| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-24 13:02 -0400 (Thu, 24 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1484/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.16.0 (landing page) Denes Turei
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
|
To the developers/maintainers of the OmnipathR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: OmnipathR |
| Version: 3.16.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings OmnipathR_3.16.0.tar.gz |
| StartedAt: 2025-04-24 01:01:35 -0400 (Thu, 24 Apr 2025) |
| EndedAt: 2025-04-24 01:26:32 -0400 (Thu, 24 Apr 2025) |
| EllapsedTime: 1497.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: OmnipathR.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings OmnipathR_3.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2025-04-24 01:02:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:02:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:02:06] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-04-24 01:02:06] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-04-24 01:02:06] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-23
[2025-04-24 01:02:06] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-23 19:13:37 UTC; unix
[2025-04-24 01:02:06] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-04-24 01:02:06] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-04-24 01:02:07] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-04-24; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-04-24 01:02:07] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-04-24 01:02:07] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.0(2025-03-21); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-04-23); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-04-24 01:02:07] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-04-24 01:02:07] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-04-24 01:02:07] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-04-24 01:02:07] [TRACE] [OmnipathR] Contains 1 files.
[2025-04-24 01:02:07] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-04-24 01:02:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:02:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:02:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-04-24 01:02:07] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-04-24 01:02:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-24 01:02:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:02:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-24 01:02:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:02:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-24 01:02:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:02:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-24 01:02:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:02:07] [TRACE] [OmnipathR] Cache locked: FALSE
It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2025-04-24 01:02:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:02:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:02:24] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-04-24 01:02:24] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-04-24 01:02:24] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-23
[2025-04-24 01:02:24] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-23 19:13:37 UTC; unix
[2025-04-24 01:02:24] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-04-24 01:02:24] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-04-24 01:02:24] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-04-24; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-04-24 01:02:24] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-04-24 01:02:24] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.0(2025-03-21); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-04-23); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-04-24 01:02:24] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-04-24 01:02:24] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-04-24 01:02:24] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-04-24 01:02:24] [TRACE] [OmnipathR] Contains 1 files.
[2025-04-24 01:02:24] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-04-24 01:02:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:02:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:02:24] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-04-24 01:02:24] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-04-24 01:02:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-24 01:02:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:02:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-24 01:02:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:02:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-24 01:02:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:02:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-24 01:02:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:02:25] [TRACE] [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: curated_ligrec_stats
> ### Title: Statistics about literature curated ligand-receptor interactions
> ### Aliases: curated_ligrec_stats
>
> ### ** Examples
>
> clr <- curated_ligrec_stats()
Warning in import_post_translational_interactions(resources = ., ...) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:05:37] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:05:37] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020],query_type=interactions]
[2025-04-24 01:05:37] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:05:37] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:05:37] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:05:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:05:37] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:37] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`.
[2025-04-24 01:05:37] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:38] [SUCCESS] [OmnipathR] Loaded 4568 interactions from cache.
Warning in (function (...) : 'function (...)
{
.Deprecated("post_translational")
post_translational(...)
}' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:05:38] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:05:38] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,fields=extra_attrs,query_type=interactions]
[2025-04-24 01:05:38] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:05:38] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:05:38] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:05:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:05:38] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-04-24 01:05:38] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`.
[2025-04-24 01:05:38] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-04-24 01:05:38] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-04-24 01:05:39] [SUCCESS] [OmnipathR] Loaded 2879 interactions from cache.
Warning in (function (...) : 'function (...)
{
.Deprecated("post_translational")
post_translational(...)
}' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:05:39] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:05:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Cellinker,fields=extra_attrs,query_type=interactions]
[2025-04-24 01:05:39] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:05:39] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:05:40] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:05:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:05:40] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-04-24 01:05:40] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`.
[2025-04-24 01:05:40] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-04-24 01:05:40] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-04-24 01:05:40] [SUCCESS] [OmnipathR] Loaded 3765 interactions from cache.
Warning in (function (...) : 'function (...)
{
.Deprecated("post_translational")
post_translational(...)
}' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:05:40] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:05:40] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=talklr,fields=extra_attrs,query_type=interactions]
[2025-04-24 01:05:40] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:05:40] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:05:41] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:05:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:05:41] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-04-24 01:05:41] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`.
[2025-04-24 01:05:41] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-04-24 01:05:41] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-04-24 01:05:42] [SUCCESS] [OmnipathR] Loaded 2484 interactions from cache.
Warning in (function (...) : 'function (...)
{
.Deprecated("post_translational")
post_translational(...)
}' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:05:42] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:05:42] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellChatDB,fields=extra_attrs,query_type=interactions]
[2025-04-24 01:05:42] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:05:42] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:05:43] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:05:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:05:43] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-04-24 01:05:43] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`.
[2025-04-24 01:05:43] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-04-24 01:05:43] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-04-24 01:05:43] [SUCCESS] [OmnipathR] Loaded 1894 interactions from cache.
[2025-04-24 01:05:43] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:05:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=SignaLink3,query_type=interactions]
[2025-04-24 01:05:43] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:05:43] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:05:44] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:05:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:05:44] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:44] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`.
[2025-04-24 01:05:44] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:44] [SUCCESS] [OmnipathR] Loaded 1796 interactions from cache.
[2025-04-24 01:05:44] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:05:44] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_function,query_type=annotations]
[2025-04-24 01:05:44] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:05:44] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:05:45] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:05:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:05:45] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2025-04-24 01:05:45] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd-1.rds`.
[2025-04-24 01:05:45] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2025-04-24 01:05:45] [SUCCESS] [OmnipathR] Loaded 2001 annotation records from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:05:45] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:05:45] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,query_type=interactions]
[2025-04-24 01:05:45] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:05:45] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:05:46] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:05:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:05:46] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:46] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:46] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:46] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:46] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:46] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:46] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:46] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-24 01:05:46] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-04-24 01:05:46] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-24 01:05:46] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-24 01:05:46] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.327778s from omnipathdb.org (47.8 Kb/s); Redirect: 0s, DNS look up: 0.00158s, Connection: 0.002591s, Pretransfer: 0.16482s, First byte at: 0.326846s
[2025-04-24 01:05:46] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 24 Apr 2025 05:05:46 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 24 Apr 2025 06:05:46 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-04-24 01:05:47] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:05:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:05:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:05:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:05:47] [INFO] [OmnipathR] Cache item `afe18d85fba82fa7d5f390113de328e13aa85e89` version 1: status changed from `unknown` to `started`.
[2025-04-24 01:05:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/afe18d85fba82fa7d5f390113de328e13aa85e89-1.rds`.
[2025-04-24 01:05:47] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/afe18d85fba82fa7d5f390113de328e13aa85e89-1.rds`.
[2025-04-24 01:05:47] [INFO] [OmnipathR] Download ready [key=afe18d85fba82fa7d5f390113de328e13aa85e89, version=1]
[2025-04-24 01:05:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:05:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:05:47] [INFO] [OmnipathR] Cache item `afe18d85fba82fa7d5f390113de328e13aa85e89` version 1: status changed from `started` to `ready`.
