Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-31 17:03:11 -0400 (Fri, 31 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 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
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 | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | 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: 1.4.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ReUseData_1.4.0.tar.gz |
StartedAt: 2024-05-31 07:23:25 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 07:26:36 -0400 (Fri, 31 May 2024) |
EllapsedTime: 191.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ReUseData.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ReUseData_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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 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 7.487 0.455 7.945 * 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-3.19-bioc/meat/ReUseData.Rcheck/00check.log’ for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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-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... 3c25b718267d20_GRCh38.primary_assembly.genome.fa.1.bt2 added 3c25b744f8a22c_GRCh38.primary_assembly.genome.fa.2.bt2 added 3c25b766cae999_GRCh38.primary_assembly.genome.fa.3.bt2 added 3c25b713844774_GRCh38.primary_assembly.genome.fa.4.bt2 added 3c25b7763bd3bd_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added 3c25b772d41733_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added 3c25b721fff352_outfile.txt added 3c25b735473ee9_GRCh37_to_GRCh38.chain added 3c25b751713a94_GRCh37_to_NCBI34.chain added 3c25b74c93abb8_GRCh37_to_NCBI35.chain added 3c25b768214865_GRCh37_to_NCBI36.chain added 3c25b7222da71b_GRCh38_to_GRCh37.chain added 3c25b71948a778_GRCh38_to_NCBI34.chain added 3c25b75d4c79f_GRCh38_to_NCBI35.chain added 3c25b756ef6e8f_GRCh38_to_NCBI36.chain added 3c25b71cacd6b1_NCBI34_to_GRCh37.chain added 3c25b71e67f2d3_NCBI34_to_GRCh38.chain added 3c25b74d633e6b_NCBI35_to_GRCh37.chain added 3c25b740084c13_NCBI35_to_GRCh38.chain added 3c25b74f999efd_NCBI36_to_GRCh37.chain added 3c25b7437e2f10_NCBI36_to_GRCh38.chain added 3c25b73538713d_GRCm38_to_NCBIM36.chain added 3c25b774a608f4_GRCm38_to_NCBIM37.chain added 3c25b72fdf5495_NCBIM36_to_GRCm38.chain added 3c25b7484f6096_NCBIM37_to_GRCm38.chain added 3c25b751b9cf5d_1000G_omni2.5.b37.vcf.gz added 3c25b75805f1d6_1000G_omni2.5.b37.vcf.gz.tbi added 3c25b717875c25_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added 3c25b7c0b6183_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added 3c25b7437cb6df_1000G_omni2.5.hg38.vcf.gz added 3c25b7214cc1c1_1000G_omni2.5.hg38.vcf.gz.tbi added 3c25b72431dea3_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added 3c25b7875590b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added 3c25b7817ab5a_af-only-gnomad.raw.sites.vcf added 3c25b737b62617_af-only-gnomad.raw.sites.vcf.idx added 3c25b77eb12cc8_Mutect2-exome-panel.vcf.idx added 3c25b77aebc28d_Mutect2-WGS-panel-b37.vcf added 3c25b759b61969_Mutect2-WGS-panel-b37.vcf.idx added 3c25b733f86bb1_small_exac_common_3.vcf added 3c25b74c5cfd21_small_exac_common_3.vcf.idx added 3c25b72649c522_1000g_pon.hg38.vcf.gz added 3c25b71c19b417_1000g_pon.hg38.vcf.gz.tbi added 3c25b76e8aa43c_af-only-gnomad.hg38.vcf.gz added 3c25b73f926c9a_af-only-gnomad.hg38.vcf.gz.tbi added 3c25b721ee7bb6_small_exac_common_3.hg38.vcf.gz added 3c25b7457a12cc_small_exac_common_3.hg38.vcf.gz.tbi added 3c25b75c3f434b_gencode.v41.annotation.gtf added 3c25b740566e8a_gencode.v42.annotation.gtf added 3c25b712dd5137_gencode.vM30.annotation.gtf added 3c25b71c478f5e_gencode.vM31.annotation.gtf added 3c25b7ff00d87_gencode.v41.transcripts.fa added 3c25b7565b8047_gencode.v41.transcripts.fa.fai added 3c25b75180009b_gencode.v42.transcripts.fa added 3c25b7496167b_gencode.v42.transcripts.fa.fai added 