Qian Liu
| Snapshot Date: 2025-04-17 13:40 -0400 (Thu, 17 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_21 |
| git_last_commit: 601a107 |
| git_last_commit_date: 2025-04-15 13:01:44 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-18 11:41 -0400 (Fri, 18 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 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
| 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 1758/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.8.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the ReUseData package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ReUseData.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: ReUseData |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ReUseData_1.8.0.tar.gz |
| StartedAt: 2025-04-18 01:54:32 -0400 (Fri, 18 Apr 2025) |
| EndedAt: 2025-04-18 01:57:24 -0400 (Fri, 18 Apr 2025) |
| EllapsedTime: 171.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ReUseData_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ReUseData.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 ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ReUseData’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dataHub-class 5.863 0.375 6.239
* 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 NOTE
See
‘/home/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.8.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ReUseData)
ReUseData.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.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'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.
> library(testthat)
> library(ReUseData)
>
> test_check("ReUseData")
Note: you need to assign a name for the recipe: rcpName <- recipeLoad('xx')
Data recipe loaded!
Use inputs() to check required input parameters before evaluation.
Check here: https://rcwl.org/dataRecipes/echo_out.html
for user instructions (e.g., eligible input values, data source, etc.)
}[1;30mINFO[0m Final process status is success
Updating data record...
outfile.txt added
Updating data record...
a80b6e03cd29_GRCh38.primary_assembly.genome.fa.1.bt2 added
a80b64c304629_GRCh38.primary_assembly.genome.fa.2.bt2 added
a80b62b84c24d_GRCh38.primary_assembly.genome.fa.3.bt2 added
a80b63466eff0_GRCh38.primary_assembly.genome.fa.4.bt2 added
a80b66c27ad9c_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
a80b662de7c67_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
a80b67c9416f7_outfile.txt added
a80b662a143af_GRCh37_to_GRCh38.chain added
a80b6699ae90f_GRCh37_to_NCBI34.chain added
a80b610dec53e_GRCh37_to_NCBI35.chain added
a80b63005dfd5_GRCh37_to_NCBI36.chain added
a80b62a04cf94_GRCh38_to_GRCh37.chain added
a80b61fb0f9a8_GRCh38_to_NCBI34.chain added
a80b65dcff8a3_GRCh38_to_NCBI35.chain added
a80b64abbf7fa_GRCh38_to_NCBI36.chain added
a80b619633374_NCBI34_to_GRCh37.chain added
a80b65726424f_NCBI34_to_GRCh38.chain added
a80b622d76950_NCBI35_to_GRCh37.chain added
a80b63a0ea872_NCBI35_to_GRCh38.chain added
a80b672eae0c4_NCBI36_to_GRCh37.chain added
a80b67f7c606c_NCBI36_to_GRCh38.chain added
a80b674653ff4_GRCm38_to_NCBIM36.chain added
a80b62fed3aea_GRCm38_to_NCBIM37.chain added
a80b6613dec05_NCBIM36_to_GRCm38.chain added
a80b61d8e0ea_NCBIM37_to_GRCm38.chain added
a80b6face218_1000G_omni2.5.b37.vcf.gz added
a80b649908e72_1000G_omni2.5.b37.vcf.gz.tbi added
a80b67f5cfb1d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