[2025-04-24 01:05:47] [SUCCESS] [OmnipathR] Downloaded 2879 interactions.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:05:47] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:05:47] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,query_type=interactions]
[2025-04-24 01:05:47] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:05:47] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:05:48] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:05:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:05:48] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:48] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/afe18d85fba82fa7d5f390113de328e13aa85e89-1.rds`.
[2025-04-24 01:05:48] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:48] [SUCCESS] [OmnipathR] Loaded 2879 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:05:48] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:05:48] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,query_type=interactions]
[2025-04-24 01:05:48] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:05:49] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:05:49] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:05:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:05:49] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:49] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/afe18d85fba82fa7d5f390113de328e13aa85e89-1.rds`.
[2025-04-24 01:05:49] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:50] [SUCCESS] [OmnipathR] Loaded 2879 interactions from cache.
Warning in (function (...) : 'function (...)
{
.Deprecated("post_translational")
post_translational(...)
}' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:05:50] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:05:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,fields=extra_attrs,query_type=interactions]
[2025-04-24 01:05:50] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:05:50] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:05:50] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:05:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:05:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-04-24 01:05:51] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`.
[2025-04-24 01:05:51] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-04-24 01:05:51] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-04-24 01:05:51] [SUCCESS] [OmnipathR] Loaded 2879 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:05:51] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:05:51] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Cellinker,query_type=interactions]
[2025-04-24 01:05:51] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:05:51] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:05:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:05:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:05:52] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:52] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:52] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:52] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:52] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:52] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:52] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:52] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-24 01:05:52] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-04-24 01:05:52] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-24 01:05:52] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-24 01:05:52] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.317793s from omnipathdb.org (49.3 Kb/s); Redirect: 0s, DNS look up: 0.001442s, Connection: 0.002458s, Pretransfer: 0.15931s, First byte at: 0.317358s
[2025-04-24 01:05:52] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 24 Apr 2025 05:05:52 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 24 Apr 2025 06:05:52 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-04-24 01:05:53] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:05:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:05:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:05:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:05:53] [INFO] [OmnipathR] Cache item `c8350370602bcfe8ed14bda96cb9bd68770c1e66` version 1: status changed from `unknown` to `started`.
[2025-04-24 01:05:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/c8350370602bcfe8ed14bda96cb9bd68770c1e66-1.rds`.
[2025-04-24 01:05:53] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/c8350370602bcfe8ed14bda96cb9bd68770c1e66-1.rds`.
[2025-04-24 01:05:53] [INFO] [OmnipathR] Download ready [key=c8350370602bcfe8ed14bda96cb9bd68770c1e66, version=1]
[2025-04-24 01:05:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:05:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:05:53] [INFO] [OmnipathR] Cache item `c8350370602bcfe8ed14bda96cb9bd68770c1e66` version 1: status changed from `started` to `ready`.
[2025-04-24 01:05:54] [SUCCESS] [OmnipathR] Downloaded 3765 interactions.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:05:54] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:05:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Cellinker,query_type=interactions]
[2025-04-24 01:05:54] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:05:54] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:05:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:05:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:05:55] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:55] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/c8350370602bcfe8ed14bda96cb9bd68770c1e66-1.rds`.
[2025-04-24 01:05:55] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:55] [SUCCESS] [OmnipathR] Loaded 3765 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:05:55] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:05:55] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Cellinker,query_type=interactions]
[2025-04-24 01:05:55] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:05:55] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:05:55] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:05:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:05:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:56] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/c8350370602bcfe8ed14bda96cb9bd68770c1e66-1.rds`.
[2025-04-24 01:05:56] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:56] [SUCCESS] [OmnipathR] Loaded 3765 interactions from cache.
Warning in (function (...) : 'function (...)
{
.Deprecated("post_translational")
post_translational(...)
}' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:05:56] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:05:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Cellinker,fields=extra_attrs,query_type=interactions]
[2025-04-24 01:05:56] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:05:56] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:05:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:05:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:05:57] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-04-24 01:05:57] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`.
[2025-04-24 01:05:57] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-04-24 01:05:57] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-04-24 01:05:57] [SUCCESS] [OmnipathR] Loaded 3765 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:05:57] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:05:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellTalkDB,query_type=interactions]
[2025-04-24 01:05:57] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:05:57] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:05:58] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:05:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:05:58] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:58] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:58] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:58] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:58] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:58] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:58] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-24 01:05:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-04-24 01:05:58] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-24 01:05:58] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-24 01:05:58] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.334855s from omnipathdb.org (46.8 Kb/s); Redirect: 0s, DNS look up: 0.00164s, Connection: 0.00249s, Pretransfer: 0.162421s, First byte at: 0.33442s
[2025-04-24 01:05:58] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 24 Apr 2025 05:05:58 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 24 Apr 2025 06:05:58 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-04-24 01:05:59] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:05:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:05:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:05:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:05:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:05:59] [INFO] [OmnipathR] Cache item `8158e608d1fd5182b9aa0a24a07fc739c59a1bf8` version 1: status changed from `unknown` to `started`.
[2025-04-24 01:05:59] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`.
[2025-04-24 01:06:00] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`.
[2025-04-24 01:06:00] [INFO] [OmnipathR] Download ready [key=8158e608d1fd5182b9aa0a24a07fc739c59a1bf8, version=1]
[2025-04-24 01:06:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:00] [INFO] [OmnipathR] Cache item `8158e608d1fd5182b9aa0a24a07fc739c59a1bf8` version 1: status changed from `started` to `ready`.
[2025-04-24 01:06:00] [SUCCESS] [OmnipathR] Downloaded 3473 interactions.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:00] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:00] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellTalkDB,query_type=interactions]
[2025-04-24 01:06:00] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:00] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:00] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:01] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:01] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`.
[2025-04-24 01:06:01] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:01] [SUCCESS] [OmnipathR] Loaded 3473 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:01] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:01] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellTalkDB,query_type=interactions]
[2025-04-24 01:06:01] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:01] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:02] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:02] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:02] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`.
[2025-04-24 01:06:02] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:02] [SUCCESS] [OmnipathR] Loaded 3473 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:02] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:02] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellTalkDB,query_type=interactions]
[2025-04-24 01:06:02] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:02] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:03] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:03] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:03] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`.
[2025-04-24 01:06:03] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:03] [SUCCESS] [OmnipathR] Loaded 3473 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:03] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellChatDB,query_type=interactions]
[2025-04-24 01:06:03] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:03] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:04] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:04] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:04] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:04] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:04] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:04] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-24 01:06:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-04-24 01:06:04] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-24 01:06:04] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-24 01:06:05] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.331214s from omnipathdb.org (47.3 Kb/s); Redirect: 0s, DNS look up: 0.001847s, Connection: 0.002686s, Pretransfer: 0.165183s, First byte at: 0.330088s
[2025-04-24 01:06:05] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 24 Apr 2025 05:06:04 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 24 Apr 2025 06:06:04 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-04-24 01:06:05] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:05] [INFO] [OmnipathR] Cache item `641434253ee9e555515168e62fe5c7e36a8596c6` version 1: status changed from `unknown` to `started`.
