Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-20 12:04 -0400 (Mon, 20 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4632 |
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 1765/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ReUseData 1.9.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | 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: 1.9.0 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReUseData_1.9.0.tar.gz |
StartedAt: 2025-10-20 03:53:22 -0400 (Mon, 20 Oct 2025) |
EndedAt: 2025-10-20 03:56:02 -0400 (Mon, 20 Oct 2025) |
EllapsedTime: 160.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ReUseData.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReUseData_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * 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 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘ReUseData/DESCRIPTION’ ... OK * this is package ‘ReUseData’ version ‘1.9.0’ * 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 5.709 0.235 5.946 * 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-3.22-bioc/meat/ReUseData.Rcheck/00check.log’ for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.9.0’ ** 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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 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... 48c963e8b0e7f_GRCh38.primary_assembly.genome.fa.1.bt2 added 48c964ce35e39_GRCh38.primary_assembly.genome.fa.2.bt2 added 48c9646295bb7_GRCh38.primary_assembly.genome.fa.3.bt2 added 48c9618a67f58_GRCh38.primary_assembly.genome.fa.4.bt2 added 48c9667d229f6_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added 48c9667e74452_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added 48c963a30f7e5_outfile.txt added 48c965da4743b_GRCh37_to_GRCh38.chain added 48c966d294ac9_GRCh37_to_NCBI34.chain added 48c9666568e93_GRCh37_to_NCBI35.chain added 48c9668b8c985_GRCh37_to_NCBI36.chain added 48c963da244b9_GRCh38_to_GRCh37.chain added 48c962fd4685c_GRCh38_to_NCBI34.chain added 48c9668f743de_GRCh38_to_NCBI35.chain added 48c9615512cdc_GRCh38_to_NCBI36.chain added 48c963759daae_NCBI34_to_GRCh37.chain added 48c96338901aa_NCBI34_to_GRCh38.chain added 48c9630b9d12d_NCBI35_to_GRCh37.chain added 48c964c793644_NCBI35_to_GRCh38.chain added 48c965bc78be8_NCBI36_to_GRCh37.chain added 48c962444fc54_NCBI36_to_GRCh38.chain added 48c962bb9c01e_GRCm38_to_NCBIM36.chain added 48c96443a670c_GRCm38_to_NCBIM37.chain added 48c963d6aa0d1_NCBIM36_to_GRCm38.chain added 48c9648888760_NCBIM37_to_GRCm38.chain added 48c96160b24ed_1000G_omni2.5.b37.vcf.gz added 48c967f786105_1000G_omni2.5.b37.vcf.gz.tbi added 48c9620b47611_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added 48c96271f4a1e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added 48c966fbd857e_1000G_omni2.5.hg38.vcf.gz added 48c9661241aa9_1000G_omni2.5.hg38.vcf.gz.tbi added 48c9665aa589d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added 48c963ca0e3b7_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added 48c96274d7661_af-only-gnomad.raw.sites.vcf added 48c967e50d7f5_af-only-gnomad.raw.sites.vcf.idx added 48c9624730dae_Mutect2-exome-panel.vcf.idx added 48c96f34bab3_Mutect2-WGS-panel-b37.vcf added 48c963881cfda_Mutect2-WGS-panel-b37.vcf.idx added 48c9621781e9_small_exac_common_3.vcf added 48c967c5e057d_small_exac_common_3.vcf.idx added 48c961ed85e6d_1000g_pon.hg38.vcf.gz added 48c966ad04b6e_1000g_pon.hg38.vcf.gz.tbi added 48c963a004a36_af-only-gnomad.hg38.vcf.gz added 48c964eacc6ca_af-only-gnomad.hg38.vcf.gz.tbi added 48c9653c78f4d_small_exac_common_3.hg38.vcf.gz added 48c964f517712_small_exac_common_3.hg38.vcf.gz.tbi added 48c96606a178_gencode.v41.annotation.gtf added 48c9675090f7_gencode.v42.annotation.gtf added 48c96b483f_gencode.vM30.annotation.gtf added 48c96527fd7bc_gencode.vM31.annotation.gtf added 48c9663181cdf_gencode.v41.transcripts.fa added 48c9624504493_gencode.v41.transcripts.fa.fai added 