Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-07-29 12:05 -0400 (Tue, 29 Jul 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4535 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4516 |
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 1737/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ReUseData 1.9.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 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: 2025-07-29 01:56:39 -0400 (Tue, 29 Jul 2025) |
EndedAt: 2025-07-29 01:59:24 -0400 (Tue, 29 Jul 2025) |
EllapsedTime: 165.2 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 24.04.2 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 5.963 0.242 6.208 * 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... 3aef9f7e60d77_GRCh38.primary_assembly.genome.fa.1.bt2 added 3aef9f58be13fd_GRCh38.primary_assembly.genome.fa.2.bt2 added 3aef9f551a2305_GRCh38.primary_assembly.genome.fa.3.bt2 added 3aef9f176bda0c_GRCh38.primary_assembly.genome.fa.4.bt2 added 3aef9f11f7643f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added 3aef9fce40cb9_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added 3aef9f72f7dedd_outfile.txt added 3aef9f35ae428f_GRCh37_to_GRCh38.chain added 3aef9f45896356_GRCh37_to_NCBI34.chain added 3aef9ffc9ec05_GRCh37_to_NCBI35.chain added 3aef9f102d28f7_GRCh37_to_NCBI36.chain added 3aef9f61cab9b_GRCh38_to_GRCh37.chain added 3aef9f45d72bc0_GRCh38_to_NCBI34.chain added 3aef9f160d1b60_GRCh38_to_NCBI35.chain added 3aef9f49b09e62_GRCh38_to_NCBI36.chain added 3aef9f727e6595_NCBI34_to_GRCh37.chain added 3aef9f4c1a5904_NCBI34_to_GRCh38.chain added 3aef9f116d2610_NCBI35_to_GRCh37.chain added 3aef9f2fd5585b_NCBI35_to_GRCh38.chain added 3aef9f2279e32a_NCBI36_to_GRCh37.chain added 3aef9f100befd_NCBI36_to_GRCh38.chain added 3aef9f1634a849_GRCm38_to_NCBIM36.chain added 3aef9f739c9e32_GRCm38_to_NCBIM37.chain added 3aef9f498beaef_NCBIM36_to_GRCm38.chain added 3aef9f662fb1c0_NCBIM37_to_GRCm38.chain added 3aef9f319e81a8_1000G_omni2.5.b37.vcf.gz added 3aef9f6cc858a8_1000G_omni2.5.b37.vcf.gz.tbi added 3aef9f36fe1e14_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added 3aef9f45027261_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added 3aef9f7b667d18_1000G_omni2.5.hg38.vcf.gz added 3aef9f5d104f32_1000G_omni2.5.hg38.vcf.gz.tbi added 3aef9f4ce87fd8_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added 3aef9f54249115_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added 3aef9f322a7238_af-only-gnomad.raw.sites.vcf added 3aef9f645459e5_af-only-gnomad.raw.sites.vcf.idx added 3aef9f661bf554_Mutect2-exome-panel.vcf.idx added 3aef9f3f0e7ef1_Mutect2-WGS-panel-b37.vcf added 3aef9f574c38c2_Mutect2-WGS-panel-b37.vcf.idx added 3aef9f1bca37e4_small_exac_common_3.vcf added 3aef9f497e247_small_exac_common_3.vcf.idx added 3aef9f671624c8_1000g_pon.hg38.vcf.gz added 3aef9f2bf760db_1000g_pon.hg38.vcf.gz.tbi added 3aef9fab48de3_af-only-gnomad.hg38.vcf.gz added 3aef9f2ced5088_af-only-gnomad.hg38.vcf.gz.tbi added 3aef9f42047c3b_small_exac_common_3.hg38.vcf.gz added 3aef9f54652c45_small_exac_common_3.hg38.vcf.gz.tbi added 3aef9f1f6bb61d_gencode.v41.annotation.gtf added 3aef9fe1ed53f_gencode.v42.annotation.gtf added 3aef9f65d25255_gencode.vM30.annotation.gtf added 3aef9f4f410e79_gencode.vM31.annotation.gtf added 3aef9f3098b869_gencode.v41.transcripts.fa added 3aef9f66d31152_gencode.v41.transcripts.fa.fai added 3aef9f6575b6c2_gencode.v42.transcripts.fa added 3aef9f2435569b_gencode.v42.transcripts.fa.fai added 3aef9f305efc41_gencode.vM30.pc_transcripts.fa added 3aef9f4ba56883_gencode.vM30.pc_transcripts.fa.fai added 3aef9f55d3d843_gencode.vM31.pc_transcripts.fa added 3aef9f1d2754e9_gencode.vM31.pc_transcripts.fa.fai added 