[2025-04-24 01:06:05] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/641434253ee9e555515168e62fe5c7e36a8596c6-1.rds`.
[2025-04-24 01:06:05] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/641434253ee9e555515168e62fe5c7e36a8596c6-1.rds`.
[2025-04-24 01:06:05] [INFO] [OmnipathR] Download ready [key=641434253ee9e555515168e62fe5c7e36a8596c6, version=1]
[2025-04-24 01:06:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:06] [INFO] [OmnipathR] Cache item `641434253ee9e555515168e62fe5c7e36a8596c6` version 1: status changed from `started` to `ready`.
[2025-04-24 01:06:06] [SUCCESS] [OmnipathR] Downloaded 1894 interactions.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:06] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellChatDB,query_type=interactions]
[2025-04-24 01:06:06] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:06] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:06] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:06] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:06] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/641434253ee9e555515168e62fe5c7e36a8596c6-1.rds`.
[2025-04-24 01:06:06] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:07] [SUCCESS] [OmnipathR] Loaded 1894 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:07] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellChatDB,query_type=interactions]
[2025-04-24 01:06:07] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:07] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:07] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:07] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:07] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/641434253ee9e555515168e62fe5c7e36a8596c6-1.rds`.
[2025-04-24 01:06:07] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:08] [SUCCESS] [OmnipathR] Loaded 1894 interactions from cache.
Warning in (function (...) : 'function (...)
{
.Deprecated("post_translational")
post_translational(...)
}' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:08] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:08] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellChatDB,fields=extra_attrs,query_type=interactions]
[2025-04-24 01:06:08] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:08] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:08] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:08] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-04-24 01:06:08] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`.
[2025-04-24 01:06:08] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-04-24 01:06:08] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-04-24 01:06:09] [SUCCESS] [OmnipathR] Loaded 1894 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:09] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellCall,query_type=interactions]
[2025-04-24 01:06:09] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:09] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:09] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:10] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:10] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:10] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:10] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:10] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:10] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:10] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:10] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-24 01:06:10] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-04-24 01:06:10] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-24 01:06:10] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-24 01:06:10] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.352973s from omnipathdb.org (44.4 Kb/s); Redirect: 0s, DNS look up: 0.001545s, Connection: 0.002208s, Pretransfer: 0.169113s, First byte at: 0.352052s
[2025-04-24 01:06:10] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 24 Apr 2025 05:06:10 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 24 Apr 2025 06:06:10 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-04-24 01:06:11] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:11] [INFO] [OmnipathR] Cache item `af0debe0cdd22707b097cd388dfd1398cccb76c8` version 1: status changed from `unknown` to `started`.
[2025-04-24 01:06:11] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/af0debe0cdd22707b097cd388dfd1398cccb76c8-1.rds`.
[2025-04-24 01:06:11] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/af0debe0cdd22707b097cd388dfd1398cccb76c8-1.rds`.
[2025-04-24 01:06:11] [INFO] [OmnipathR] Download ready [key=af0debe0cdd22707b097cd388dfd1398cccb76c8, version=1]
[2025-04-24 01:06:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:11] [INFO] [OmnipathR] Cache item `af0debe0cdd22707b097cd388dfd1398cccb76c8` version 1: status changed from `started` to `ready`.
[2025-04-24 01:06:11] [SUCCESS] [OmnipathR] Downloaded 1000 interactions.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:11] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:11] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellCall,query_type=interactions]
[2025-04-24 01:06:11] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:11] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:12] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:12] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:12] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/af0debe0cdd22707b097cd388dfd1398cccb76c8-1.rds`.
[2025-04-24 01:06:12] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:12] [SUCCESS] [OmnipathR] Loaded 1000 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:12] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:12] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellCall,query_type=interactions]
[2025-04-24 01:06:12] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:12] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:12] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:13] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/af0debe0cdd22707b097cd388dfd1398cccb76c8-1.rds`.
[2025-04-24 01:06:13] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:13] [SUCCESS] [OmnipathR] Loaded 1000 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:13] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:13] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellCall,query_type=interactions]
[2025-04-24 01:06:13] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:13] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:13] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:13] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/af0debe0cdd22707b097cd388dfd1398cccb76c8-1.rds`.
[2025-04-24 01:06:13] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:14] [SUCCESS] [OmnipathR] Loaded 1000 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:14] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:14] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=connectomeDB2020,query_type=interactions]
[2025-04-24 01:06:14] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:14] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:14] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:14] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:14] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:14] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:14] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:14] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:14] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:14] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:14] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-24 01:06:14] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-04-24 01:06:14] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-24 01:06:15] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-24 01:06:15] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.33604s from omnipathdb.org (46.6 Kb/s); Redirect: 0s, DNS look up: 0.001467s, Connection: 0.002203s, Pretransfer: 0.178765s, First byte at: 0.335503s
[2025-04-24 01:06:15] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 24 Apr 2025 05:06:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 24 Apr 2025 06:06:15 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-04-24 01:06:16] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:16] [INFO] [OmnipathR] Cache item `d08eb76734c005daabb6eb3c832a55e330672026` version 1: status changed from `unknown` to `started`.
[2025-04-24 01:06:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/d08eb76734c005daabb6eb3c832a55e330672026-1.rds`.
[2025-04-24 01:06:16] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/d08eb76734c005daabb6eb3c832a55e330672026-1.rds`.
[2025-04-24 01:06:16] [INFO] [OmnipathR] Download ready [key=d08eb76734c005daabb6eb3c832a55e330672026, version=1]
[2025-04-24 01:06:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:16] [INFO] [OmnipathR] Cache item `d08eb76734c005daabb6eb3c832a55e330672026` version 1: status changed from `started` to `ready`.
[2025-04-24 01:06:16] [SUCCESS] [OmnipathR] Downloaded 2313 interactions.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:16] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:16] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=connectomeDB2020,query_type=interactions]
[2025-04-24 01:06:16] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:16] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:17] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:17] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:17] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/d08eb76734c005daabb6eb3c832a55e330672026-1.rds`.
[2025-04-24 01:06:17] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:17] [SUCCESS] [OmnipathR] Loaded 2313 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:17] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=connectomeDB2020,query_type=interactions]
[2025-04-24 01:06:17] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:17] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:18] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:18] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:18] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/d08eb76734c005daabb6eb3c832a55e330672026-1.rds`.
[2025-04-24 01:06:18] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:18] [SUCCESS] [OmnipathR] Loaded 2313 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:18] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:18] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=connectomeDB2020,query_type=interactions]
[2025-04-24 01:06:18] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:18] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:19] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:19] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:19] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/d08eb76734c005daabb6eb3c832a55e330672026-1.rds`.
