Qian Liu
| Snapshot Date: 2025-04-16 13:40 -0400 (Wed, 16 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 2025-04-17 11:47 -0400 (Thu, 17 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" | 4667 |
| 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: ReUseData |
| Version: 1.8.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ReUseData_1.8.0.tar.gz |
| StartedAt: 2025-04-17 10:39:43 -0000 (Thu, 17 Apr 2025) |
| EndedAt: 2025-04-17 10:42:30 -0000 (Thu, 17 Apr 2025) |
| EllapsedTime: 167.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ReUseData_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 8.919 0.635 9.588
getCloudData 3.330 0.207 7.646
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* 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/R/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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...
2fe215ae378ce_GRCh38.primary_assembly.genome.fa.1.bt2 added
2fe21514513710_GRCh38.primary_assembly.genome.fa.2.bt2 added
2fe21534be9154_GRCh38.primary_assembly.genome.fa.3.bt2 added
2fe21519952585_GRCh38.primary_assembly.genome.fa.4.bt2 added
2fe2153c76d9af_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2fe21544938cd7_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2fe215ca8811b_outfile.txt added
2fe2152bc31894_GRCh37_to_GRCh38.chain added
2fe21575ec8aa2_GRCh37_to_NCBI34.chain added
2fe2154e7b6d11_GRCh37_to_NCBI35.chain added
2fe21522079115_GRCh37_to_NCBI36.chain added
2fe2156baf16d4_GRCh38_to_GRCh37.chain added
2fe21539092241_GRCh38_to_NCBI34.chain added
2fe2154b21f0c2_GRCh38_to_NCBI35.chain added
2fe215e4c06c1_GRCh38_to_NCBI36.chain added
2fe2154e6adc62_NCBI34_to_GRCh37.chain added
2fe2154d34b66c_NCBI34_to_GRCh38.chain added
2fe2151fc46fa1_NCBI35_to_GRCh37.chain added
2fe2155b15c217_NCBI35_to_GRCh38.chain added
2fe215776bb978_NCBI36_to_GRCh37.chain added
2fe215704fc29a_NCBI36_to_GRCh38.chain added
2fe2153101e208_GRCm38_to_NCBIM36.chain added
2fe215101a21e_GRCm38_to_NCBIM37.chain added
2fe21529c9676f_NCBIM36_to_GRCm38.chain added
2fe215248a6ae4_NCBIM37_to_GRCm38.chain added
2fe2151a987ef2_1000G_omni2.5.b37.vcf.gz added
2fe2152a741081_1000G_omni2.5.b37.vcf.gz.tbi added
2fe215426e37ad_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2fe215643417c2_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2fe215218a0a4_1000G_omni2.5.hg38.vcf.gz added
2fe215a7bf472_1000G_omni2.5.hg38.vcf.gz.tbi added
2fe2156f179090_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2fe2151669d7b5_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2fe2153f3a85c7_af-only-gnomad.raw.sites.vcf added
2fe2158acb615_af-only-gnomad.raw.sites.vcf.idx added
2fe21552e0b164_Mutect2-exome-panel.vcf.idx added
2fe2153ce129e_Mutect2-WGS-panel-b37.vcf added
2fe21515553730_Mutect2-WGS-panel-b37.vcf.idx added
2fe2157ea3c9f8_small_exac_common_3.vcf added
2fe21579ba9d40_small_exac_common_3.vcf.idx added
2fe21563d0a441_1000g_pon.hg38.vcf.gz added
2fe21520ab5b0d_1000g_pon.hg38.vcf.gz.tbi added
2fe2156569b415_af-only-gnomad.hg38.vcf.gz added
2fe2151cd9c683_af-only-gnomad.hg38.vcf.gz.tbi added
2fe2156bcd4bd0_small_exac_common_3.hg38.vcf.gz added
2fe21573b5bad6_small_exac_common_3.hg38.vcf.gz.tbi added
2fe2156b44a2e5_gencode.v41.annotation.gtf added
2fe2153902023c_gencode.v42.annotation.gtf added
2fe215137a2a77_gencode.vM30.annotation.gtf added
2fe215465a64fc_gencode.vM31.annotation.gtf added
2fe215306dbbb4_gencode.v41.transcripts.fa added
2fe2153c9ed11_gencode.v41.transcripts.fa.fai added
2fe215775c4705_gencode.v42.transcripts.fa added
2fe215316f5dd2_gencode.v42.transcripts.fa.fai added
2fe2152d935481_gencode.vM30.pc_transcripts.fa added
2fe2151be6b1e9_gencode.vM30.pc_transcripts.fa.fai added
