Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-30 12:05 -0400 (Sat, 30 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
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 1742/2320 | 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 12.7.1 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: 2025-08-30 02:16:47 -0400 (Sat, 30 Aug 2025) |
EndedAt: 2025-08-30 02:19:36 -0400 (Sat, 30 Aug 2025) |
EllapsedTime: 169.2 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 (2025-06-13) * 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 6.122 0.233 6.359 * 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 (2025-06-13) -- "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... 1e085c1c5ff2cd_GRCh38.primary_assembly.genome.fa.1.bt2 added 1e085c445d0562_GRCh38.primary_assembly.genome.fa.2.bt2 added 1e085c67ef217c_GRCh38.primary_assembly.genome.fa.3.bt2 added 1e085c7262ccb8_GRCh38.primary_assembly.genome.fa.4.bt2 added 1e085c4c4b91e9_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added 1e085c7e5d4523_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added 1e085c5fa208b4_outfile.txt added 1e085c6c01e830_GRCh37_to_GRCh38.chain added 1e085c531ddadf_GRCh37_to_NCBI34.chain added 1e085c74e11a6e_GRCh37_to_NCBI35.chain added 1e085c17c248b6_GRCh37_to_NCBI36.chain added 1e085c66923497_GRCh38_to_GRCh37.chain added 1e085c549f54fd_GRCh38_to_NCBI34.chain added 1e085c1444881d_GRCh38_to_NCBI35.chain added 1e085cdb7cf99_GRCh38_to_NCBI36.chain added 1e085c50fc4998_NCBI34_to_GRCh37.chain added 1e085c76b33126_NCBI34_to_GRCh38.chain added 1e085c7c11ef24_NCBI35_to_GRCh37.chain added 1e085c4aeb2c66_NCBI35_to_GRCh38.chain added 1e085c31f8d0a7_NCBI36_to_GRCh37.chain added 1e085c618e0726_NCBI36_to_GRCh38.chain added 1e085c32240049_GRCm38_to_NCBIM36.chain added 1e085c3dee042_GRCm38_to_NCBIM37.chain added 1e085c3083dada_NCBIM36_to_GRCm38.chain added 1e085cbfafd38_NCBIM37_to_GRCm38.chain added 1e085c69821e3a_1000G_omni2.5.b37.vcf.gz added 1e085c7eec6f7a_1000G_omni2.5.b37.vcf.gz.tbi added 1e085c656835d6_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added 1e085c7361f640_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added 1e085c6a311838_1000G_omni2.5.hg38.vcf.gz added 1e085c124f2bd_1000G_omni2.5.hg38.vcf.gz.tbi added 1e085cfc1e90d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added 1e085c2e8e1d9a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added 1e085c6914143a_af-only-gnomad.raw.sites.vcf added 1e085c224b5c5_af-only-gnomad.raw.sites.vcf.idx added 1e085c7ad9af84_Mutect2-exome-panel.vcf.idx added 1e085c6771595d_Mutect2-WGS-panel-b37.vcf added 1e085c61c6be79_Mutect2-WGS-panel-b37.vcf.idx added 1e085c66db97b4_small_exac_common_3.vcf added 1e085c3a8f343d_small_exac_common_3.vcf.idx added 1e085c56a7d8e7_1000g_pon.hg38.vcf.gz added 1e085c7e9de06a_1000g_pon.hg38.vcf.gz.tbi added 1e085c212168d4_af-only-gnomad.hg38.vcf.gz added 1e085c2b472de4_af-only-gnomad.hg38.vcf.gz.tbi added 1e085c12e26887_small_exac_common_3.hg38.vcf.gz added 1e085c2ed9386d_small_exac_common_3.hg38.vcf.gz.tbi added 1e085c7c43777c_gencode.v41.annotation.gtf added 1e085c99599ae_gencode.v42.annotation.gtf added 1e085c2aeb2791_gencode.vM30.annotation.gtf added 1e085c472ea3e3_gencode.vM31.annotation.gtf added 1e085c3b8e6a55_gencode.v41.transcripts.fa added 1e085cc792eb7_gencode.v41.transcripts.fa.fai added 1e085c7952a42c_gencode.v42.transcripts.fa added 1e085c3f6d4a98_gencode.v42.transcripts.fa.fai added 1e085c3cfd0992_gencode.vM30.pc_transcripts.fa added 1e085c54da164_gencode.vM30.pc_transcripts.fa.fai added 1e085c28ef68d2_gencode.vM31.pc_transcripts.fa added 1e085c3be9790c_gencode.vM31.pc_transcripts.fa.fai added 