[2025-04-24 01:06:19] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:19] [SUCCESS] [OmnipathR] Loaded 2313 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:19] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:19] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Guide2Pharma,query_type=interactions]
[2025-04-24 01:06:19] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:19] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:20] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:20] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:20] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:20] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:20] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:20] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:20] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:20] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:20] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-24 01:06:20] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-04-24 01:06:20] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-24 01:06:21] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-24 01:06:21] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.316594s from omnipathdb.org (49.5 Kb/s); Redirect: 0s, DNS look up: 0.001646s, Connection: 0.002382s, Pretransfer: 0.158181s, First byte at: 0.316176s
[2025-04-24 01:06:21] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 24 Apr 2025 05:06:21 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 24 Apr 2025 06:06:21 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-04-24 01:06:21] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:21] [INFO] [OmnipathR] Cache item `11b0dd49c2e8541d966f577a8aacd52c71112987` version 1: status changed from `unknown` to `started`.
[2025-04-24 01:06:21] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/11b0dd49c2e8541d966f577a8aacd52c71112987-1.rds`.
[2025-04-24 01:06:21] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/11b0dd49c2e8541d966f577a8aacd52c71112987-1.rds`.
[2025-04-24 01:06:21] [INFO] [OmnipathR] Download ready [key=11b0dd49c2e8541d966f577a8aacd52c71112987, version=1]
[2025-04-24 01:06:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:21] [INFO] [OmnipathR] Cache item `11b0dd49c2e8541d966f577a8aacd52c71112987` version 1: status changed from `started` to `ready`.
[2025-04-24 01:06:22] [SUCCESS] [OmnipathR] Downloaded 672 interactions.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:22] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:22] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Guide2Pharma,query_type=interactions]
[2025-04-24 01:06:22] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:22] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:22] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:22] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:22] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/11b0dd49c2e8541d966f577a8aacd52c71112987-1.rds`.
[2025-04-24 01:06:22] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:22] [SUCCESS] [OmnipathR] Loaded 672 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:22] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:22] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Guide2Pharma,query_type=interactions]
[2025-04-24 01:06:22] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:22] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:23] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:23] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:23] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/11b0dd49c2e8541d966f577a8aacd52c71112987-1.rds`.
[2025-04-24 01:06:23] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:23] [SUCCESS] [OmnipathR] Loaded 672 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:23] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:23] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Guide2Pharma,query_type=interactions]
[2025-04-24 01:06:23] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:23] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:24] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:24] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:24] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/11b0dd49c2e8541d966f577a8aacd52c71112987-1.rds`.
[2025-04-24 01:06:24] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:24] [SUCCESS] [OmnipathR] Loaded 672 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:24] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:24] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Baccin2019,query_type=interactions]
[2025-04-24 01:06:24] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:24] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:25] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:25] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:25] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:25] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:25] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:25] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:25] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:25] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:25] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-24 01:06:25] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-04-24 01:06:25] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-24 01:06:26] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-24 01:06:26] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.34778s from omnipathdb.org (45 Kb/s); Redirect: 0s, DNS look up: 0.001845s, Connection: 0.002433s, Pretransfer: 0.191128s, First byte at: 0.346837s
[2025-04-24 01:06:26] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 24 Apr 2025 05:06:25 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 24 Apr 2025 06:06:25 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-04-24 01:06:26] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:27] [INFO] [OmnipathR] Cache item `f963006a054fdbb2fcbd5a63e731087e21fb4b31` version 1: status changed from `unknown` to `started`.
[2025-04-24 01:06:27] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f963006a054fdbb2fcbd5a63e731087e21fb4b31-1.rds`.
[2025-04-24 01:06:27] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f963006a054fdbb2fcbd5a63e731087e21fb4b31-1.rds`.
[2025-04-24 01:06:27] [INFO] [OmnipathR] Download ready [key=f963006a054fdbb2fcbd5a63e731087e21fb4b31, version=1]
[2025-04-24 01:06:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:27] [INFO] [OmnipathR] Cache item `f963006a054fdbb2fcbd5a63e731087e21fb4b31` version 1: status changed from `started` to `ready`.
[2025-04-24 01:06:27] [SUCCESS] [OmnipathR] Downloaded 1676 interactions.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:27] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:27] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Baccin2019,query_type=interactions]
[2025-04-24 01:06:27] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:27] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:28] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:28] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:28] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/f963006a054fdbb2fcbd5a63e731087e21fb4b31-1.rds`.
[2025-04-24 01:06:28] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:28] [SUCCESS] [OmnipathR] Loaded 1676 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:28] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:28] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Baccin2019,query_type=interactions]
[2025-04-24 01:06:28] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:28] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:29] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:29] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:29] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/f963006a054fdbb2fcbd5a63e731087e21fb4b31-1.rds`.
[2025-04-24 01:06:29] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:29] [SUCCESS] [OmnipathR] Loaded 1676 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:29] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:29] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Baccin2019,query_type=interactions]
[2025-04-24 01:06:29] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:29] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:30] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:30] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:30] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/f963006a054fdbb2fcbd5a63e731087e21fb4b31-1.rds`.
[2025-04-24 01:06:30] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:30] [SUCCESS] [OmnipathR] Loaded 1676 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:30] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:30] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Kirouac2010,query_type=interactions]
[2025-04-24 01:06:30] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:30] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:31] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:31] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:31] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:31] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:31] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:31] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:31] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:31] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:31] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-24 01:06:31] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-04-24 01:06:31] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-24 01:06:31] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-24 01:06:31] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.314994s from omnipathdb.org (49.7 Kb/s); Redirect: 0s, DNS look up: 0.001389s, Connection: 0.002137s, Pretransfer: 0.158792s, First byte at: 0.313994s
[2025-04-24 01:06:31] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 24 Apr 2025 05:06:31 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 24 Apr 2025 06:06:31 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-04-24 01:06:31] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:31] [INFO] [OmnipathR] Cache item `e59c495f650b38ab64da89e0da5af6ff096901b8` version 1: status changed from `unknown` to `started`.
[2025-04-24 01:06:31] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/e59c495f650b38ab64da89e0da5af6ff096901b8-1.rds`.
[2025-04-24 01:06:31] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/e59c495f650b38ab64da89e0da5af6ff096901b8-1.rds`.
[2025-04-24 01:06:31] [INFO] [OmnipathR] Download ready [key=e59c495f650b38ab64da89e0da5af6ff096901b8, version=1]
[2025-04-24 01:06:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:32] [INFO] [OmnipathR] Cache item `e59c495f650b38ab64da89e0da5af6ff096901b8` version 1: status changed from `started` to `ready`.
[2025-04-24 01:06:32] [SUCCESS] [OmnipathR] Downloaded 152 interactions.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:32] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:32] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Kirouac2010,query_type=interactions]
[2025-04-24 01:06:32] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:32] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:32] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:32] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:32] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/e59c495f650b38ab64da89e0da5af6ff096901b8-1.rds`.