a80b664fad2a0_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
a80b6223e91c6_1000G_omni2.5.hg38.vcf.gz added
a80b6695a2a65_1000G_omni2.5.hg38.vcf.gz.tbi added
a80b672fe9fca_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
a80b66e6ed7f0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
a80b614deecb2_af-only-gnomad.raw.sites.vcf added
a80b627658fba_af-only-gnomad.raw.sites.vcf.idx added
a80b65a96858c_Mutect2-exome-panel.vcf.idx added
a80b677bd691a_Mutect2-WGS-panel-b37.vcf added
a80b623f9a6b1_Mutect2-WGS-panel-b37.vcf.idx added
a80b63d37c93b_small_exac_common_3.vcf added
a80b661585229_small_exac_common_3.vcf.idx added
a80b634d86bf0_1000g_pon.hg38.vcf.gz added
a80b66d3da910_1000g_pon.hg38.vcf.gz.tbi added
a80b6b5d21bd_af-only-gnomad.hg38.vcf.gz added
a80b654896598_af-only-gnomad.hg38.vcf.gz.tbi added
a80b64b0da1b4_small_exac_common_3.hg38.vcf.gz added
a80b6561919b7_small_exac_common_3.hg38.vcf.gz.tbi added
a80b66dec990c_gencode.v41.annotation.gtf added
a80b62233e403_gencode.v42.annotation.gtf added
a80b678f08307_gencode.vM30.annotation.gtf added
a80b627fb417f_gencode.vM31.annotation.gtf added
a80b6151ec4c8_gencode.v41.transcripts.fa added
a80b6786ce373_gencode.v41.transcripts.fa.fai added
a80b61c608173_gencode.v42.transcripts.fa added
a80b6450bffb2_gencode.v42.transcripts.fa.fai added
a80b659aacf78_gencode.vM30.pc_transcripts.fa added
a80b61e39625d_gencode.vM30.pc_transcripts.fa.fai added
a80b654b8e1ca_gencode.vM31.pc_transcripts.fa added
a80b6233b5deb_gencode.vM31.pc_transcripts.fa.fai added
a80b61d965d7a_GRCh38.primary_assembly.genome.fa.1.ht2 added
a80b639b3b46b_GRCh38.primary_assembly.genome.fa.2.ht2 added
a80b64579efb1_GRCh38.primary_assembly.genome.fa.3.ht2 added
a80b66f087e0_GRCh38.primary_assembly.genome.fa.4.ht2 added
a80b62cb25435_GRCh38.primary_assembly.genome.fa.5.ht2 added
a80b633e8c7a1_GRCh38.primary_assembly.genome.fa.6.ht2 added
a80b61bcf7492_GRCh38.primary_assembly.genome.fa.7.ht2 added
a80b65417e3ef_GRCh38.primary_assembly.genome.fa.8.ht2 added
a80b6e7f4d2e_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
a80b6138cddac_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
a80b678118aa0_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
a80b64bb71669_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
a80b674e52fd5_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
a80b62ce9f690_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
a80b638f4bf7a_GRCh38_full_analysis_set_plus_decoy_hla.fa added
a80b6425192_GRCh38.primary_assembly.genome.fa.fai added
a80b61735c29_GRCh38.primary_assembly.genome.fa.amb added
a80b6402612e_GRCh38.primary_assembly.genome.fa.ann added
a80b6565b6b4a_GRCh38.primary_assembly.genome.fa.bwt added
a80b66f5ff535_GRCh38.primary_assembly.genome.fa.pac added
a80b626364531_GRCh38.primary_assembly.genome.fa.sa added
a80b64f4bee51_GRCh38.primary_assembly.genome.fa added
a80b6175b36b4_hs37d5.fa.fai added
a80b63b5509f9_hs37d5.fa.amb added
a80b647b8d1c5_hs37d5.fa.ann added
a80b633bbb827_hs37d5.fa.bwt added
a80b66109ac_hs37d5.fa.pac added
a80b62163a13d_hs37d5.fa.sa added
a80b651f51a84_hs37d5.fa added
a80b65519eb76_complete_ref_lens.bin added
a80b6449eff28_ctable.bin added
a80b66f8b77ff_ctg_offsets.bin added
a80b6ecd9fe1_duplicate_clusters.tsv added
a80b6a18eeda_info.json added
a80b6767bffdf_mphf.bin added
a80b63b7ff416_pos.bin added
a80b63e01b67b_pre_indexing.log added
a80b6124b7471_rank.bin added
a80b6f97d805_ref_indexing.log added
a80b64c8103a9_refAccumLengths.bin added