1e085c6ab5d73a_GRCh38.primary_assembly.genome.fa.1.ht2 added 1e085c1c515f13_GRCh38.primary_assembly.genome.fa.2.ht2 added 1e085c261a9144_GRCh38.primary_assembly.genome.fa.3.ht2 added 1e085c6bdac9f8_GRCh38.primary_assembly.genome.fa.4.ht2 added 1e085c2c134820_GRCh38.primary_assembly.genome.fa.5.ht2 added 1e085c54a8aedf_GRCh38.primary_assembly.genome.fa.6.ht2 added 1e085c54eede32_GRCh38.primary_assembly.genome.fa.7.ht2 added 1e085c2e37fde6_GRCh38.primary_assembly.genome.fa.8.ht2 added 1e085c4f825e63_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added 1e085c3c60378f_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added 1e085cffebc5f_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added 1e085c365df617_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added 1e085c76ef6bcc_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added 1e085c66a69547_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added 1e085c34fbd681_GRCh38_full_analysis_set_plus_decoy_hla.fa added 1e085c1810d4a0_GRCh38.primary_assembly.genome.fa.fai added 1e085c11edc32b_GRCh38.primary_assembly.genome.fa.amb added 1e085c47de3f09_GRCh38.primary_assembly.genome.fa.ann added 1e085c46ea0d0e_GRCh38.primary_assembly.genome.fa.bwt added 1e085ce313aa8_GRCh38.primary_assembly.genome.fa.pac added 1e085c5173d8b7_GRCh38.primary_assembly.genome.fa.sa added 1e085c71d5349f_GRCh38.primary_assembly.genome.fa added 1e085c555fde8b_hs37d5.fa.fai added 1e085cd02430c_hs37d5.fa.amb added 1e085c7e4e6357_hs37d5.fa.ann added 1e085c4eb282b7_hs37d5.fa.bwt added 1e085c4c6f8da4_hs37d5.fa.pac added 1e085c3b4b6ce9_hs37d5.fa.sa added 1e085c5400241c_hs37d5.fa added 1e085c755ef677_complete_ref_lens.bin added 1e085c7734e5f5_ctable.bin added 1e085c3eb5fb56_ctg_offsets.bin added 1e085c11b0558a_duplicate_clusters.tsv added 1e085c1d4f773a_info.json added 1e085c2a90c54e_mphf.bin added 1e085c3dc39daa_pos.bin added 1e085c71f82619_pre_indexing.log added 1e085c7f7fa380_rank.bin added 1e085c6bfb9b90_ref_indexing.log added 1e085c417a847c_refAccumLengths.bin added 1e085c3bdfdb10_reflengths.bin added 1e085c7bfa57f0_refseq.bin added 1e085c77d87a93_seq.bin added 1e085c32cf46dc_versionInfo.json added 1e085c62a0ed37_salmon_index added 1e085c2cd45114_chrLength.txt added 1e085c4ae01b7d_chrName.txt added 1e085c748eb062_chrNameLength.txt added 1e085c74b2901d_chrStart.txt added 1e085c11ca288b_exonGeTrInfo.tab added 1e085c2bfeb0a_exonInfo.tab added 1e085c462668d4_geneInfo.tab added 1e085c39f5d2a_Genome added 1e085c581fc995_genomeParameters.txt added 1e085c5328abe1_Log.out added 1e085c1edc081_SA added 1e085c26d24c4d_SAindex added 1e085c1f983985_sjdbInfo.txt added 1e085c3d392d6a_sjdbList.fromGTF.out.tab added 1e085c7ad27069_sjdbList.out.tab added 1e085c14f72ffc_transcriptInfo.tab added 1e085c346e1360_GRCh38.GENCODE.v42_100 added 1e085c39886bbf_knownGene_hg38.sql added 1e085c26a78586_knownGene_hg38.txt added 1e085c51bd8a9a_refGene_hg38.sql added 1e085c6419310e_refGene_hg38.txt added 1e085c646b2331_knownGene_mm39.sql added 1e085c43b5b0b3_knownGene_mm39.txt added 1e085c6398d48e_refGene_mm39.sql added 1e085c5066bec1_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/RtmpSAnYzu/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 18.818 1.322 20.512
ReUseData.Rcheck/ReUseData-Ex.timings
name | user | system | elapsed | |
dataHub-class | 6.122 | 0.233 | 6.359 | |
dataSearch | 1.158 | 0.009 | 1.167 | |
dataUpdate | 0 | 0 | 0 | |
getCloudData | 2.812 | 0.122 | 3.864 | |
getData | 0 | 0 | 0 | |
meta_data | 0.001 | 0.000 | 0.001 | |
recipeHub-class | 0.131 | 0.019 | 0.151 | |
recipeLoad | 1.309 | 0.091 | 1.403 | |
recipeMake | 0 | 0 | 0 | |
recipeSearch | 0.550 | 0.010 | 0.561 | |
recipeUpdate | 0 | 0 | 0 | |