Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-04 12:04 -0400 (Sat, 04 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" | 4853 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4640 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4585 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
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 1757/2341 | 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: 2025-10-04 03:24:21 -0400 (Sat, 04 Oct 2025) |
EndedAt: 2025-10-04 03:27:06 -0400 (Sat, 04 Oct 2025) |
EllapsedTime: 164.2 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 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 6.042 0.26 6.303 * 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... eef6b514aae62_GRCh38.primary_assembly.genome.fa.1.bt2 added eef6b5ebfd3e6_GRCh38.primary_assembly.genome.fa.2.bt2 added eef6b39e6aea3_GRCh38.primary_assembly.genome.fa.3.bt2 added eef6b506ffd2f_GRCh38.primary_assembly.genome.fa.4.bt2 added eef6b4cdb9e8d_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added eef6b4c2dd899_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added eef6b1a015366_outfile.txt added eef6b6e0d67bf_GRCh37_to_GRCh38.chain added eef6b3e5f9a9b_GRCh37_to_NCBI34.chain added eef6b13a4f64a_GRCh37_to_NCBI35.chain added eef6b51aa2c9a_GRCh37_to_NCBI36.chain added eef6b3357195b_GRCh38_to_GRCh37.chain added eef6b18466415_GRCh38_to_NCBI34.chain added eef6b7ac27433_GRCh38_to_NCBI35.chain added eef6b17205fa9_GRCh38_to_NCBI36.chain added eef6b3e4426aa_NCBI34_to_GRCh37.chain added eef6b1b32a01d_NCBI34_to_GRCh38.chain added eef6b3ab465cc_NCBI35_to_GRCh37.chain added eef6b7dca6ff3_NCBI35_to_GRCh38.chain added eef6b7691acf3_NCBI36_to_GRCh37.chain added eef6b5c507c7d_NCBI36_to_GRCh38.chain added eef6b311b1b3f_GRCm38_to_NCBIM36.chain added eef6b4a90d19_GRCm38_to_NCBIM37.chain added eef6b5b6108c5_NCBIM36_to_GRCm38.chain added eef6b61fc25b8_NCBIM37_to_GRCm38.chain added eef6b4fa3262f_1000G_omni2.5.b37.vcf.gz added eef6b22b673ea_1000G_omni2.5.b37.vcf.gz.tbi added eef6b202b1a24_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added eef6b61d56a4f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added eef6b129626b5_1000G_omni2.5.hg38.vcf.gz added eef6b4fd440a1_1000G_omni2.5.hg38.vcf.gz.tbi added eef6b332018b2_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added eef6b7155fa9b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added eef6b9baef44_af-only-gnomad.raw.sites.vcf added eef6b39015e1_af-only-gnomad.raw.sites.vcf.idx added eef6b3e319928_Mutect2-exome-panel.vcf.idx added eef6b55e8c7dd_Mutect2-WGS-panel-b37.vcf added eef6b1d916947_Mutect2-WGS-panel-b37.vcf.idx added eef6b2c3f00e7_small_exac_common_3.vcf added eef6b14486279_small_exac_common_3.vcf.idx added eef6b31365f91_1000g_pon.hg38.vcf.gz added eef6b7de92d82_1000g_pon.hg38.vcf.gz.tbi added eef6b479f7bd4_af-only-gnomad.hg38.vcf.gz added eef6b497cc3a6_af-only-gnomad.hg38.vcf.gz.tbi added eef6b78aba1b5_small_exac_common_3.hg38.vcf.gz added eef6b5ebfdb7d_small_exac_common_3.hg38.vcf.gz.tbi added eef6b7c0ea50_gencode.v41.annotation.gtf added eef6b13de41d2_gencode.v42.annotation.gtf added eef6b1974414a_gencode.vM30.annotation.gtf added eef6b58b5a44_gencode.vM31.annotation.gtf added eef6ba6feec5_gencode.v41.transcripts.fa added eef6b75c4bdc7_gencode.v41.transcripts.fa.fai added eef6b36a67583_gencode.v42.transcripts.fa added eef6bf18fbde_gencode.v42.transcripts.fa.fai added eef6b5125c68c_gencode.vM30.pc_transcripts.fa added eef6b18a29b3b_gencode.vM30.pc_transcripts.fa.fai added eef6b5ebc220d_gencode.vM31.pc_transcripts.fa added eef6b73dc3a76_gencode.vM31.pc_transcripts.fa.fai