Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-16 11:39 -0400 (Thu, 16 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
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 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.7.5 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReUseData_1.8.0.tar.gz |
StartedAt: 2025-10-14 09:04:55 -0400 (Tue, 14 Oct 2025) |
EndedAt: 2025-10-14 09:09:06 -0400 (Tue, 14 Oct 2025) |
EllapsedTime: 251.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ReUseData.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReUseData_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’ * using R version 4.5.1 RC (2025-06-05 r88288) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * 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 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 12.153 1.261 13.660 getCloudData 4.677 0.214 6.131 * 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 ‘/Users/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck/00check.log’ for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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... 91267ca17082_GRCh38.primary_assembly.genome.fa.1.bt2 added 91264ae1a6ba_GRCh38.primary_assembly.genome.fa.2.bt2 added 9126248923be_GRCh38.primary_assembly.genome.fa.3.bt2 added 91262789a1af_GRCh38.primary_assembly.genome.fa.4.bt2 added 91263cd5fc70_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added 91264b03c44_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added 91264e4496c3_outfile.txt added 912679060459_GRCh37_to_GRCh38.chain added 91267a07ad21_GRCh37_to_NCBI34.chain added 9126df7901e_GRCh37_to_NCBI35.chain added 91267816a8bb_GRCh37_to_NCBI36.chain added 9126179fca95_GRCh38_to_GRCh37.chain added 91267bad0850_GRCh38_to_NCBI34.chain added 91261cfcfb9f_GRCh38_to_NCBI35.chain added 912624eb9297_GRCh38_to_NCBI36.chain added 912665e50a70_NCBI34_to_GRCh37.chain added 912620107353_NCBI34_to_GRCh38.chain added 912618035e97_NCBI35_to_GRCh37.chain added 912653717d2_NCBI35_to_GRCh38.chain added 912663fcdeaa_NCBI36_to_GRCh37.chain added 91266e7e9e2e_NCBI36_to_GRCh38.chain added 91263ac316ae_GRCm38_to_NCBIM36.chain added 91265e0617a5_GRCm38_to_NCBIM37.chain added 912661fa81dc_NCBIM36_to_GRCm38.chain added 9126563c4c5_NCBIM37_to_GRCm38.chain added 9126590b6446_1000G_omni2.5.b37.vcf.gz added 91267ae45d55_1000G_omni2.5.b37.vcf.gz.tbi added 912626abb67b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added 912653595912_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added 9126ee6d77e_1000G_omni2.5.hg38.vcf.gz added 9126554d98d6_1000G_omni2.5.hg38.vcf.gz.tbi added 9126596d355a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added 912610c9d594_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added 912632e4f028_af-only-gnomad.raw.sites.vcf added 91265452ec32_af-only-gnomad.raw.sites.vcf.idx added 91261010f1de_Mutect2-exome-panel.vcf.idx added 912648772e0f_Mutect2-WGS-panel-b37.vcf added 9126870fff4_Mutect2-WGS-panel-b37.vcf.idx added 912632b3f080_small_exac_common_3.vcf added 912643727d81_small_exac_common_3.vcf.idx added 9126118dc2bf_1000g_pon.hg38.vcf.gz added 912671ec9299_1000g_pon.hg38.vcf.gz.tbi added 9126628cb53d_af-only-gnomad.hg38.vcf.gz added 91263ceea57_af-only-gnomad.hg38.vcf.gz.tbi added 912657af7b5_small_exac_common_3.hg38.vcf.gz added 91264c1c8ee2_small_exac_common_3.hg38.vcf.gz.tbi added 912666e8be77_gencode.v41.annotation.gtf added 91263a30ab69_gencode.v42.annotation.gtf added 912651459857_gencode.vM30.annotation.gtf added 91263014a170_gencode.vM31.annotation.gtf added 91261a72d8b9_gencode.v41.transcripts.fa added 912669f2673f_gencode.v41.transcripts.fa.fai added 912629588f70_gencode.v42.transcripts.fa added 912675311744_gencode.v42.transcripts.fa.fai added 