Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-14 12:07 -0400 (Tue, 14 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" | 4864 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4610 |
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 1762/2346 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: ReUseData |
Version: 1.9.0 |
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_1.9.0.tar.gz |
StartedAt: 2025-10-14 11:56:07 -0000 (Tue, 14 Oct 2025) |
EndedAt: 2025-10-14 11:58:49 -0000 (Tue, 14 Oct 2025) |
EllapsedTime: 161.1 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_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’ * using R version 4.5.0 (2025-04-11) * 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) * using session charset: UTF-8 * using option ‘--no-vignettes’ * 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 8.986 0.287 9.307 getCloudData 3.593 0.399 8.732 * 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-3.22-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-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six" 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... 2a521c1ff0a4cd_GRCh38.primary_assembly.genome.fa.1.bt2 added 2a521c67f75963_GRCh38.primary_assembly.genome.fa.2.bt2 added 2a521c5c24c9e_GRCh38.primary_assembly.genome.fa.3.bt2 added 2a521c50a524ed_GRCh38.primary_assembly.genome.fa.4.bt2 added 2a521c2cc2273_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added 2a521c40164527_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added 2a521c1ccd4675_outfile.txt added 2a521c2c7259b2_GRCh37_to_GRCh38.chain added 2a521c3cd0ed5b_GRCh37_to_NCBI34.chain added 2a521c2855ca17_GRCh37_to_NCBI35.chain added 2a521c45c78f49_GRCh37_to_NCBI36.chain added 2a521c3d635135_GRCh38_to_GRCh37.chain added 2a521c56f617d6_GRCh38_to_NCBI34.chain added 2a521c2c350ccd_GRCh38_to_NCBI35.chain added 2a521c326e066e_GRCh38_to_NCBI36.chain added 2a521c1e1139e2_NCBI34_to_GRCh37.chain added 2a521c493bede8_NCBI34_to_GRCh38.chain added 2a521c69931ad7_NCBI35_to_GRCh37.chain added 2a521c34beb078_NCBI35_to_GRCh38.chain added 2a521c69c67449_NCBI36_to_GRCh37.chain added 2a521c60a6317c_NCBI36_to_GRCh38.chain added 2a521c2add13cb_GRCm38_to_NCBIM36.chain added 2a521c1be7c7cd_GRCm38_to_NCBIM37.chain added 2a521c6bd674a6_NCBIM36_to_GRCm38.chain added 2a521c4f2f0a4b_NCBIM37_to_GRCm38.chain added 2a521c6baf6ede_1000G_omni2.5.b37.vcf.gz added 2a521c7d8bc02e_1000G_omni2.5.b37.vcf.gz.tbi added 2a521c62d26952_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added 2a521c3e138ee8_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added 2a521c2c4458a4_1000G_omni2.5.hg38.vcf.gz added 2a521c24f0262c_1000G_omni2.5.hg38.vcf.gz.tbi added 2a521c5e0433b5_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added 2a521c143bb207_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added 2a521c2ab272ca_af-only-gnomad.raw.sites.vcf added 2a521c2ea958a2_af-only-gnomad.raw.sites.vcf.idx added 2a521c1707d47a_Mutect2-exome-panel.vcf.idx added 2a521c6ac8b7f1_Mutect2-WGS-panel-b37.vcf added 2a521c4b769f17_Mutect2-WGS-panel-b37.vcf.idx added 2a521c437a2e2d_small_exac_common_3.vcf added 2a521c2799a54c_small_exac_common_3.vcf.idx added 2a521c73cc692e_1000g_pon.hg38.vcf.gz added 2a521c941bd76_1000g_pon.hg38.vcf.gz.tbi added 2a521c64fcf682_af-only-gnomad.hg38.vcf.gz added 2a521c4ac28104_af-only-gnomad.hg38.vcf.gz.tbi added 2a521c3576ca43_small_exac_common_3.hg38.vcf.gz added 2a521c176afcf0_small_exac_common_3.hg38.vcf.gz.tbi added 2a521c68d3bae6_gencode.v41.annotation.gtf added 2a521c7eb2b82b_gencode.v42.annotation.gtf added 2a521cfe17c7_gencode.vM30.annotation.gtf added 2a521c1d926b5e_gencode.vM31.annotation.gtf added 2a521c68792c74_gencode.v41.transcripts.fa added 2a521c61a44943_gencode.v41.transcripts.fa.fai added 2a521c486f7f29_gencode.v42.transcripts.fa added 2a521c460f441_gencode.v42.transcripts.fa.fai added 