[2025-04-24 01:06:32] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:32] [SUCCESS] [OmnipathR] Loaded 152 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:32] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:32] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Kirouac2010,query_type=interactions]
[2025-04-24 01:06:32] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:32] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:33] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:33] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:33] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/e59c495f650b38ab64da89e0da5af6ff096901b8-1.rds`.
[2025-04-24 01:06:33] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:33] [SUCCESS] [OmnipathR] Loaded 152 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:33] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:33] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Kirouac2010,query_type=interactions]
[2025-04-24 01:06:33] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:33] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:34] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:34] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:34] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/e59c495f650b38ab64da89e0da5af6ff096901b8-1.rds`.
[2025-04-24 01:06:34] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:34] [SUCCESS] [OmnipathR] Loaded 152 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:34] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:34] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Ramilowski2015,query_type=interactions]
[2025-04-24 01:06:34] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:34] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:35] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:35] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:35] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:35] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:35] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:35] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:35] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:35] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:35] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-24 01:06:35] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-04-24 01:06:35] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-24 01:06:35] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-24 01:06:35] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.326324s from omnipathdb.org (48 Kb/s); Redirect: 0s, DNS look up: 0.00182s, Connection: 0.002487s, Pretransfer: 0.1634s, First byte at: 0.325457s
[2025-04-24 01:06:36] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 24 Apr 2025 05:06:35 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 24 Apr 2025 06:06:35 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-04-24 01:06:36] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:37] [INFO] [OmnipathR] Cache item `78bff68f8413d6211070111914db1b8b2b98ad54` version 1: status changed from `unknown` to `started`.
[2025-04-24 01:06:37] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/78bff68f8413d6211070111914db1b8b2b98ad54-1.rds`.
[2025-04-24 01:06:37] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/78bff68f8413d6211070111914db1b8b2b98ad54-1.rds`.
[2025-04-24 01:06:37] [INFO] [OmnipathR] Download ready [key=78bff68f8413d6211070111914db1b8b2b98ad54, version=1]
[2025-04-24 01:06:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:37] [INFO] [OmnipathR] Cache item `78bff68f8413d6211070111914db1b8b2b98ad54` version 1: status changed from `started` to `ready`.
[2025-04-24 01:06:37] [SUCCESS] [OmnipathR] Downloaded 1946 interactions.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:37] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:37] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Ramilowski2015,query_type=interactions]
[2025-04-24 01:06:37] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:37] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:38] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:38] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:38] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/78bff68f8413d6211070111914db1b8b2b98ad54-1.rds`.
[2025-04-24 01:06:38] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:38] [SUCCESS] [OmnipathR] Loaded 1946 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:38] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:38] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Ramilowski2015,query_type=interactions]
[2025-04-24 01:06:38] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:38] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:39] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:39] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:39] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/78bff68f8413d6211070111914db1b8b2b98ad54-1.rds`.
[2025-04-24 01:06:39] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:39] [SUCCESS] [OmnipathR] Loaded 1946 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:39] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Ramilowski2015,query_type=interactions]
[2025-04-24 01:06:39] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:39] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:40] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:40] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:40] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/78bff68f8413d6211070111914db1b8b2b98ad54-1.rds`.
[2025-04-24 01:06:40] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:40] [SUCCESS] [OmnipathR] Loaded 1946 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:40] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:40] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=scConnect,query_type=interactions]
[2025-04-24 01:06:40] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:40] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:41] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:41] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:41] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:41] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:41] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:41] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:41] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:41] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:41] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-24 01:06:41] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-04-24 01:06:41] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-24 01:06:41] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-24 01:06:41] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.32862s from omnipathdb.org (47.7 Kb/s); Redirect: 0s, DNS look up: 0.001769s, Connection: 0.002603s, Pretransfer: 0.164375s, First byte at: 0.327722s
[2025-04-24 01:06:41] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 24 Apr 2025 05:06:41 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 24 Apr 2025 06:06:41 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-04-24 01:06:42] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:42] [INFO] [OmnipathR] Cache item `4d3e24d35f89a47701b9f0e9d5da90ec2aee0874` version 1: status changed from `unknown` to `started`.
[2025-04-24 01:06:42] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/4d3e24d35f89a47701b9f0e9d5da90ec2aee0874-1.rds`.
[2025-04-24 01:06:42] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/4d3e24d35f89a47701b9f0e9d5da90ec2aee0874-1.rds`.
[2025-04-24 01:06:42] [INFO] [OmnipathR] Download ready [key=4d3e24d35f89a47701b9f0e9d5da90ec2aee0874, version=1]
[2025-04-24 01:06:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:42] [INFO] [OmnipathR] Cache item `4d3e24d35f89a47701b9f0e9d5da90ec2aee0874` version 1: status changed from `started` to `ready`.
[2025-04-24 01:06:42] [SUCCESS] [OmnipathR] Downloaded 479 interactions.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:42] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:42] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=scConnect,query_type=interactions]
[2025-04-24 01:06:42] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:42] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:43] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:43] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:43] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/4d3e24d35f89a47701b9f0e9d5da90ec2aee0874-1.rds`.
[2025-04-24 01:06:43] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:43] [SUCCESS] [OmnipathR] Loaded 479 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:43] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=scConnect,query_type=interactions]
[2025-04-24 01:06:43] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:43] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:43] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:43] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:43] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/4d3e24d35f89a47701b9f0e9d5da90ec2aee0874-1.rds`.
[2025-04-24 01:06:43] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:44] [SUCCESS] [OmnipathR] Loaded 479 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:44] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:44] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=scConnect,query_type=interactions]
[2025-04-24 01:06:44] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:44] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:44] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:44] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:44] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/4d3e24d35f89a47701b9f0e9d5da90ec2aee0874-1.rds`.
[2025-04-24 01:06:44] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:44] [SUCCESS] [OmnipathR] Loaded 479 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:44] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:44] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=talklr,query_type=interactions]
[2025-04-24 01:06:44] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:44] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:45] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:45] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:45] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:45] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:45] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:45] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:45] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:45] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:45] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-24 01:06:45] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-04-24 01:06:45] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-24 01:06:46] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-24 01:06:46] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.297764s from omnipathdb.org (52.6 Kb/s); Redirect: 0s, DNS look up: 0.001429s, Connection: 0.00198s, Pretransfer: 0.148467s, First byte at: 0.297314s
[2025-04-24 01:06:46] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 24 Apr 2025 05:06:45 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 24 Apr 2025 06:06:45 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-04-24 01:06:46] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:47] [INFO] [OmnipathR] Cache item `2fed349a0caf2a5e7555cbd27caa66d55fd06302` version 1: status changed from `unknown` to `started`.
[2025-04-24 01:06:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/2fed349a0caf2a5e7555cbd27caa66d55fd06302-1.rds`.
[2025-04-24 01:06:47] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/2fed349a0caf2a5e7555cbd27caa66d55fd06302-1.rds`.
[2025-04-24 01:06:47] [INFO] [OmnipathR] Download ready [key=2fed349a0caf2a5e7555cbd27caa66d55fd06302, version=1]
[2025-04-24 01:06:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:47] [INFO] [OmnipathR] Cache item `2fed349a0caf2a5e7555cbd27caa66d55fd06302` version 1: status changed from `started` to `ready`.
