Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:39:54 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
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 1723/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ReUseData 1.3.2 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.3.2 |
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_1.3.2.tar.gz |
StartedAt: 2024-03-27 23:33:22 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 23:36:08 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 165.4 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_1.3.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * 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 ‘1.3.2’ * 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 8.024 0.956 9.14 * 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 Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 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... 7c4c5b965867_GRCh38.primary_assembly.genome.fa.1.bt2 added 7c4c6b86012a_GRCh38.primary_assembly.genome.fa.2.bt2 added 7c4c2ab6a38c_GRCh38.primary_assembly.genome.fa.3.bt2 added 7c4c3cab523c_GRCh38.primary_assembly.genome.fa.4.bt2 added 7c4c13a40042_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added 7c4c740cf720_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added 7c4c7f349165_outfile.txt added 7c4c5435bf21_GRCh37_to_GRCh38.chain added 7c4c14973ab8_GRCh37_to_NCBI34.chain added 7c4c54901097_GRCh37_to_NCBI35.chain added 7c4c3e3154e0_GRCh37_to_NCBI36.chain added 7c4c18bb5e06_GRCh38_to_GRCh37.chain added 7c4c3519e899_GRCh38_to_NCBI34.chain added 7c4c37f5b00b_GRCh38_to_NCBI35.chain added 7c4c62f8bee0_GRCh38_to_NCBI36.chain added 7c4c38bb96e3_NCBI34_to_GRCh37.chain added 7c4c23af2e2e_NCBI34_to_GRCh38.chain added 7c4c4200e04f_NCBI35_to_GRCh37.chain added 7c4c47868463_NCBI35_to_GRCh38.chain added 7c4c505da444_NCBI36_to_GRCh37.chain added 7c4c33cb9594_NCBI36_to_GRCh38.chain added 7c4c7ac9421c_GRCm38_to_NCBIM36.chain added 7c4c33137b3e_GRCm38_to_NCBIM37.chain added 7c4c44003da4_NCBIM36_to_GRCm38.chain added 7c4c6bcefcdc_NCBIM37_to_GRCm38.chain added 7c4c623b06cf_1000G_omni2.5.b37.vcf.gz added 7c4c113c326b_1000G_omni2.5.b37.vcf.gz.tbi added 7c4c71217a4_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added 7c4c34ce139c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added 7c4c456981d9_1000G_omni2.5.hg38.vcf.gz added 7c4c11cbf129_1000G_omni2.5.hg38.vcf.gz.tbi added 7c4c6445c3df_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added 7c4c203e98e7_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added 7c4c6da8763a_af-only-gnomad.raw.sites.vcf added 7c4c4eea1214_af-only-gnomad.raw.sites.vcf.idx added 7c4c69490785_Mutect2-exome-panel.vcf.idx added 7c4c398ce2c3_Mutect2-WGS-panel-b37.vcf added 7c4c507b8db9_Mutect2-WGS-panel-b37.vcf.idx added 7c4c5f9595f6_small_exac_common_3.vcf added 7c4c55a87a80_small_exac_common_3.vcf.idx added 7c4c2802956f_1000g_pon.hg38.vcf.gz added 7c4c41a0beee_1000g_pon.hg38.vcf.gz.tbi added 7c4c20571ceb_af-only-gnomad.hg38.vcf.gz added 7c4c372b98e3_af-only-gnomad.hg38.vcf.gz.tbi added 7c4cf427b61_small_exac_common_3.hg38.vcf.gz added 7c4c55b2251a_small_exac_common_3.hg38.vcf.gz.tbi added 7c4c22a1f9ea_gencode.v41.annotation.gtf added 7c4c381e8369_gencode.v42.annotation.gtf added 7c4c5b457f47_gencode.vM30.annotation.gtf added 7c4c2fa73d21_gencode.vM31.annotation.gtf added 7c4cc9e59f8_gencode.v41.transcripts.fa added 7c4c7024af40_gencode.v41.transcripts.fa.fai added 7c4c786dcc44_gencode.v42.transcripts.fa added 7c4c707dc220_gencode.v42.transcripts.fa.fai added 7c4c5053fc92_gencode.vM30.pc_transcripts.fa added 7c4c39eafe71_gencode.vM30.pc_transcripts.fa.fai added 