3c25b763ad4dc_gencode.vM30.pc_transcripts.fa added 3c25b719cf6132_gencode.vM30.pc_transcripts.fa.fai added 3c25b7564fe5d8_gencode.vM31.pc_transcripts.fa added 3c25b75e40c6b2_gencode.vM31.pc_transcripts.fa.fai added 3c25b73156bd57_GRCh38.primary_assembly.genome.fa.1.ht2 added 3c25b7625b475b_GRCh38.primary_assembly.genome.fa.2.ht2 added 3c25b721bd7d91_GRCh38.primary_assembly.genome.fa.3.ht2 added 3c25b752a37f18_GRCh38.primary_assembly.genome.fa.4.ht2 added 3c25b768d25fe_GRCh38.primary_assembly.genome.fa.5.ht2 added 3c25b72a32d69c_GRCh38.primary_assembly.genome.fa.6.ht2 added 3c25b75abb2a73_GRCh38.primary_assembly.genome.fa.7.ht2 added 3c25b73e434c16_GRCh38.primary_assembly.genome.fa.8.ht2 added 3c25b728e40365_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added 3c25b755a6ed00_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added 3c25b717f9657f_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added 3c25b75cdc6f16_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added 3c25b72203ea22_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added 3c25b73e432aa1_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added 3c25b778f6232d_GRCh38_full_analysis_set_plus_decoy_hla.fa added 3c25b7108e8e5e_GRCh38.primary_assembly.genome.fa.fai added 3c25b77dd5973c_GRCh38.primary_assembly.genome.fa.amb added 3c25b71ae49ee4_GRCh38.primary_assembly.genome.fa.ann added 3c25b75608a12a_GRCh38.primary_assembly.genome.fa.bwt added 3c25b75a14da87_GRCh38.primary_assembly.genome.fa.pac added 3c25b75b3b0d6e_GRCh38.primary_assembly.genome.fa.sa added 3c25b768e5f261_GRCh38.primary_assembly.genome.fa added 3c25b7765c69e6_hs37d5.fa.fai added 3c25b76b2b1af5_hs37d5.fa.amb added 3c25b73f4172a8_hs37d5.fa.ann added 3c25b747dc6a81_hs37d5.fa.bwt added 3c25b76fc13171_hs37d5.fa.pac added 3c25b7457c4784_hs37d5.fa.sa added 3c25b761abcbb3_hs37d5.fa added 3c25b746111749_complete_ref_lens.bin added 3c25b723bd0e36_ctable.bin added 3c25b71302890a_ctg_offsets.bin added 3c25b7286c5ea5_duplicate_clusters.tsv added 3c25b7457a8bc7_info.json added 3c25b765a60823_mphf.bin added 3c25b72ef984a3_pos.bin added 3c25b76fad6264_pre_indexing.log added 3c25b740613296_rank.bin added 3c25b76d3cd0b9_ref_indexing.log added 3c25b7189165c9_refAccumLengths.bin added 3c25b716081f96_reflengths.bin added 3c25b75363639_refseq.bin added 3c25b7756dd4df_seq.bin added 3c25b7380c09b8_versionInfo.json added 3c25b7437960da_salmon_index added 3c25b76e63f80d_chrLength.txt added 3c25b7489a9817_chrName.txt added 3c25b7414ef816_chrNameLength.txt added 3c25b794896f1_chrStart.txt added 3c25b71ea33941_exonGeTrInfo.tab added 3c25b71b63d29e_exonInfo.tab added 3c25b76483a45f_geneInfo.tab added 3c25b77892ba3_Genome added 3c25b711c03c84_genomeParameters.txt added 3c25b74faebf54_Log.out added 3c25b746ca9e4b_SA added 3c25b7599ca705_SAindex added 3c25b73f6ff0c5_sjdbInfo.txt added 3c25b7c46e5d0_sjdbList.fromGTF.out.tab added 3c25b73b4872b9_sjdbList.out.tab added 3c25b7581080f_transcriptInfo.tab added 3c25b73003f406_GRCh38.GENCODE.v42_100 added 3c25b74e4afbc3_knownGene_hg38.sql added 3c25b72ded66b4_knownGene_hg38.txt added 3c25b7757e7fce_refGene_hg38.sql added 3c25b733f103e6_refGene_hg38.txt added 3c25b75ce6eb57_knownGene_mm39.sql added 3c25b7652be232_knownGene_mm39.txt added 3c25b77452367c_refGene_mm39.sql added 3c25b74a23bc11_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/RtmppGtZCJ/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 22.557 1.940 24.934
ReUseData.Rcheck/ReUseData-Ex.timings
name | user | system | elapsed | |
dataHub-class | 7.487 | 0.455 | 7.945 | |
dataSearch | 1.354 | 0.060 | 1.414 | |
dataUpdate | 0.000 | 0.001 | 0.001 | |
getCloudData | 2.922 | 0.185 | 3.575 | |
getData | 0 | 0 | 0 | |
meta_data | 0.001 | 0.000 | 0.001 | |
recipeHub-class | 0.136 | 0.012 | 0.147 | |
recipeLoad | 1.477 | 0.052 | 1.531 | |
recipeMake | 0 | 0 | 0 | |
recipeSearch | 0.634 | 0.039 | 0.675 | |
recipeUpdate | 0 | 0 | 0 | |