added eef6b38cdb55f_GRCh38.primary_assembly.genome.fa.1.ht2 added eef6b40918c5d_GRCh38.primary_assembly.genome.fa.2.ht2 added eef6b672612b_GRCh38.primary_assembly.genome.fa.3.ht2 added eef6b8a1f600_GRCh38.primary_assembly.genome.fa.4.ht2 added eef6b73b1a50f_GRCh38.primary_assembly.genome.fa.5.ht2 added eef6b77c85bc6_GRCh38.primary_assembly.genome.fa.6.ht2 added eef6b125ce544_GRCh38.primary_assembly.genome.fa.7.ht2 added eef6b7741baf0_GRCh38.primary_assembly.genome.fa.8.ht2 added eef6b35f9f4ee_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added eef6b6845ad22_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added eef6b14d32437_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added eef6b6238f5d6_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added eef6b7c8e0f9b_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added eef6b460983c8_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added eef6b60222358_GRCh38_full_analysis_set_plus_decoy_hla.fa added eef6b442d8b6f_GRCh38.primary_assembly.genome.fa.fai added eef6bf86476e_GRCh38.primary_assembly.genome.fa.amb added eef6b58cdc50d_GRCh38.primary_assembly.genome.fa.ann added eef6b22ed66ed_GRCh38.primary_assembly.genome.fa.bwt added eef6b174731bf_GRCh38.primary_assembly.genome.fa.pac added eef6b6cac06df_GRCh38.primary_assembly.genome.fa.sa added eef6b3c61a837_GRCh38.primary_assembly.genome.fa added eef6b1cd28c03_hs37d5.fa.fai added eef6b771bf5a4_hs37d5.fa.amb added eef6b322665fe_hs37d5.fa.ann added eef6b53790186_hs37d5.fa.bwt added eef6b634f183_hs37d5.fa.pac added eef6b34c2c8a_hs37d5.fa.sa added eef6b6c1b9cc1_hs37d5.fa added eef6b64f11390_complete_ref_lens.bin added eef6b77286700_ctable.bin added eef6b24e95220_ctg_offsets.bin added eef6b25829fed_duplicate_clusters.tsv added eef6b7d9ac82b_info.json added eef6b2d8b4821_mphf.bin added eef6b193444fc_pos.bin added eef6b756323f1_pre_indexing.log added eef6b3fe82d65_rank.bin added eef6b1075ffec_ref_indexing.log added eef6b2b5d18df_refAccumLengths.bin added eef6b282dda87_reflengths.bin added eef6b25492423_refseq.bin added eef6bd960eb5_seq.bin added eef6b24bbea22_versionInfo.json added eef6b6b52a7eb_salmon_index added eef6b6db8320d_chrLength.txt added eef6b68e97592_chrName.txt added eef6b7ad8ef5a_chrNameLength.txt added eef6b4685f71a_chrStart.txt added eef6bbd6dc7f_exonGeTrInfo.tab added eef6b12202119_exonInfo.tab added eef6b3331fdf9_geneInfo.tab added eef6b483884b6_Genome added eef6b2ef2ad1c_genomeParameters.txt added eef6b2a4df39e_Log.out added eef6b7a5eeab4_SA added eef6b26baea2_SAindex added eef6b3082e521_sjdbInfo.txt added eef6b7dab173e_sjdbList.fromGTF.out.tab added eef6b6e874b63_sjdbList.out.tab added eef6b1573f8b1_transcriptInfo.tab added eef6b74d37e3e_GRCh38.GENCODE.v42_100 added eef6b13709d83_knownGene_hg38.sql added eef6b3af6989f_knownGene_hg38.txt added eef6b726e4669_refGene_hg38.sql added eef6b40fbe5a4_refGene_hg38.txt added eef6b542add9b_knownGene_mm39.sql added eef6b67d16a5a_knownGene_mm39.txt added eef6be4130a_refGene_mm39.sql added eef6b64a0dd88_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/RtmpVfmNv0/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 17.991 1.028 19.488
ReUseData.Rcheck/ReUseData-Ex.timings
name | user | system | elapsed | |
dataHub-class | 6.042 | 0.260 | 6.303 | |
dataSearch | 1.083 | 0.009 | 1.093 | |
dataUpdate | 0 | 0 | 0 | |
getCloudData | 2.688 | 0.135 | 3.826 | |
getData | 0 | 0 | 0 | |
meta_data | 0.001 | 0.000 | 0.000 | |
recipeHub-class | 0.124 | 0.000 | 0.124 | |
recipeLoad | 1.234 | 0.050 | 1.284 | |
recipeMake | 0 | 0 | 0 | |
recipeSearch | 0.536 | 0.009 | 0.546 | |
recipeUpdate | 0 | 0 | 0 | |