7c4c72e6ca6b_gencode.vM31.pc_transcripts.fa added 7c4cdf371bc_gencode.vM31.pc_transcripts.fa.fai added 7c4c69aff4cb_GRCh38.primary_assembly.genome.fa.1.ht2 added 7c4c1ef071a2_GRCh38.primary_assembly.genome.fa.2.ht2 added 7c4c3bb4528c_GRCh38.primary_assembly.genome.fa.3.ht2 added 7c4c3b9783f3_GRCh38.primary_assembly.genome.fa.4.ht2 added 7c4c5857e515_GRCh38.primary_assembly.genome.fa.5.ht2 added 7c4c7280f302_GRCh38.primary_assembly.genome.fa.6.ht2 added 7c4c6fd24308_GRCh38.primary_assembly.genome.fa.7.ht2 added 7c4c552efb92_GRCh38.primary_assembly.genome.fa.8.ht2 added 7c4c7f8659ee_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added 7c4c4d7a59aa_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added 7c4c1b94cfa3_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added 7c4c46cbe47a_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added 7c4c740529e5_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added 7c4c7f01b4e4_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added 7c4c490b25e0_GRCh38_full_analysis_set_plus_decoy_hla.fa added 7c4c7ae3ba96_GRCh38.primary_assembly.genome.fa.fai added 7c4c7cef0ce1_GRCh38.primary_assembly.genome.fa.amb added 7c4c3236c7db_GRCh38.primary_assembly.genome.fa.ann added 7c4c2a7b149e_GRCh38.primary_assembly.genome.fa.bwt added 7c4c7686a6db_GRCh38.primary_assembly.genome.fa.pac added 7c4c234b0a8_GRCh38.primary_assembly.genome.fa.sa added 7c4c5139e6b9_GRCh38.primary_assembly.genome.fa added 7c4c305aa558_hs37d5.fa.fai added 7c4cf1d4d35_hs37d5.fa.amb added 7c4c4cb7da53_hs37d5.fa.ann added 7c4c3a5ea67e_hs37d5.fa.bwt added 7c4c1c04b822_hs37d5.fa.pac added 7c4c79d4ce8c_hs37d5.fa.sa added 7c4c24487d1_hs37d5.fa added 7c4c6130ab80_complete_ref_lens.bin added 7c4c424b9259_ctable.bin added 7c4c6f75330f_ctg_offsets.bin added 7c4c776b56f3_duplicate_clusters.tsv added 7c4c2819a8c5_info.json added 7c4c2c973214_mphf.bin added 7c4c7a58d5ea_pos.bin added 7c4c5e443466_pre_indexing.log added 7c4c4fcc44e3_rank.bin added 7c4c6bbebc02_ref_indexing.log added 7c4c37295e91_refAccumLengths.bin added 7c4c7cff9de1_reflengths.bin added 7c4c71d65ee3_refseq.bin added 7c4c30efc378_seq.bin added 7c4c4d0a1461_versionInfo.json added 7c4c50c013ca_salmon_index added 7c4c72535c30_chrLength.txt added 7c4c3ec98df3_chrName.txt added 7c4c22866cb9_chrNameLength.txt added 7c4c274bf764_chrStart.txt added 7c4c6c5eda63_exonGeTrInfo.tab added 7c4c4753d12a_exonInfo.tab added 7c4c4fc940fb_geneInfo.tab added 7c4c25c947a9_Genome added 7c4c417fbba0_genomeParameters.txt added 7c4c28f726f8_Log.out added 7c4c7a1f78ca_SA added 7c4c28335469_SAindex added 7c4c41eace1d_sjdbInfo.txt added 7c4c1e81f3ba_sjdbList.fromGTF.out.tab added 7c4c65a847fb_sjdbList.out.tab added 7c4cb0de3e1_transcriptInfo.tab added 7c4c3cebce72_GRCh38.GENCODE.v42_100 added 7c4c1d3ebd9d_knownGene_hg38.sql added 7c4c2129d6b_knownGene_hg38.txt added 7c4c141cdcdd_refGene_hg38.sql added 7c4c72e83b7b_refGene_hg38.txt added 7c4c6c99432c_knownGene_mm39.sql added 7c4c42093567_knownGene_mm39.txt added 7c4c6a911f0f_refGene_mm39.sql added 7c4c5d8e4871_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/RtmpwO4pjB/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 26.133 3.562 30.956
ReUseData.Rcheck/ReUseData-Ex.timings
name | user | system | elapsed | |
dataHub-class | 8.024 | 0.956 | 9.140 | |
dataSearch | 1.436 | 0.067 | 1.518 | |
dataUpdate | 0.000 | 0.001 | 0.001 | |
getCloudData | 3.048 | 0.176 | 4.102 | |
getData | 0.000 | 0.000 | 0.001 | |
meta_data | 0.001 | 0.000 | 0.001 | |
recipeHub-class | 0.162 | 0.015 | 0.179 | |
recipeLoad | 1.619 | 0.111 | 1.750 | |
recipeMake | 0.000 | 0.001 | 0.001 | |
recipeSearch | 0.723 | 0.049 | 0.780 | |
recipeUpdate | 0 | 0 | 0 | |