2a521c4d7abde9_gencode.vM30.pc_transcripts.fa added 2a521c179e8975_gencode.vM30.pc_transcripts.fa.fai added 2a521c70106320_gencode.vM31.pc_transcripts.fa added 2a521c4b067e18_gencode.vM31.pc_transcripts.fa.fai added 2a521c7a70f2c7_GRCh38.primary_assembly.genome.fa.1.ht2 added 2a521c2e23f208_GRCh38.primary_assembly.genome.fa.2.ht2 added 2a521c774ad6bc_GRCh38.primary_assembly.genome.fa.3.ht2 added 2a521c1f6118f3_GRCh38.primary_assembly.genome.fa.4.ht2 added 2a521cc2825bd_GRCh38.primary_assembly.genome.fa.5.ht2 added 2a521cb8688c3_GRCh38.primary_assembly.genome.fa.6.ht2 added 2a521c4a138bbe_GRCh38.primary_assembly.genome.fa.7.ht2 added 2a521c3ad17e5f_GRCh38.primary_assembly.genome.fa.8.ht2 added 2a521c228e5d3e_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added 2a521c34dc43af_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added 2a521c6481d76_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added 2a521c66088b6b_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added 2a521c5c75e8fc_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added 2a521c7a1486a4_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added 2a521c6f4a48e1_GRCh38_full_analysis_set_plus_decoy_hla.fa added 2a521c4172df7e_GRCh38.primary_assembly.genome.fa.fai added 2a521c44d707a9_GRCh38.primary_assembly.genome.fa.amb added 2a521c24c11324_GRCh38.primary_assembly.genome.fa.ann added 2a521c58dddc6e_GRCh38.primary_assembly.genome.fa.bwt added 2a521c2daac28f_GRCh38.primary_assembly.genome.fa.pac added 2a521c2373cb4f_GRCh38.primary_assembly.genome.fa.sa added 2a521c59dbf435_GRCh38.primary_assembly.genome.fa added 2a521c4b3d2dee_hs37d5.fa.fai added 2a521cbecf7c3_hs37d5.fa.amb added 2a521c3b803d78_hs37d5.fa.ann added 2a521c13acad17_hs37d5.fa.bwt added 2a521c104dec05_hs37d5.fa.pac added 2a521c8fafb62_hs37d5.fa.sa added 2a521c2b4b368c_hs37d5.fa added 2a521c5e4f25_complete_ref_lens.bin added 2a521c5401797a_ctable.bin added 2a521c25bc2953_ctg_offsets.bin added 2a521c2e82412d_duplicate_clusters.tsv added 2a521c4b4c5036_info.json added 2a521c451d4247_mphf.bin added 2a521c3aaa66ea_pos.bin added 2a521c56d2d8f9_pre_indexing.log added 2a521cf30ce05_rank.bin added 2a521c757be549_ref_indexing.log added 2a521c79613637_refAccumLengths.bin added 2a521c440d11b4_reflengths.bin added 2a521c7bc402bf_refseq.bin added 2a521c5f69c1a2_seq.bin added 2a521c2082fab0_versionInfo.json added 2a521c75d88963_salmon_index added 2a521c4eb40a83_chrLength.txt added 2a521c61f5da2e_chrName.txt added 2a521c3aaf910c_chrNameLength.txt added 2a521c73751da7_chrStart.txt added 2a521c3ad3b69c_exonGeTrInfo.tab added 2a521c685a539c_exonInfo.tab added 2a521c16e8e8f6_geneInfo.tab added 2a521c14afaad1_Genome added 2a521c3397818a_genomeParameters.txt added 2a521c22d5e0ba_Log.out added 2a521c502fe84a_SA added 2a521c47442ea1_SAindex added 2a521c3323ccbf_sjdbInfo.txt added 2a521c592ae3ac_sjdbList.fromGTF.out.tab added 2a521c728f652e_sjdbList.out.tab added 2a521c33821be4_transcriptInfo.tab added 2a521c2d2c5d26_GRCh38.GENCODE.v42_100 added 2a521c184b8e81_knownGene_hg38.sql added 2a521c62045d11_knownGene_hg38.txt added 2a521c7878ad5c_refGene_hg38.sql added 2a521c5d68d0c8_refGene_hg38.txt added 2a521c1caec3fb_knownGene_mm39.sql added 2a521c4f4b8655_knownGene_mm39.txt added 2a521c6c999ecd_refGene_mm39.sql added 2a521c122aa944_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/RtmpnrmSee/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 25.436 2.093 30.637
ReUseData.Rcheck/ReUseData-Ex.timings
name | user | system | elapsed | |
dataHub-class | 8.986 | 0.287 | 9.307 | |
dataSearch | 1.739 | 0.052 | 1.796 | |
dataUpdate | 0 | 0 | 0 | |
getCloudData | 3.593 | 0.399 | 8.732 | |
getData | 0.001 | 0.000 | 0.000 | |
meta_data | 0.001 | 0.000 | 0.001 | |
recipeHub-class | 0.202 | 0.004 | 0.209 | |
recipeLoad | 2.086 | 0.076 | 2.173 | |
recipeMake | 0 | 0 | 0 | |
recipeSearch | 0.854 | 0.040 | 0.896 | |
recipeUpdate | 0.000 | 0.000 | 0.001 | |