912669eead77_gencode.vM30.pc_transcripts.fa added 912634be95f6_gencode.vM30.pc_transcripts.fa.fai added 91264c676487_gencode.vM31.pc_transcripts.fa added 912617f90241_gencode.vM31.pc_transcripts.fa.fai added 91265d0305b2_GRCh38.primary_assembly.genome.fa.1.ht2 added 9126716b18d2_GRCh38.primary_assembly.genome.fa.2.ht2 added 91262e2abd2a_GRCh38.primary_assembly.genome.fa.3.ht2 added 912677e92813_GRCh38.primary_assembly.genome.fa.4.ht2 added 91266c4634e5_GRCh38.primary_assembly.genome.fa.5.ht2 added 9126753addeb_GRCh38.primary_assembly.genome.fa.6.ht2 added 91266bbfab6d_GRCh38.primary_assembly.genome.fa.7.ht2 added 9126748fb85e_GRCh38.primary_assembly.genome.fa.8.ht2 added 91267915f1b_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added 912658fae97e_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added 912640f77cd5_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added 91263824a545_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added 91266dde71ce_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added 91262701c3bc_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added 912664d97fa5_GRCh38_full_analysis_set_plus_decoy_hla.fa added 912634b5d5d_GRCh38.primary_assembly.genome.fa.fai added 912648de865b_GRCh38.primary_assembly.genome.fa.amb added 9126946e5bd_GRCh38.primary_assembly.genome.fa.ann added 9126d94e00d_GRCh38.primary_assembly.genome.fa.bwt added 912629017c72_GRCh38.primary_assembly.genome.fa.pac added 912620913566_GRCh38.primary_assembly.genome.fa.sa added 91261d48cc3e_GRCh38.primary_assembly.genome.fa added 912616590977_hs37d5.fa.fai added 91262f7c6f17_hs37d5.fa.amb added 91261261675c_hs37d5.fa.ann added 912638c8d271_hs37d5.fa.bwt added 912687015d7_hs37d5.fa.pac added 912676a9da94_hs37d5.fa.sa added 912694d6769_hs37d5.fa added 912638c02344_complete_ref_lens.bin added 91264e4b6277_ctable.bin added 9126372d9ac9_ctg_offsets.bin added 9126130d1e6c_duplicate_clusters.tsv added 912642484e39_info.json added 91261907a22e_mphf.bin added 9126442886d8_pos.bin added 912640acf1dd_pre_indexing.log added 91261a3b0557_rank.bin added 912618dba035_ref_indexing.log added 91267af30452_refAccumLengths.bin added 912668a0e28d_reflengths.bin added 91261a79cca5_refseq.bin added 9126326a7237_seq.bin added 91266a7092bc_versionInfo.json added 91264b1ab3c_salmon_index added 91262c60f28c_chrLength.txt added 912610d3dc17_chrName.txt added 9126451672a2_chrNameLength.txt added 912644c00d1d_chrStart.txt added 91261c9d0e2e_exonGeTrInfo.tab added 9126b0dfcaf_exonInfo.tab added 912643484ad4_geneInfo.tab added 91263f28c6ce_Genome added 9126e141ec7_genomeParameters.txt added 91264af0a209_Log.out added 91267c1e234e_SA added 91261ea0158b_SAindex added 91261fe66862_sjdbInfo.txt added 91264fcf0a4a_sjdbList.fromGTF.out.tab added 912621aca935_sjdbList.out.tab added 91264e98e7d8_transcriptInfo.tab added 9126189d3e38_GRCh38.GENCODE.v42_100 added 91267b5fdb27_knownGene_hg38.sql added 9126522d1cb8_knownGene_hg38.txt added 9126fb89e2e_refGene_hg38.sql added 91262198e612_refGene_hg38.txt added 91263d28b8f9_knownGene_mm39.sql added 91263c8802cd_knownGene_mm39.txt added 912656fffc7_refGene_mm39.sql added 91267c01649a_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/RtmpJf0WxQ/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 41.536 5.082 47.776
ReUseData.Rcheck/ReUseData-Ex.timings
name | user | system | elapsed | |
dataHub-class | 12.153 | 1.261 | 13.660 | |
dataSearch | 2.461 | 0.080 | 2.602 | |
dataUpdate | 0.000 | 0.001 | 0.002 | |
getCloudData | 4.677 | 0.214 | 6.131 | |
getData | 0.001 | 0.002 | 0.001 | |
meta_data | 0.001 | 0.000 | 0.002 | |
recipeHub-class | 0.254 | 0.023 | 0.278 | |
recipeLoad | 2.812 | 0.141 | 2.978 | |
recipeMake | 0.000 | 0.001 | 0.001 | |
recipeSearch | 1.159 | 0.053 | 1.215 | |
recipeUpdate | 0.000 | 0.000 | 0.001 | |