Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-04 11:39:50 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4479 |
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 | ![]() | ||||||||
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 | ||||||||||
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: 2024-05-04 00:22:38 -0400 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 00:25:30 -0400 (Sat, 04 May 2024) |
EllapsedTime: 172.1 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 beta (2024-04-14 r86421) * 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 8.430 1.003 9.591 getCloudData 3.105 0.182 10.041 * 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 beta (2024-04-14 r86421) -- "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... 117af88cf9c7_GRCh38.primary_assembly.genome.fa.1.bt2 added 117af5f627c33_GRCh38.primary_assembly.genome.fa.2.bt2 added 117af3ac82931_GRCh38.primary_assembly.genome.fa.3.bt2 added 117af2b086e1d_GRCh38.primary_assembly.genome.fa.4.bt2 added 117af367547fd_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added 117af4dc94ef9_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added 117af5b5fe554_outfile.txt added 117af74c91ca9_GRCh37_to_GRCh38.chain added 117af3f78d725_GRCh37_to_NCBI34.chain added 117af1674deb1_GRCh37_to_NCBI35.chain added 117af52c841fb_GRCh37_to_NCBI36.chain added 117af5963f032_GRCh38_to_GRCh37.chain added 117af302e9077_GRCh38_to_NCBI34.chain added 117af410e8d57_GRCh38_to_NCBI35.chain added 117af22616c1f_GRCh38_to_NCBI36.chain added 117af2a0178db_NCBI34_to_GRCh37.chain added 117af46a58768_NCBI34_to_GRCh38.chain added 117af1d5ce114_NCBI35_to_GRCh37.chain added 117af3cbcf71b_NCBI35_to_GRCh38.chain added 117af1a032cc4_NCBI36_to_GRCh37.chain added 117af46700533_NCBI36_to_GRCh38.chain added 117af64657b65_GRCm38_to_NCBIM36.chain added 117af42885761_GRCm38_to_NCBIM37.chain added 117af520c367_NCBIM36_to_GRCm38.chain added 117af29fca1d2_NCBIM37_to_GRCm38.chain added 117af8e3f787_1000G_omni2.5.b37.vcf.gz added 117af2e8fc4a0_1000G_omni2.5.b37.vcf.gz.tbi added 117af60b5fc41_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added 117af4bc44101_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added 117af4187cf83_1000G_omni2.5.hg38.vcf.gz added 117af3b48c311_1000G_omni2.5.hg38.vcf.gz.tbi added 117af25feaf7f_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added 117af73b3ce55_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added 117af21af69cb_af-only-gnomad.raw.sites.vcf added 117af34a9fb4_af-only-gnomad.raw.sites.vcf.idx added 117af183ae41c_Mutect2-exome-panel.vcf.idx added 117af4255f6b1_Mutect2-WGS-panel-b37.vcf added 117af19b7007d_Mutect2-WGS-panel-b37.vcf.idx added 117af3d811bbb_small_exac_common_3.vcf added 117af6743b188_small_exac_common_3.vcf.idx added 117afd3c8caf_1000g_pon.hg38.vcf.gz added 117af2383bf3_1000g_pon.hg38.vcf.gz.tbi added 117af39e7cfa8_af-only-gnomad.hg38.vcf.gz added 117af21f23c4b_af-only-gnomad.hg38.vcf.gz.tbi added 117af26547156_small_exac_common_3.hg38.vcf.gz added 117af71dcd8c2_small_exac_common_3.hg38.vcf.gz.tbi added 117af5a1ae2f4_gencode.v41.annotation.gtf added 117af1b2a2f63_gencode.v42.annotation.gtf added 117af6e8d1a83_gencode.vM30.annotation.gtf added 117af71c7c728_gencode.vM31.annotation.gtf added 117af72e44d73_gencode.v41.transcripts.fa added 117af6a98f3f2_gencode.v41.transcripts.fa.fai added 117af5fb7cb8a_gencode.v42.transcripts.fa added 117af1b94021e_gencode.v42.transcripts.fa.fai added 117af12170db7_gencode.vM30.pc_transcripts.fa added 117af278572a8_gencode.vM30.pc_transcripts.fa.fai added 