2fe2154c07dcc4_gencode.vM31.pc_transcripts.fa added
2fe21558076502_gencode.vM31.pc_transcripts.fa.fai added
2fe2155e54e996_GRCh38.primary_assembly.genome.fa.1.ht2 added
2fe215303bf487_GRCh38.primary_assembly.genome.fa.2.ht2 added
2fe2155a2005a7_GRCh38.primary_assembly.genome.fa.3.ht2 added
2fe21568d0de09_GRCh38.primary_assembly.genome.fa.4.ht2 added
2fe2151f538517_GRCh38.primary_assembly.genome.fa.5.ht2 added
2fe2157089dd5c_GRCh38.primary_assembly.genome.fa.6.ht2 added
2fe215280b63d0_GRCh38.primary_assembly.genome.fa.7.ht2 added
2fe21528003b2d_GRCh38.primary_assembly.genome.fa.8.ht2 added
2fe215436a8ec0_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2fe2152bd9766e_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2fe2153d55725d_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2fe215420e58b8_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2fe215259413ae_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2fe2152126169f_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2fe21562b9b3c6_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2fe215afdc7c3_GRCh38.primary_assembly.genome.fa.fai added
2fe2153dffdd22_GRCh38.primary_assembly.genome.fa.amb added
2fe2154e86ff96_GRCh38.primary_assembly.genome.fa.ann added
2fe2157eb38299_GRCh38.primary_assembly.genome.fa.bwt added
2fe21529448007_GRCh38.primary_assembly.genome.fa.pac added
2fe21578901d2_GRCh38.primary_assembly.genome.fa.sa added
2fe215122dad11_GRCh38.primary_assembly.genome.fa added
2fe2156f9ee504_hs37d5.fa.fai added
2fe21537f6bd87_hs37d5.fa.amb added
2fe21515f79a22_hs37d5.fa.ann added
2fe21566fb2c09_hs37d5.fa.bwt added
2fe21569661b59_hs37d5.fa.pac added
2fe215438aeea3_hs37d5.fa.sa added
2fe2152e1ddf2_hs37d5.fa added
2fe215356df81e_complete_ref_lens.bin added
2fe2151b9253a6_ctable.bin added
2fe2156136c788_ctg_offsets.bin added
2fe21565a9eca5_duplicate_clusters.tsv added
2fe21575b2594d_info.json added
2fe2154a07a591_mphf.bin added
2fe2154fd71bc_pos.bin added
2fe215663c36a9_pre_indexing.log added
2fe21572130961_rank.bin added
2fe2152cfdace9_ref_indexing.log added
2fe21529a6c569_refAccumLengths.bin added
2fe2151dec7fcf_reflengths.bin added
2fe2156a531f47_refseq.bin added
2fe2156bb51e21_seq.bin added
2fe2154380937e_versionInfo.json added
2fe215b7935e6_salmon_index added
2fe2154e6ed1e7_chrLength.txt added
2fe2154e7e5b41_chrName.txt added
2fe21549791308_chrNameLength.txt added
2fe2151cf5d17d_chrStart.txt added
2fe2154d31dddb_exonGeTrInfo.tab added
2fe21572bd930f_exonInfo.tab added
2fe215247ed350_geneInfo.tab added
2fe2155f5f8aec_Genome added
2fe215625c7813_genomeParameters.txt added
2fe2155c7590d7_Log.out added
2fe2157557250e_SA added
2fe2154957a41c_SAindex added
2fe21545dbac30_sjdbInfo.txt added
2fe21538e213b2_sjdbList.fromGTF.out.tab added
2fe2154c39820e_sjdbList.out.tab added
2fe2157b49a44e_transcriptInfo.tab added
2fe21554746758_GRCh38.GENCODE.v42_100 added
2fe2152d704997_knownGene_hg38.sql added
2fe21560f390f3_knownGene_hg38.txt added
2fe2154a26c0a5_refGene_hg38.sql added
2fe2157777ef28_refGene_hg38.txt added
2fe21565f102b0_knownGene_mm39.sql added
2fe2153062f74e_knownGene_mm39.txt added
2fe215698af88a_refGene_mm39.sql added
2fe21512eeaf99_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:
/home/biocbuild/tmp/RtmpsRtIZh/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
30.077 1.690 33.790
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 8.919 | 0.635 | 9.588 | |
| dataSearch | 1.658 | 0.048 | 1.709 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 3.330 | 0.207 | 7.646 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.167 | 0.008 | 0.176 | |
| recipeLoad | 1.876 | 0.076 | 1.961 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.772 | 0.036 | 0.809 | |
| recipeUpdate | 0 | 0 | 0 | |