[2025-04-24 01:06:47] [SUCCESS] [OmnipathR] Downloaded 2484 interactions.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:47] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:47] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=talklr,query_type=interactions]
[2025-04-24 01:06:47] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:47] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:48] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:48] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:48] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/2fed349a0caf2a5e7555cbd27caa66d55fd06302-1.rds`.
[2025-04-24 01:06:48] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:48] [SUCCESS] [OmnipathR] Loaded 2484 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:48] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:48] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=talklr,query_type=interactions]
[2025-04-24 01:06:48] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:48] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:49] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:49] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:49] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/2fed349a0caf2a5e7555cbd27caa66d55fd06302-1.rds`.
[2025-04-24 01:06:49] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:49] [SUCCESS] [OmnipathR] Loaded 2484 interactions from cache.
Warning in (function (...) : 'function (...)
{
.Deprecated("post_translational")
post_translational(...)
}' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:49] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:49] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=talklr,fields=extra_attrs,query_type=interactions]
[2025-04-24 01:06:49] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:49] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:50] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:50] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-04-24 01:06:50] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`.
[2025-04-24 01:06:50] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-04-24 01:06:50] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-04-24 01:06:50] [SUCCESS] [OmnipathR] Loaded 2484 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:51] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:51] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=ICELLNET,query_type=interactions]
[2025-04-24 01:06:51] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:51] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:51] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:51] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:51] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:51] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:51] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:51] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:52] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:52] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-24 01:06:52] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-04-24 01:06:52] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-24 01:06:52] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-24 01:06:52] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.340496s from omnipathdb.org (46 Kb/s); Redirect: 0s, DNS look up: 0.001762s, Connection: 0.00233s, Pretransfer: 0.169809s, First byte at: 0.339652s
[2025-04-24 01:06:52] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 24 Apr 2025 05:06:52 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 24 Apr 2025 06:06:52 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-04-24 01:06:52] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:53] [INFO] [OmnipathR] Cache item `d78f1e5d23782453249e01fb0379efde9c053131` version 1: status changed from `unknown` to `started`.
[2025-04-24 01:06:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/d78f1e5d23782453249e01fb0379efde9c053131-1.rds`.
[2025-04-24 01:06:53] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/d78f1e5d23782453249e01fb0379efde9c053131-1.rds`.
[2025-04-24 01:06:53] [INFO] [OmnipathR] Download ready [key=d78f1e5d23782453249e01fb0379efde9c053131, version=1]
[2025-04-24 01:06:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:53] [INFO] [OmnipathR] Cache item `d78f1e5d23782453249e01fb0379efde9c053131` version 1: status changed from `started` to `ready`.
[2025-04-24 01:06:53] [SUCCESS] [OmnipathR] Downloaded 1018 interactions.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:53] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:53] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=ICELLNET,query_type=interactions]
[2025-04-24 01:06:53] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:53] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:53] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:54] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:54] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/d78f1e5d23782453249e01fb0379efde9c053131-1.rds`.
[2025-04-24 01:06:54] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:54] [SUCCESS] [OmnipathR] Loaded 1018 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:54] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=ICELLNET,query_type=interactions]
[2025-04-24 01:06:54] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:54] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:54] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:54] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/d78f1e5d23782453249e01fb0379efde9c053131-1.rds`.
[2025-04-24 01:06:54] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:55] [SUCCESS] [OmnipathR] Loaded 1018 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:55] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:55] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=ICELLNET,query_type=interactions]
[2025-04-24 01:06:55] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:55] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:55] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:55] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:55] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/d78f1e5d23782453249e01fb0379efde9c053131-1.rds`.
[2025-04-24 01:06:55] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:55] [SUCCESS] [OmnipathR] Loaded 1018 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:56] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=EMBRACE,query_type=interactions]
[2025-04-24 01:06:56] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:56] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:56] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:56] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:56] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:56] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:56] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-24 01:06:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-04-24 01:06:56] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-24 01:06:57] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-24 01:06:57] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.317145s from omnipathdb.org (49.4 Kb/s); Redirect: 0s, DNS look up: 0.001477s, Connection: 0.002207s, Pretransfer: 0.157952s, First byte at: 0.316235s
[2025-04-24 01:06:57] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 24 Apr 2025 05:06:56 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 24 Apr 2025 06:06:56 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-04-24 01:06:57] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:57] [INFO] [OmnipathR] Cache item `ef7eb533b45a8e6a8f4b6e928698c193d947a86b` version 1: status changed from `unknown` to `started`.
[2025-04-24 01:06:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/ef7eb533b45a8e6a8f4b6e928698c193d947a86b-1.rds`.
[2025-04-24 01:06:57] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/ef7eb533b45a8e6a8f4b6e928698c193d947a86b-1.rds`.
[2025-04-24 01:06:57] [INFO] [OmnipathR] Download ready [key=ef7eb533b45a8e6a8f4b6e928698c193d947a86b, version=1]
[2025-04-24 01:06:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:06:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:58] [INFO] [OmnipathR] Cache item `ef7eb533b45a8e6a8f4b6e928698c193d947a86b` version 1: status changed from `started` to `ready`.
[2025-04-24 01:06:58] [SUCCESS] [OmnipathR] Downloaded 1707 interactions.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:58] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=EMBRACE,query_type=interactions]
[2025-04-24 01:06:58] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:58] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:58] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:58] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:58] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/ef7eb533b45a8e6a8f4b6e928698c193d947a86b-1.rds`.
[2025-04-24 01:06:58] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:59] [SUCCESS] [OmnipathR] Loaded 1707 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:06:59] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:06:59] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=EMBRACE,query_type=interactions]
[2025-04-24 01:06:59] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:06:59] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:06:59] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:06:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:06:59] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:06:59] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/ef7eb533b45a8e6a8f4b6e928698c193d947a86b-1.rds`.
[2025-04-24 01:06:59] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:00] [SUCCESS] [OmnipathR] Loaded 1707 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:07:00] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:07:00] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=EMBRACE,query_type=interactions]
[2025-04-24 01:07:00] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:07:00] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:07:00] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:07:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:07:00] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:00] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/ef7eb533b45a8e6a8f4b6e928698c193d947a86b-1.rds`.
[2025-04-24 01:07:00] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:00] [SUCCESS] [OmnipathR] Loaded 1707 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:07:01] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:07:01] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=LRdb,query_type=interactions]
[2025-04-24 01:07:01] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:07:01] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:07:01] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:07:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:07:01] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:01] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:01] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:01] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:01] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:01] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:01] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:01] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-24 01:07:01] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-04-24 01:07:01] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-24 01:07:02] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-24 01:07:02] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.330998s from omnipathdb.org (47.3 Kb/s); Redirect: 0s, DNS look up: 0.001352s, Connection: 0.002109s, Pretransfer: 0.165658s, First byte at: 0.330601s
[2025-04-24 01:07:02] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 24 Apr 2025 05:07:02 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 24 Apr 2025 06:07:02 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-04-24 01:07:03] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:07:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:07:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:07:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:07:03] [INFO] [OmnipathR] Cache item `0ae240e6276d9da6cd5c362b0e477962ece2e997` version 1: status changed from `unknown` to `started`.