3aef9f2a38697_GRCh38.primary_assembly.genome.fa.1.ht2 added 3aef9f1ad64aa4_GRCh38.primary_assembly.genome.fa.2.ht2 added 3aef9f188dd201_GRCh38.primary_assembly.genome.fa.3.ht2 added 3aef9f5fb3d5c9_GRCh38.primary_assembly.genome.fa.4.ht2 added 3aef9f67beca7d_GRCh38.primary_assembly.genome.fa.5.ht2 added 3aef9f6cb26317_GRCh38.primary_assembly.genome.fa.6.ht2 added 3aef9f11de4801_GRCh38.primary_assembly.genome.fa.7.ht2 added 3aef9f4c132462_GRCh38.primary_assembly.genome.fa.8.ht2 added 3aef9f52ce586b_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added 3aef9f50ecc6f2_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added 3aef9f235f5d24_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added 3aef9f6e98904f_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added 3aef9f5584a93a_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added 3aef9fa7581ec_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added 3aef9f1a8ff12a_GRCh38_full_analysis_set_plus_decoy_hla.fa added 3aef9f6039371d_GRCh38.primary_assembly.genome.fa.fai added 3aef9f3762d274_GRCh38.primary_assembly.genome.fa.amb added 3aef9f5c946d66_GRCh38.primary_assembly.genome.fa.ann added 3aef9f349e6362_GRCh38.primary_assembly.genome.fa.bwt added 3aef9f56ce8892_GRCh38.primary_assembly.genome.fa.pac added 3aef9f6ab342a5_GRCh38.primary_assembly.genome.fa.sa added 3aef9f1a70b5b8_GRCh38.primary_assembly.genome.fa added 3aef9f260f970b_hs37d5.fa.fai added 3aef9f1b4bfb0f_hs37d5.fa.amb added 3aef9f143c70a_hs37d5.fa.ann added 3aef9fb854dcd_hs37d5.fa.bwt added 3aef9f3f8151aa_hs37d5.fa.pac added 3aef9f31a2c34c_hs37d5.fa.sa added 3aef9f572ab650_hs37d5.fa added 3aef9f155529ee_complete_ref_lens.bin added 3aef9f4eca1835_ctable.bin added 3aef9f59ce3ce7_ctg_offsets.bin added 3aef9f302b7492_duplicate_clusters.tsv added 3aef9f6757ea37_info.json added 3aef9f398212b1_mphf.bin added 3aef9f17ea3f0f_pos.bin added 3aef9f540a4d4e_pre_indexing.log added 3aef9f4b605ab2_rank.bin added 3aef9f63fd6371_ref_indexing.log added 3aef9f26d8a5b9_refAccumLengths.bin added 3aef9f1c4d21a5_reflengths.bin added 3aef9f75cc096_refseq.bin added 3aef9f15713609_seq.bin added 3aef9f71d1cadf_versionInfo.json added 3aef9f11d24282_salmon_index added 3aef9f30012733_chrLength.txt added 3aef9f520b01fc_chrName.txt added 3aef9f493514f7_chrNameLength.txt added 3aef9fc959499_chrStart.txt added 3aef9f6a9655e_exonGeTrInfo.tab added 3aef9f20039d89_exonInfo.tab added 3aef9f7748d73f_geneInfo.tab added 3aef9f211a1b16_Genome added 3aef9f46133494_genomeParameters.txt added 3aef9f1294d24e_Log.out added 3aef9f225de221_SA added 3aef9f51988261_SAindex added 3aef9f521623f8_sjdbInfo.txt added 3aef9f5400a56d_sjdbList.fromGTF.out.tab added 3aef9f28c338b2_sjdbList.out.tab added 3aef9f676b4de6_transcriptInfo.tab added 3aef9f22cabda2_GRCh38.GENCODE.v42_100 added 3aef9f2917599_knownGene_hg38.sql added 3aef9f1796c279_knownGene_hg38.txt added 3aef9fa22a7d9_refGene_hg38.sql added 3aef9f3c13884a_refGene_hg38.txt added 3aef9f2f810188_knownGene_mm39.sql added 3aef9f5e2cf527_knownGene_mm39.txt added 3aef9f773e2fd_refGene_mm39.sql added 3aef9f137e64fa_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/RtmpfMwV1z/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 19.202 1.855 21.351
ReUseData.Rcheck/ReUseData-Ex.timings
name | user | system | elapsed | |
dataHub-class | 5.963 | 0.242 | 6.208 | |
dataSearch | 1.113 | 0.013 | 1.126 | |
dataUpdate | 0.001 | 0.000 | 0.000 | |
getCloudData | 2.638 | 0.103 | 3.306 | |
getData | 0 | 0 | 0 | |
meta_data | 0.001 | 0.000 | 0.001 | |
recipeHub-class | 0.134 | 0.002 | 0.137 | |
recipeLoad | 1.238 | 0.011 | 1.251 | |
recipeMake | 0.000 | 0.000 | 0.001 | |
recipeSearch | 0.526 | 0.005 | 0.530 | |
recipeUpdate | 0 | 0 | 0 | |