48c967e3997da_gencode.v42.transcripts.fa added 48c96275283eb_gencode.v42.transcripts.fa.fai added 48c9661bae565_gencode.vM30.pc_transcripts.fa added 48c9646c21f3a_gencode.vM30.pc_transcripts.fa.fai added 48c963d5da8d9_gencode.vM31.pc_transcripts.fa added 48c966133466a_gencode.vM31.pc_transcripts.fa.fai added 48c966776954b_GRCh38.primary_assembly.genome.fa.1.ht2 added 48c96647cf2f7_GRCh38.primary_assembly.genome.fa.2.ht2 added 48c9650f0cbe8_GRCh38.primary_assembly.genome.fa.3.ht2 added 48c96489aaff5_GRCh38.primary_assembly.genome.fa.4.ht2 added 48c964a274b94_GRCh38.primary_assembly.genome.fa.5.ht2 added 48c96d91afa0_GRCh38.primary_assembly.genome.fa.6.ht2 added 48c966fe82656_GRCh38.primary_assembly.genome.fa.7.ht2 added 48c9648782389_GRCh38.primary_assembly.genome.fa.8.ht2 added 48c963204bd4e_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added 48c967f1ce109_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added 48c96f9f364_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added 48c96341c3f37_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added 48c967b7ae686_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added 48c961fd251d1_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added 48c961eec8aa5_GRCh38_full_analysis_set_plus_decoy_hla.fa added 48c96357b30bc_GRCh38.primary_assembly.genome.fa.fai added 48c966e7f189b_GRCh38.primary_assembly.genome.fa.amb added 48c9672b419f2_GRCh38.primary_assembly.genome.fa.ann added 48c964cca7cf_GRCh38.primary_assembly.genome.fa.bwt added 48c967485ba14_GRCh38.primary_assembly.genome.fa.pac added 48c967a04aaea_GRCh38.primary_assembly.genome.fa.sa added 48c964d7f00e_GRCh38.primary_assembly.genome.fa added 48c96470591d0_hs37d5.fa.fai added 48c965d1cc7c9_hs37d5.fa.amb added 48c96292834a2_hs37d5.fa.ann added 48c96453f29ab_hs37d5.fa.bwt added 48c9646f4bb5_hs37d5.fa.pac added 48c96ae31a07_hs37d5.fa.sa added 48c96c0148e5_hs37d5.fa added 48c9641ccf48e_complete_ref_lens.bin added 48c966c166071_ctable.bin added 48c967377de31_ctg_offsets.bin added 48c962649e785_duplicate_clusters.tsv added 48c963d072c5a_info.json added 48c963c128e26_mphf.bin added 48c9670713319_pos.bin added 48c964a98dbfa_pre_indexing.log added 48c962bfab47c_rank.bin added 48c9638e956a2_ref_indexing.log added 48c967c9d9948_refAccumLengths.bin added 48c962b179585_reflengths.bin added 48c9639e34a06_refseq.bin added 48c9630b9d87f_seq.bin added 48c9626927c0c_versionInfo.json added 48c9659b59bd8_salmon_index added 48c964fa66324_chrLength.txt added 48c965c0dacc8_chrName.txt added 48c964834b473_chrNameLength.txt added 48c96425a7d17_chrStart.txt added 48c9660da5497_exonGeTrInfo.tab added 48c963cba6e87_exonInfo.tab added 48c963c5f2801_geneInfo.tab added 48c9665b244a6_Genome added 48c963c00058_genomeParameters.txt added 48c96197befca_Log.out added 48c96eda7948_SA added 48c9648ff2a03_SAindex added 48c961deb3b7f_sjdbInfo.txt added 48c9619bd934f_sjdbList.fromGTF.out.tab added 48c96550072e8_sjdbList.out.tab added 48c965fb8300d_transcriptInfo.tab added 48c965d3f3c0_GRCh38.GENCODE.v42_100 added 48c9648785119_knownGene_hg38.sql added 48c966021792_knownGene_hg38.txt added 48c9642db201a_refGene_hg38.sql added 48c9648adf3f_refGene_hg38.txt added 48c9676734aab_knownGene_mm39.sql added 48c96d73fc14_knownGene_mm39.txt added 48c96308593bb_refGene_mm39.sql added 48c962f5ca14e_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/RtmpAkdfMv/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 17.737 0.908 19.145
ReUseData.Rcheck/ReUseData-Ex.timings
name | user | system | elapsed | |
dataHub-class | 5.709 | 0.235 | 5.946 | |
dataSearch | 1.136 | 0.010 | 1.147 | |
dataUpdate | 0 | 0 | 0 | |
getCloudData | 2.621 | 0.104 | 3.761 | |
getData | 0.001 | 0.000 | 0.000 | |
meta_data | 0.001 | 0.000 | 0.001 | |
recipeHub-class | 0.124 | 0.004 | 0.129 | |
recipeLoad | 1.250 | 0.018 | 1.268 | |
recipeMake | 0 | 0 | 0 | |
recipeSearch | 0.519 | 0.005 | 0.524 | |
recipeUpdate | 0.001 | 0.000 | 0.000 | |