[2025-04-24 01:07:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/0ae240e6276d9da6cd5c362b0e477962ece2e997-1.rds`.
[2025-04-24 01:07:03] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/0ae240e6276d9da6cd5c362b0e477962ece2e997-1.rds`.
[2025-04-24 01:07:03] [INFO] [OmnipathR] Download ready [key=0ae240e6276d9da6cd5c362b0e477962ece2e997, version=1]
[2025-04-24 01:07:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:07:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:07:03] [INFO] [OmnipathR] Cache item `0ae240e6276d9da6cd5c362b0e477962ece2e997` version 1: status changed from `started` to `ready`.
[2025-04-24 01:07:03] [SUCCESS] [OmnipathR] Downloaded 3310 interactions.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:07:03] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:07:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=LRdb,query_type=interactions]
[2025-04-24 01:07:03] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:07:03] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:07:04] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:07:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:07:04] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:04] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/0ae240e6276d9da6cd5c362b0e477962ece2e997-1.rds`.
[2025-04-24 01:07:04] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:04] [SUCCESS] [OmnipathR] Loaded 3310 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:07:04] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:07:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=LRdb,query_type=interactions]
[2025-04-24 01:07:04] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:07:04] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:07:05] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:07:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:07:05] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:05] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/0ae240e6276d9da6cd5c362b0e477962ece2e997-1.rds`.
[2025-04-24 01:07:05] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:05] [SUCCESS] [OmnipathR] Loaded 3310 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:07:05] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:07:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=LRdb,query_type=interactions]
[2025-04-24 01:07:05] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:07:05] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:07:06] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:07:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:07:06] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:06] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/0ae240e6276d9da6cd5c362b0e477962ece2e997-1.rds`.
[2025-04-24 01:07:06] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:06] [SUCCESS] [OmnipathR] Loaded 3310 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:07:06] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:07:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=iTALK,query_type=interactions]
[2025-04-24 01:07:06] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:07:06] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:07:07] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:07:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:07:07] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:07] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:07] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:07] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:07] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:07] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:07] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:07] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-24 01:07:07] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-04-24 01:07:07] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-24 01:07:07] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-24 01:07:07] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.305811s from omnipathdb.org (51.2 Kb/s); Redirect: 0s, DNS look up: 0.001968s, Connection: 0.002718s, Pretransfer: 0.151358s, First byte at: 0.305262s
[2025-04-24 01:07:07] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 24 Apr 2025 05:07:07 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 24 Apr 2025 06:07:07 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-04-24 01:07:08] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:07:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:07:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:07:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:07:08] [INFO] [OmnipathR] Cache item `b5d1617be0762d096dbf001209e826bff4794c4d` version 1: status changed from `unknown` to `started`.
[2025-04-24 01:07:08] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/b5d1617be0762d096dbf001209e826bff4794c4d-1.rds`.
[2025-04-24 01:07:09] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/b5d1617be0762d096dbf001209e826bff4794c4d-1.rds`.
[2025-04-24 01:07:09] [INFO] [OmnipathR] Download ready [key=b5d1617be0762d096dbf001209e826bff4794c4d, version=1]
[2025-04-24 01:07:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:07:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:07:09] [INFO] [OmnipathR] Cache item `b5d1617be0762d096dbf001209e826bff4794c4d` version 1: status changed from `started` to `ready`.
[2025-04-24 01:07:09] [SUCCESS] [OmnipathR] Downloaded 2639 interactions.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:07:09] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:07:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=iTALK,query_type=interactions]
[2025-04-24 01:07:09] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:07:09] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:07:09] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:07:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:07:10] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:10] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/b5d1617be0762d096dbf001209e826bff4794c4d-1.rds`.
[2025-04-24 01:07:10] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:10] [SUCCESS] [OmnipathR] Loaded 2639 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:07:10] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:07:10] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=iTALK,query_type=interactions]
[2025-04-24 01:07:10] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:07:10] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-24 01:07:11] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-24 01:07:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:07:11] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:11] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/b5d1617be0762d096dbf001209e826bff4794c4d-1.rds`.
[2025-04-24 01:07:11] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-04-24 01:07:11] [SUCCESS] [OmnipathR] Loaded 2639 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-04-24 01:07:11] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-24 01:07:11] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=iTALK,query_type=interactions]
[2025-04-24 01:07:11] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-24 01:07:11] [TRACE] [OmnipathR] Orthology targets:
Warning in file(con, "r") :
URL 'https://omnipathdb.org/resources': status was 'Server returned nothing (no headers, no data)'
Error in `map()`:
ℹ In index: 16.
Caused by error in `map()`:
ℹ In index: 4.
Caused by error in `map()`:
ℹ In index: 1.
Caused by error in `file()`:
! cannot open the connection to 'https://omnipathdb.org/resources'
Backtrace:
▆
1. ├─OmnipathR::curated_ligrec_stats()
2. │ └─... %>% unnest_wider(col = data)
3. ├─OmnipathR:::unnest_wider(., col = data)
4. │ └─base::eval(call[[tbl_name]], parent.frame())
5. │ └─base::eval(call[[tbl_name]], parent.frame())
6. ├─tibble::tibble(resource = names(.), data = .)
7. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)
8. │ └─rlang::eval_tidy(xs[[j]], mask)
9. ├─rlang::set_names(map(., stats_one_resource, curated), .)
10. ├─purrr::map(., stats_one_resource, curated)
11. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
12. │ ├─purrr:::with_indexed_errors(...)
13. │ │ └─base::withCallingHandlers(...)
14. │ ├─purrr:::call_with_cleanup(...)
15. │ └─OmnipathR (local) .f(.x[[i]], ...)
16. │ └─... %>% ...
17. ├─purrr::map(., nrow)
18. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
19. │ └─purrr:::vctrs_vec_compat(.x, .purrr_user_env)
20. ├─rlang::set_names(...)
21. ├─purrr::map(...)
22. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
23. │ ├─purrr:::with_indexed_errors(...)
24. │ │ └─base::withCallingHandlers(...)
25. │ ├─purrr:::call_with_cleanup(...)
26. │ └─OmnipathR (local) .f(.x[[i]], ...)
27. │ └─get(sprintf("%s_one_resource", field))(resource, curated)
28. │ └─OmnipathR:::literature_one_resource(resource = resource)
29. │ ├─... %>% with_references(resources = resource)
30. │ └─OmnipathR::import_post_translational_interactions(resources = resource)
31. │ └─OmnipathR::post_translational(...)
32. │ ├─rlang::exec(omnipath_query, !!!args)
33. │ └─OmnipathR (local) `<fn>`(resources = "iTALK", query_type = "interactions", datasets = `<chr>`)
34. │ └─environment() %>% as.list %>% c(list(...)) %>% ...
