Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-07-28 12:06 -0400 (Mon, 28 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" | 4536 |
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" | 4512 |
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: 2025-07-28 01:40:43 -0400 (Mon, 28 Jul 2025) |
EndedAt: 2025-07-28 01:43:27 -0400 (Mon, 28 Jul 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 (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 6.127 0.245 6.374 * 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... 3afd7c3b07605_GRCh38.primary_assembly.genome.fa.1.bt2 added 3afd7ceb99448_GRCh38.primary_assembly.genome.fa.2.bt2 added 3afd7c7fd9eadb_GRCh38.primary_assembly.genome.fa.3.bt2 added 3afd7c78177566_GRCh38.primary_assembly.genome.fa.4.bt2 added 3afd7c6161011f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added 3afd7c4068fad_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added 3afd7c6d2c54ca_outfile.txt added 3afd7c77911702_GRCh37_to_GRCh38.chain added 3afd7c18770b59_GRCh37_to_NCBI34.chain added 3afd7c57739997_GRCh37_to_NCBI35.chain added 3afd7c74b420fc_GRCh37_to_NCBI36.chain added 3afd7c397b6244_GRCh38_to_GRCh37.chain added 3afd7c4413ac7_GRCh38_to_NCBI34.chain added 3afd7c509c530c_GRCh38_to_NCBI35.chain added 3afd7c738b49a_GRCh38_to_NCBI36.chain added 3afd7c79876a6f_NCBI34_to_GRCh37.chain added 3afd7c77fb29cc_NCBI34_to_GRCh38.chain added 3afd7c6c633a32_NCBI35_to_GRCh37.chain added 3afd7c1722a1c7_NCBI35_to_GRCh38.chain added 3afd7c7bade397_NCBI36_to_GRCh37.chain added 3afd7c450096a9_NCBI36_to_GRCh38.chain added 3afd7c7b153080_GRCm38_to_NCBIM36.chain added 3afd7c7e7c4ce7_GRCm38_to_NCBIM37.chain added 3afd7c3baec9d5_NCBIM36_to_GRCm38.chain added 3afd7c1ae7be2_NCBIM37_to_GRCm38.chain added 3afd7c450801f9_1000G_omni2.5.b37.vcf.gz added 3afd7c1d44e572_1000G_omni2.5.b37.vcf.gz.tbi added 3afd7c41f9d4e9_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added 3afd7c52f9f0a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added 3afd7c6b1f5dbf_1000G_omni2.5.hg38.vcf.gz added 3afd7c60cc081a_1000G_omni2.5.hg38.vcf.gz.tbi added 3afd7c8e01510_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added 3afd7c79d8f208_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added 3afd7c60a5f2f5_af-only-gnomad.raw.sites.vcf added 3afd7cf78a76_af-only-gnomad.raw.sites.vcf.idx added 3afd7c5b39f327_Mutect2-exome-panel.vcf.idx added 3afd7c64ac82a2_Mutect2-WGS-panel-b37.vcf added 3afd7c6e23df41_Mutect2-WGS-panel-b37.vcf.idx added 3afd7c52cb0a29_small_exac_common_3.vcf added 3afd7c7d238dfb_small_exac_common_3.vcf.idx added 3afd7c459778d8_1000g_pon.hg38.vcf.gz added 3afd7c477f2b26_1000g_pon.hg38.vcf.gz.tbi added 3afd7c369ef03f_af-only-gnomad.hg38.vcf.gz added 3afd7c49d8b39f_af-only-gnomad.hg38.vcf.gz.tbi added 3afd7c181b7e32_small_exac_common_3.hg38.vcf.gz added 3afd7c3dd7a4da_small_exac_common_3.hg38.vcf.gz.tbi added 3afd7c43601e0e_gencode.v41.annotation.gtf added 3afd7c1016a7fe_gencode.v42.annotation.gtf added 3afd7c2a3adf0c_gencode.vM30.annotation.gtf added 3afd7c5a82bfd6_gencode.vM31.annotation.gtf added 3afd7cbc48b95_gencode.v41.transcripts.fa added 3afd7c6f3b75b5_gencode.v41.transcripts.fa.fai added 3afd7c5597f056_gencode.v42.transcripts.fa added 3afd7ca40d87d_gencode.v42.transcripts.fa.fai added 3afd7c2aea3f8a_gencode.vM30.pc_transcripts.fa added 3afd7c57466c38_gencode.vM30.pc_transcripts.fa.fai added 3afd7c4f48da76_gencode.vM31.pc_transcripts.fa added 3afd7c482f24fc_gencode.vM31.pc_transcripts.fa.fai added 3afd7c19404121_GRCh38.primary_assembly.genome.fa.1.ht2 added 3afd7c54787981_GRCh38.primary_assembly.genome.fa.2.ht2 