Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-30 11:35:51 -0400 (Thu, 30 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4518 |
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 1745/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ReUseData 1.4.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.4.0 |
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_1.4.0.tar.gz |
StartedAt: 2024-05-29 23:12:40 -0400 (Wed, 29 May 2024) |
EndedAt: 2024-05-29 23:15:28 -0400 (Wed, 29 May 2024) |
EllapsedTime: 168.0 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_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ReUseData/DESCRIPTION’ ... OK * this is package ‘ReUseData’ version ‘1.4.0’ * 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 8.504 1.051 9.785 * 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-3.19-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/4.4-x86_64/Resources/library’ * installing *source* package ‘ReUseData’ ... ** 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 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 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... dc204c7bf4ed_GRCh38.primary_assembly.genome.fa.1.bt2 added dc205e0d1ad5_GRCh38.primary_assembly.genome.fa.2.bt2 added dc202e5cc630_GRCh38.primary_assembly.genome.fa.3.bt2 added dc204cd79117_GRCh38.primary_assembly.genome.fa.4.bt2 added dc205c76a46a_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added dc2071245a92_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added dc209b66146_outfile.txt added dc2024ac3fa5_GRCh37_to_GRCh38.chain added dc2028867c72_GRCh37_to_NCBI34.chain added dc2015543527_GRCh37_to_NCBI35.chain added dc204b6d9e61_GRCh37_to_NCBI36.chain added dc209b918f7_GRCh38_to_GRCh37.chain added dc205716051d_GRCh38_to_NCBI34.chain added dc2066a9df95_GRCh38_to_NCBI35.chain added dc201a95e3db_GRCh38_to_NCBI36.chain added dc2066a24c7f_NCBI34_to_GRCh37.chain added dc20294c5a7d_NCBI34_to_GRCh38.chain added dc2053c8d9b9_NCBI35_to_GRCh37.chain added dc20274e2ba8_NCBI35_to_GRCh38.chain added dc207d1436c0_NCBI36_to_GRCh37.chain added dc203a16b767_NCBI36_to_GRCh38.chain added dc202962e8fc_GRCm38_to_NCBIM36.chain added dc201cae0d9e_GRCm38_to_NCBIM37.chain added dc2067000ec7_NCBIM36_to_GRCm38.chain added dc2034ca5fa5_NCBIM37_to_GRCm38.chain added dc20524d64b6_1000G_omni2.5.b37.vcf.gz added dc20570f12f0_1000G_omni2.5.b37.vcf.gz.tbi added dc201ea47737_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added dc203f8ecb98_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added dc2037d888c1_1000G_omni2.5.hg38.vcf.gz added dc2068fa538b_1000G_omni2.5.hg38.vcf.gz.tbi added dc20a830085_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added dc201e972127_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added dc2054019721_af-only-gnomad.raw.sites.vcf added dc203469229d_af-only-gnomad.raw.sites.vcf.idx added dc20625f8c4c_Mutect2-exome-panel.vcf.idx added dc206ef40408_Mutect2-WGS-panel-b37.vcf added dc205634e220_Mutect2-WGS-panel-b37.vcf.idx added dc2029e9cf17_small_exac_common_3.vcf added dc20351b0480_small_exac_common_3.vcf.idx added dc20c48abd_1000g_pon.hg38.vcf.gz added dc2067707eaf_1000g_pon.hg38.vcf.gz.tbi added dc20a8d4837_af-only-gnomad.hg38.vcf.gz added dc204180184a_af-only-gnomad.hg38.vcf.gz.tbi added dc2040bac3de_small_exac_common_3.hg38.vcf.gz added dc2025914505_small_exac_common_3.hg38.vcf.gz.tbi added dc20644a5e87_gencode.v41.annotation.gtf added dc204e842481_gencode.v42.annotation.gtf added dc204578b96c_gencode.vM30.annotation.gtf added dc2078d58515_gencode.vM31.annotation.gtf added dc20a1463ad_gencode.v41.transcripts.fa added dc20409bf806_gencode.v41.transcripts.fa.fai added dc203fb8730d_gencode.v42.transcripts.fa added dc2066897b29_gencode.v42.transcripts.fa.fai added