35. ├─OmnipathR::with_references(., resources = resource)
36. │ └─... %>% distinct(across(everything()))
37. ├─dplyr::distinct(., across(everything()))
38. ├─dplyr::bind_rows(.)
39. │ └─rlang::list2(...)
40. ├─purrr::map(., .with_references, data = data)
41. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
42. │ ├─purrr:::with_indexed_errors(...)
43. │ │ └─base::withCallingHandlers(...)
44. │ ├─purrr:::call_with_cleanup(...)
45. │ └─OmnipathR (local) .f(.x[[i]], ...)
46. │ └─data %>% filter(predicate(references))
47. ├─dplyr::filter(., predicate(references))
48. ├─OmnipathR:::omnipath_check_param(.)
49. │ └─OmnipathR::resources(param$query_type)
50. │ └─OmnipathR:::safe_json(path = resources_url)
51. │ └─base::readLines(con = path, encoding = encoding)
52. │ └─base::file(con, "r")
53. └─base::.handleSimpleError(...)
54. └─purrr (local) h(simpleError(msg, call))
55. └─cli::cli_abort(...)
56. └─rlang::abort(...)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotation_categories 75.265 0.072 76.755
curated_ligand_receptor_interactions 6.510 0.855 16.766
all_uniprots 1.615 0.322 21.101
annotated_network 1.437 0.404 26.776
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.16.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2025-04-23 15:13:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 15:13:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 15:13:51] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-04-23 15:13:51] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-04-23 15:13:51] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-23 [2025-04-23 15:13:51] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-23 19:13:37 UTC; unix [2025-04-23 15:13:51] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-04-23 15:13:51] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-04-23 15:13:52] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-04-23; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto] [2025-04-23 15:13:52] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-04-23 15:13:52] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.0(2025-03-21); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-04-23); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-04-23 15:13:52] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-04-23 15:13:52] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-23 15:13:52] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-04-23 15:13:52] [TRACE] [OmnipathR] Contains 8 files. [2025-04-23 15:13:52] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-23 15:13:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 15:13:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 15:13:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-04-23 15:13:52] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-04-23 15:13:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-23 15:13:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 15:13:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-23 15:13:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 15:13:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-23 15:13:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 15:13:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-23 15:13:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 15:13:52] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-04-23 15:13:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 15:13:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 15:13:54] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-04-23 15:13:54] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-04-23 15:13:54] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-23 [2025-04-23 15:13:54] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-23 19:13:37 UTC; unix [2025-04-23 15:13:54] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-04-23 15:13:54] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-04-23 15:13:55] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-04-23; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto] [2025-04-23 15:13:55] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-04-23 15:13:55] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.0(2025-03-21); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-04-23); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-04-23 15:13:55] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-04-23 15:13:55] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-23 15:13:55] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-04-23 15:13:55] [TRACE] [OmnipathR] Contains 1 files. [2025-04-23 15:13:55] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-23 15:13:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-23 15:13:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 15:13:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-04-23 15:13:55] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-04-23 15:13:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-23 15:13:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 15:13:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-23 15:13:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 15:13:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-23 15:13:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 15:13:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-23 15:13:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-23 15:13:55] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #!/usr/bin/env Rscript
>
> #
> # This file is part of the `OmnipathR` R package
> #
> # Copyright
> # 2018-2024
> # Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> # File author(s): Alberto Valdeolivas
> # Dénes Türei (turei.denes@gmail.com)
> # Attila Gábor
> #
> # Distributed under the MIT (Expat) License.
> # See accompanying file `LICENSE` or find a copy at
> # https://directory.fsf.org/wiki/License:Expat
> #
> # Website: https://r.omnipathdb.org/
> # Git repo: https://github.com/saezlab/OmnipathR
> #
>
>
> library(testthat)
> library(OmnipathR)
[2025-04-24 01:08:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:08:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:08:29] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-04-24 01:08:29] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-04-24 01:08:29] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-23
[2025-04-24 01:08:29] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-23 19:13:37 UTC; unix
[2025-04-24 01:08:29] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-04-24 01:08:29] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-04-24 01:08:29] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-04-24; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-04-24 01:08:29] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-04-24 01:08:30] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-04-23); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); testthat 3.2.3(2025-01-13); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-04-24 01:08:30] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-04-24 01:08:30] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-04-24 01:08:30] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-04-24 01:08:30] [TRACE] [OmnipathR] Contains 33 files.
[2025-04-24 01:08:30] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-04-24 01:08:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-24 01:08:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:08:30] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-04-24 01:08:30] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-04-24 01:08:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-24 01:08:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:08:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-24 01:08:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:08:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-24 01:08:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:08:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-24 01:08:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-24 01:08:30] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 38 ]
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 38 ]
>
> proc.time()
user system elapsed
25.878 3.077 157.877
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.000 | 0.000 | 0.001 | |
| all_uniprot_acs | 0.015 | 0.001 | 0.016 | |
| all_uniprots | 1.615 | 0.322 | 21.101 | |
| ancestors | 0.008 | 0.001 | 0.010 | |
| annotated_network | 1.437 | 0.404 | 26.776 | |
| annotation_categories | 75.265 | 0.072 | 76.755 | |
| annotation_resources | 0.168 | 0.016 | 0.964 | |
| annotations | 0.647 | 0.098 | 1.578 | |
| biomart_query | 1.009 | 0.051 | 2.009 | |
| bioplex1 | 0.009 | 0.001 | 0.009 | |
| bioplex2 | 0.007 | 0.001 | 0.008 | |
| bioplex3 | 0.006 | 0.001 | 0.008 | |
| bioplex_all | 0.007 | 0.001 | 0.008 | |
| bioplex_hct116_1 | 0.007 | 0.001 | 0.007 | |
| bma_motif_es | 0.681 | 0.073 | 1.694 | |
| bma_motif_vs | 0.208 | 0.004 | 0.924 | |
| chalmers_gem | 0.009 | 0.000 | 0.009 | |
| chalmers_gem_id_mapping_table | 0.008 | 0.000 | 0.008 | |
| chalmers_gem_id_type | 0.002 | 0.000 | 0.002 | |
| chalmers_gem_metabolites | 0.008 | 0.000 | 0.008 | |
| chalmers_gem_network | 0.009 | 0.000 | 0.008 | |
| chalmers_gem_raw | 0.008 | 0.000 | 0.008 | |
| chalmers_gem_reactions | 0.007 | 0.001 | 0.008 | |
| common_name | 0.030 | 0.001 | 0.031 | |
| complex_genes | 0.715 | 0.030 | 2.642 | |
| complex_resources | 0.171 | 0.005 | 0.823 | |
| complexes | 0.236 | 0.004 | 0.908 | |
| consensuspathdb_download | 0 | 0 | 0 | |
| consensuspathdb_raw_table | 0.007 | 0.001 | 0.008 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 6.510 | 0.855 | 16.766 | |