a80b625d8521e_reflengths.bin added
a80b67a962a6_refseq.bin added
a80b618381a13_seq.bin added
a80b61abd81f3_versionInfo.json added
a80b634935936_salmon_index added
a80b6512cd98d_chrLength.txt added
a80b61affd386_chrName.txt added
a80b63606b55f_chrNameLength.txt added
a80b6552f3abb_chrStart.txt added
a80b6715b3ed0_exonGeTrInfo.tab added
a80b62566aa95_exonInfo.tab added
a80b67b657fec_geneInfo.tab added
a80b640a72d21_Genome added
a80b63cc1e149_genomeParameters.txt added
a80b636ba89e6_Log.out added
a80b685ffee6_SA added
a80b6707d9971_SAindex added
a80b6371b9392_sjdbInfo.txt added
a80b629c3a024_sjdbList.fromGTF.out.tab added
a80b64272b3f5_sjdbList.out.tab added
a80b6c357f08_transcriptInfo.tab added
a80b66e629f4c_GRCh38.GENCODE.v42_100 added
a80b631fe2bf4_knownGene_hg38.sql added
a80b61b031eea_knownGene_hg38.txt added
a80b6787b8e26_refGene_hg38.sql added
a80b6287a2bd3_refGene_hg38.txt added
a80b656831300_knownGene_mm39.sql added
a80b6367d44a2_knownGene_mm39.txt added
a80b63ac5a045_refGene_mm39.sql added
a80b6661aeb06_refGene_mm39.txt added
trying URL 'https://storage.googleapis.com/reusedata/echo/outfile.txt'
Content type 'text/plain' length 30 bytes
==================================================
downloaded 30 bytes
trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.yml'
Content type 'application/x-yaml' length 151 bytes
==================================================
downloaded 151 bytes
trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.cwl'
Content type 'application/octet-stream' length 1152 bytes
==================================================
downloaded 1152 bytes
trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.md5'
Content type 'application/octet-stream' length 45 bytes
==================================================
downloaded 45 bytes
trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.sh'
Content type 'application/x-shellscript' length 68 bytes
==================================================
downloaded 68 bytes
Data is downloaded:
/tmp/RtmpbefzqP/test_gcpData/outfile.txt
}[1;30mINFO[0m Final process status is success
NOTE: existing caches will be removed and regenerated!
Updating recipes...
STAR_index.R added
bowtie2_index.R added
echo_out.R added
ensembl_liftover.R added
gcp_broad_gatk_hg19.R added
gcp_broad_gatk_hg38.R added
gcp_gatk_mutect2_b37.R added
gcp_gatk_mutect2_hg38.R added
gencode_annotation.R added
gencode_genome_grch38.R added
gencode_transcripts.R added
hisat2_index.R added
reference_genome.R added
salmon_index.R added
ucsc_database.R added
Data recipe loaded!
Use inputs(ensembl_liftover) to check required input parameters before evaluation.
Check here: https://rcwl.org/dataRecipes/ensembl_liftover.html
for user instructions (e.g., eligible input values, data source, etc.)
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 44 ]
> Sys.setenv(cachePath = file.path(tempdir(), "cache"))
>
>
>
> proc.time()
user system elapsed
20.141 1.575 21.792
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.863 | 0.375 | 6.239 | |
| dataSearch | 1.104 | 0.019 | 1.123 | |
| dataUpdate | 0.000 | 0.001 | 0.001 | |
| getCloudData | 2.809 | 0.166 | 3.411 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.001 | 0.001 | |
| recipeHub-class | 0.129 | 0.002 | 0.131 | |
| recipeLoad | 1.311 | 0.098 | 1.409 | |
| recipeMake | 0.000 | 0.001 | 0.000 | |
| recipeSearch | 0.554 | 0.049 | 0.604 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |