Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-09-29 11:39 -0400 (Mon, 29 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4827 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4580 |
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 1758/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ReUseData 1.8.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | 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: 1.8.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReUseData_1.8.0.tar.gz |
StartedAt: 2025-09-26 08:52:29 -0400 (Fri, 26 Sep 2025) |
EndedAt: 2025-09-26 08:57:14 -0400 (Fri, 26 Sep 2025) |
EllapsedTime: 285.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ReUseData.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReUseData_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’ * using R version 4.5.1 RC (2025-06-05 r88288) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ReUseData/DESCRIPTION’ ... OK * this is package ‘ReUseData’ version ‘1.8.0’ * 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 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 12.260 1.295 18.655 getCloudData 4.548 0.200 5.988 * 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 ‘/Users/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck/00check.log’ for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.8.0’ ** 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 RC (2025-06-05 r88288) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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... eb4d100b1787_GRCh38.primary_assembly.genome.fa.1.bt2 added eb4d4835a84b_GRCh38.primary_assembly.genome.fa.2.bt2 added eb4d3abbf8f6_GRCh38.primary_assembly.genome.fa.3.bt2 added eb4dad5fc9a_GRCh38.primary_assembly.genome.fa.4.bt2 added eb4d66bae804_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added eb4d78d6934c_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added eb4d4f60a08e_outfile.txt added eb4d50ccf358_GRCh37_to_GRCh38.chain added eb4d3f7c3fd9_GRCh37_to_NCBI34.chain added eb4d7643e01e_GRCh37_to_NCBI35.chain added eb4d622f0e3a_GRCh37_to_NCBI36.chain added eb4d7f4f3431_GRCh38_to_GRCh37.chain added eb4d28ebbe43_GRCh38_to_NCBI34.chain added eb4dd1835b2_GRCh38_to_NCBI35.chain added eb4d306d3fd5_GRCh38_to_NCBI36.chain added eb4d5479d1c9_NCBI34_to_GRCh37.chain added eb4d9bc0e73_NCBI34_to_GRCh38.chain added eb4d1958a503_NCBI35_to_GRCh37.chain added eb4dab974f5_NCBI35_to_GRCh38.chain added eb4d15ad8653_NCBI36_to_GRCh37.chain added eb4d334dbe43_NCBI36_to_GRCh38.chain added eb4d35063b05_GRCm38_to_NCBIM36.chain added eb4d2c0ce075_GRCm38_to_NCBIM37.chain added eb4d16437eb_NCBIM36_to_GRCm38.chain added eb4d5a932603_NCBIM37_to_GRCm38.chain added eb4d72a4bd69_1000G_omni2.5.b37.vcf.gz added eb4d1d8f734c_1000G_omni2.5.b37.vcf.gz.tbi added eb4d34da91bd_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added eb4d79962a66_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added eb4d71b9cce6_1000G_omni2.5.hg38.vcf.gz added eb4d5d3b4a5e_1000G_omni2.5.hg38.vcf.gz.tbi added eb4d5f8f9123_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added eb4d4a81c1d8_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added eb4dcdd721f_af-only-gnomad.raw.sites.vcf added eb4d1e6f57d2_af-only-gnomad.raw.sites.vcf.idx added eb4d1feeab9a_Mutect2-exome-panel.vcf.idx added eb4d6e441bd6_Mutect2-WGS-panel-b37.vcf added eb4d397fb728_Mutect2-WGS-panel-b37.vcf.idx added eb4d6fd1c095_small_exac_common_3.vcf added eb4d33baaf8d_small_exac_common_3.vcf.idx added eb4d255b6c83_1000g_pon.hg38.vcf.gz added eb4d15311f9e_1000g_pon.hg38.vcf.gz.tbi added eb4d4c12c8f0_af-only-gnomad.hg38.vcf.gz added eb4d65462b94_af-only-gnomad.hg38.vcf.gz.tbi added eb4d61d7357d_small_exac_common_3.hg38.vcf.gz added eb4d77f8d3b9_small_exac_common_3.hg38.vcf.gz.tbi added eb4d71145437_gencode.v41.annotation.gtf added eb4d6da520e0_gencode.v42.annotation.gtf added eb4d74118a5c_gencode.vM30.annotation.gtf added eb4d2b92d98c_gencode.vM31.annotation.gtf