added 3afd7c334e82bc_GRCh38.primary_assembly.genome.fa.3.ht2 added 3afd7c7a0c493b_GRCh38.primary_assembly.genome.fa.4.ht2 added 3afd7c5d588e91_GRCh38.primary_assembly.genome.fa.5.ht2 added 3afd7c2d2774c4_GRCh38.primary_assembly.genome.fa.6.ht2 added 3afd7c5ab23c31_GRCh38.primary_assembly.genome.fa.7.ht2 added 3afd7c5e501907_GRCh38.primary_assembly.genome.fa.8.ht2 added 3afd7c86167eb_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added 3afd7c3f5ebed3_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added 3afd7c4c73f848_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added 3afd7c5b2c7215_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added 3afd7c3c824ccf_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added 3afd7c120b7120_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added 3afd7c22ab9d3b_GRCh38_full_analysis_set_plus_decoy_hla.fa added 3afd7c73213d0e_GRCh38.primary_assembly.genome.fa.fai added 3afd7c5be424bf_GRCh38.primary_assembly.genome.fa.amb added 3afd7c3ac71b6d_GRCh38.primary_assembly.genome.fa.ann added 3afd7c30f8e1e8_GRCh38.primary_assembly.genome.fa.bwt added 3afd7c1f4442ce_GRCh38.primary_assembly.genome.fa.pac added 3afd7c4addc36b_GRCh38.primary_assembly.genome.fa.sa added 3afd7c5b33c0f5_GRCh38.primary_assembly.genome.fa added 3afd7c79c702a4_hs37d5.fa.fai added 3afd7c56a24f00_hs37d5.fa.amb added 3afd7c4a6f36aa_hs37d5.fa.ann added 3afd7c4f5ef2fa_hs37d5.fa.bwt added 3afd7c60e3277d_hs37d5.fa.pac added 3afd7c75597635_hs37d5.fa.sa added 3afd7c26a55f32_hs37d5.fa added 3afd7c302c01f4_complete_ref_lens.bin added 3afd7c3d889b31_ctable.bin added 3afd7c3fe5a053_ctg_offsets.bin added 3afd7c4a47b75_duplicate_clusters.tsv added 3afd7c70d71ded_info.json added 3afd7c39f1e98e_mphf.bin added 3afd7c61fd0a06_pos.bin added 3afd7c1dfe92b1_pre_indexing.log added 3afd7c14a425bf_rank.bin added 3afd7c404d230d_ref_indexing.log added 3afd7c265ffa9d_refAccumLengths.bin added 3afd7c5402e493_reflengths.bin added 3afd7ccc11b56_refseq.bin added 3afd7c18c6cb2_seq.bin added 3afd7c10853162_versionInfo.json added 3afd7c1ecc8c76_salmon_index added 3afd7c243809ed_chrLength.txt added 3afd7c3a66e70_chrName.txt added 3afd7c7ab0b136_chrNameLength.txt added 3afd7c5eff255a_chrStart.txt added 3afd7c349f5059_exonGeTrInfo.tab added 3afd7c19f4f404_exonInfo.tab added 3afd7c29dce8c5_geneInfo.tab added 3afd7cfd3114e_Genome added 3afd7c13bbf6a8_genomeParameters.txt added 3afd7c7f37c5_Log.out added 3afd7c5a4247f8_SA added 3afd7c631ae9a2_SAindex added 3afd7c61625f43_sjdbInfo.txt added 3afd7c4f9bbe2d_sjdbList.fromGTF.out.tab added 3afd7c9c048d4_sjdbList.out.tab added 3afd7c118e6137_transcriptInfo.tab added 3afd7cd24595f_GRCh38.GENCODE.v42_100 added 3afd7c49a5e927_knownGene_hg38.sql added 3afd7c1632dcac_knownGene_hg38.txt added 3afd7c7dfb774c_refGene_hg38.sql added 3afd7c397d2b5_refGene_hg38.txt added 3afd7c782fe6b2_knownGene_mm39.sql added 3afd7c1bfa09fe_knownGene_mm39.txt added 3afd7c183bf875_refGene_mm39.sql added 3afd7c387d09bf_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/RtmpAaKwZk/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 18.954 1.402 20.697
ReUseData.Rcheck/ReUseData-Ex.timings
name | user | system | elapsed | |
dataHub-class | 6.127 | 0.245 | 6.374 | |
dataSearch | 1.191 | 0.013 | 1.205 | |
dataUpdate | 0.001 | 0.001 | 0.000 | |
getCloudData | 2.739 | 0.073 | 3.776 | |
getData | 0.001 | 0.000 | 0.000 | |
meta_data | 0.000 | 0.000 | 0.001 | |
recipeHub-class | 0.125 | 0.001 | 0.127 | |
recipeLoad | 1.263 | 0.020 | 1.284 | |
recipeMake | 0.001 | 0.000 | 0.000 | |
recipeSearch | 0.594 | 0.010 | 0.604 | |
recipeUpdate | 0 | 0 | 0 | |