dc204bf4f556_gencode.vM30.pc_transcripts.fa added dc203f17080f_gencode.vM30.pc_transcripts.fa.fai added dc201123125_gencode.vM31.pc_transcripts.fa added dc20515874af_gencode.vM31.pc_transcripts.fa.fai added dc20654b6e2_GRCh38.primary_assembly.genome.fa.1.ht2 added dc2023b2b2ad_GRCh38.primary_assembly.genome.fa.2.ht2 added dc2028f08e2a_GRCh38.primary_assembly.genome.fa.3.ht2 added dc2049057c65_GRCh38.primary_assembly.genome.fa.4.ht2 added dc20729f057_GRCh38.primary_assembly.genome.fa.5.ht2 added dc205261e36d_GRCh38.primary_assembly.genome.fa.6.ht2 added dc20189a335c_GRCh38.primary_assembly.genome.fa.7.ht2 added dc2033a1e9a2_GRCh38.primary_assembly.genome.fa.8.ht2 added dc204af1a529_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added dc203e924d2f_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added dc20770968c0_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added dc20abc524e_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added dc2051bf8463_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added dc20748ca982_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added dc203eccd195_GRCh38_full_analysis_set_plus_decoy_hla.fa added dc2078d3ad68_GRCh38.primary_assembly.genome.fa.fai added dc20111dc4d1_GRCh38.primary_assembly.genome.fa.amb added dc2039647e1e_GRCh38.primary_assembly.genome.fa.ann added dc2074940101_GRCh38.primary_assembly.genome.fa.bwt added dc2020ce2472_GRCh38.primary_assembly.genome.fa.pac added dc203dbac931_GRCh38.primary_assembly.genome.fa.sa added dc2031eecfa0_GRCh38.primary_assembly.genome.fa added dc2035812afc_hs37d5.fa.fai added dc20332d21d5_hs37d5.fa.amb added dc2058084132_hs37d5.fa.ann added dc205f066c5_hs37d5.fa.bwt added dc2069eb128e_hs37d5.fa.pac added dc20480f5ef5_hs37d5.fa.sa added dc2069234bc8_hs37d5.fa added dc20c446d65_complete_ref_lens.bin added dc20606a082d_ctable.bin added dc20513ef3ce_ctg_offsets.bin added dc207bf8830d_duplicate_clusters.tsv added dc2078640a10_info.json added dc206fd0de2f_mphf.bin added dc2079ab1902_pos.bin added dc204ff710b5_pre_indexing.log added dc20656a0416_rank.bin added dc201332745e_ref_indexing.log added dc205575d12a_refAccumLengths.bin added dc2029f7483b_reflengths.bin added dc2029a72f03_refseq.bin added dc201eff8352_seq.bin added dc2019068c64_versionInfo.json added dc207ceb0611_salmon_index added dc2029db8629_chrLength.txt added dc20b450337_chrName.txt added dc205fd615a8_chrNameLength.txt added dc206027f9bf_chrStart.txt added dc20607d9bea_exonGeTrInfo.tab added dc2056875123_exonInfo.tab added dc204ddffd36_geneInfo.tab added dc202c690c2b_Genome added dc20249df1d4_genomeParameters.txt added dc207d6fa813_Log.out added dc202d83b7bb_SA added dc2022936d55_SAindex added dc207ceef92e_sjdbInfo.txt added dc202d297b16_sjdbList.fromGTF.out.tab added dc207e4ff883_sjdbList.out.tab added dc203444a13e_transcriptInfo.tab added dc205b60841_GRCh38.GENCODE.v42_100 added dc2071d7e654_knownGene_hg38.sql added dc201552cf30_knownGene_hg38.txt added dc206fa0633f_refGene_hg38.sql added dc20ad3f65a_refGene_hg38.txt added dc2061d29443_knownGene_mm39.sql added dc204803ece1_knownGene_mm39.txt added dc2079b4ccb6_refGene_mm39.sql added dc204cebff26_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/RtmpYivN20/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 26.987 3.723 31.860
ReUseData.Rcheck/ReUseData-Ex.timings
name | user | system | elapsed | |
dataHub-class | 8.504 | 1.051 | 9.785 | |
dataSearch | 1.574 | 0.076 | 1.671 | |
dataUpdate | 0 | 0 | 0 | |
getCloudData | 3.211 | 0.193 | 4.305 | |
getData | 0.000 | 0.000 | 0.001 | |
meta_data | 0.001 | 0.001 | 0.001 | |
recipeHub-class | 0.157 | 0.015 | 0.174 | |
recipeLoad | 1.725 | 0.119 | 1.864 | |
recipeMake | 0.000 | 0.001 | 0.000 | |
recipeSearch | 0.745 | 0.051 | 0.804 | |
recipeUpdate | 0 | 0 | 0 | |