added eb4d36088cad_gencode.v41.transcripts.fa added eb4d6b4bcd91_gencode.v41.transcripts.fa.fai added eb4d3da5219f_gencode.v42.transcripts.fa added eb4d24426d57_gencode.v42.transcripts.fa.fai added eb4d5187d5a_gencode.vM30.pc_transcripts.fa added eb4dacda253_gencode.vM30.pc_transcripts.fa.fai added eb4d425bfcaf_gencode.vM31.pc_transcripts.fa added eb4d252a6732_gencode.vM31.pc_transcripts.fa.fai added eb4d2dd16ae_GRCh38.primary_assembly.genome.fa.1.ht2 added eb4dfbfafa_GRCh38.primary_assembly.genome.fa.2.ht2 added eb4d1f1a3397_GRCh38.primary_assembly.genome.fa.3.ht2 added eb4d71310e74_GRCh38.primary_assembly.genome.fa.4.ht2 added eb4d4bac1bba_GRCh38.primary_assembly.genome.fa.5.ht2 added eb4d10507726_GRCh38.primary_assembly.genome.fa.6.ht2 added eb4d12be6828_GRCh38.primary_assembly.genome.fa.7.ht2 added eb4d12a823b5_GRCh38.primary_assembly.genome.fa.8.ht2 added eb4d5cc049a4_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added eb4d5422dd8e_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added eb4d3cffc0c9_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added eb4d3ac9eb68_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added eb4d1e7e16ff_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added eb4d6817cefc_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added eb4d731637c7_GRCh38_full_analysis_set_plus_decoy_hla.fa added eb4d37a824d8_GRCh38.primary_assembly.genome.fa.fai added eb4dafd74_GRCh38.primary_assembly.genome.fa.amb added eb4d5185cab1_GRCh38.primary_assembly.genome.fa.ann added eb4d26be5447_GRCh38.primary_assembly.genome.fa.bwt added eb4d198f1530_GRCh38.primary_assembly.genome.fa.pac added eb4db80f6c_GRCh38.primary_assembly.genome.fa.sa added eb4d33fc7bd2_GRCh38.primary_assembly.genome.fa added eb4d52532a8_hs37d5.fa.fai added eb4d4d20b63b_hs37d5.fa.amb added eb4d1e9c030c_hs37d5.fa.ann added eb4d148c1887_hs37d5.fa.bwt added eb4d799e519a_hs37d5.fa.pac added eb4d8ff93d7_hs37d5.fa.sa added eb4d43430cde_hs37d5.fa added eb4d6701e551_complete_ref_lens.bin added eb4d2d765dac_ctable.bin added eb4d35ffde85_ctg_offsets.bin added eb4d316a0975_duplicate_clusters.tsv added eb4d2892f9ab_info.json added eb4d49455e5c_mphf.bin added eb4d69360f98_pos.bin added eb4d5c39fa1e_pre_indexing.log added eb4d6253f6df_rank.bin added eb4d7674dce7_ref_indexing.log added eb4d7252fe72_refAccumLengths.bin added eb4d26bf2901_reflengths.bin added eb4d501d1486_refseq.bin added eb4d252e9281_seq.bin added eb4d14946639_versionInfo.json added eb4d1ac332bd_salmon_index added eb4d5382405_chrLength.txt added eb4d28c4c6f0_chrName.txt added eb4dee0cb79_chrNameLength.txt added eb4d484e7c90_chrStart.txt added eb4d18d3f706_exonGeTrInfo.tab added eb4d3feb7a6_exonInfo.tab added eb4d47caf556_geneInfo.tab added eb4d5db105ec_Genome added eb4d10fbf902_genomeParameters.txt added eb4de98fb04_Log.out added eb4d5d87cb18_SA added eb4d7e26c4a0_SAindex added eb4d23372514_sjdbInfo.txt added eb4d7963561b_sjdbList.fromGTF.out.tab added eb4d68aa44df_sjdbList.out.tab added eb4d28fc228_transcriptInfo.tab added eb4d2c13d168_GRCh38.GENCODE.v42_100 added eb4d49191973_knownGene_hg38.sql added eb4ded5f283_knownGene_hg38.txt added eb4d247e11_refGene_hg38.sql added eb4d5bd08e29_refGene_hg38.txt added eb4d592554d6_knownGene_mm39.sql added eb4d21e4db53_knownGene_mm39.txt added eb4d37fb3787_refGene_mm39.sql added eb4d4dfa9cc7_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/RtmpG4GfWF/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 42.620 5.544 59.514
ReUseData.Rcheck/ReUseData-Ex.timings
name | user | system | elapsed | |
dataHub-class | 12.260 | 1.295 | 18.655 | |
dataSearch | 2.372 | 0.082 | 2.464 | |
dataUpdate | 0.001 | 0.001 | 0.001 | |
getCloudData | 4.548 | 0.200 | 5.988 | |
getData | 0.001 | 0.001 | 0.002 | |
meta_data | 0.001 | 0.000 | 0.002 | |
recipeHub-class | 0.244 | 0.020 | 1.135 | |
recipeLoad | 2.898 | 0.142 | 3.665 | |
recipeMake | 0.001 | 0.002 | 0.002 | |
recipeSearch | 1.201 | 0.057 | 1.292 | |
recipeUpdate | 0.000 | 0.001 | 0.001 | |