117af2a2a87dd_gencode.vM31.pc_transcripts.fa added 117af4e3dd3cb_gencode.vM31.pc_transcripts.fa.fai added 117af3d1bdc8e_GRCh38.primary_assembly.genome.fa.1.ht2 added 117af702d0df9_GRCh38.primary_assembly.genome.fa.2.ht2 added 117af1df08ff8_GRCh38.primary_assembly.genome.fa.3.ht2 added 117af1c7bf223_GRCh38.primary_assembly.genome.fa.4.ht2 added 117afd55e671_GRCh38.primary_assembly.genome.fa.5.ht2 added 117af28c0b8e_GRCh38.primary_assembly.genome.fa.6.ht2 added 117af384a98f0_GRCh38.primary_assembly.genome.fa.7.ht2 added 117af297ed16f_GRCh38.primary_assembly.genome.fa.8.ht2 added 117af44e7e3b1_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added 117af54159cce_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added 117af56e9c382_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added 117afd22b862_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added 117af627730aa_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added 117af7f1c1b66_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added 117afe4b06bc_GRCh38_full_analysis_set_plus_decoy_hla.fa added 117af5fa727f8_GRCh38.primary_assembly.genome.fa.fai added 117af57313bd7_GRCh38.primary_assembly.genome.fa.amb added 117af614fccf9_GRCh38.primary_assembly.genome.fa.ann added 117af3e1a2158_GRCh38.primary_assembly.genome.fa.bwt added 117af25833842_GRCh38.primary_assembly.genome.fa.pac added 117af49e2884b_GRCh38.primary_assembly.genome.fa.sa added 117af376219d2_GRCh38.primary_assembly.genome.fa added 117af98d4666_hs37d5.fa.fai added 117af1a08d770_hs37d5.fa.amb added 117af3a78076a_hs37d5.fa.ann added 117af1e2ede23_hs37d5.fa.bwt added 117af16f9db50_hs37d5.fa.pac added 117af6dad6cf8_hs37d5.fa.sa added 117af14cd4609_hs37d5.fa added 117af30b1038a_complete_ref_lens.bin added 117af355f71ff_ctable.bin added 117afd3537b9_ctg_offsets.bin added 117af20dd5975_duplicate_clusters.tsv added 117af241c212e_info.json added 117af32c66587_mphf.bin added 117af7f339c1b_pos.bin added 117af154df1db_pre_indexing.log added 117af30416bca_rank.bin added 117af170bb386_ref_indexing.log added 117af1372e3c_refAccumLengths.bin added 117af4dbc65c3_reflengths.bin added 117afbbd0d14_refseq.bin added 117af28a5a211_seq.bin added 117af12331ef0_versionInfo.json added 117af5a3427e5_salmon_index added 117af162759a7_chrLength.txt added 117af716eee4d_chrName.txt added 117af29df3b69_chrNameLength.txt added 117af7eb57ff8_chrStart.txt added 117af3de4b3c5_exonGeTrInfo.tab added 117af71d66a41_exonInfo.tab added 117af33da0bca_geneInfo.tab added 117af303c155e_Genome added 117af389ee70f_genomeParameters.txt added 117af4853a6d3_Log.out added 117af6bed8bbd_SA added 117af38715ca6_SAindex added 117af1a79b33d_sjdbInfo.txt added 117af2be6775f_sjdbList.fromGTF.out.tab added 117af27a7147d_sjdbList.out.tab added 117af4a322ee1_transcriptInfo.tab added 117af24a3dbd5_GRCh38.GENCODE.v42_100 added 117af1b58fbe_knownGene_hg38.sql added 117af36f003d2_knownGene_hg38.txt added 117af478aec2b_refGene_hg38.sql added 117af71971fbe_refGene_hg38.txt added 117af78a52d34_knownGene_mm39.sql added 117af243aeecd_knownGene_mm39.txt added 117af1913e750_refGene_mm39.sql added 117af69b7420c_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/Rtmpgbc9c4/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 26.618 3.724 32.020
ReUseData.Rcheck/ReUseData-Ex.timings
name | user | system | elapsed | |
dataHub-class | 8.430 | 1.003 | 9.591 | |
dataSearch | 1.554 | 0.073 | 1.646 | |
dataUpdate | 0 | 0 | 0 | |
getCloudData | 3.105 | 0.182 | 10.041 | |
getData | 0.000 | 0.001 | 0.001 | |
meta_data | 0.001 | 0.000 | 0.001 | |
recipeHub-class | 0.166 | 0.015 | 0.185 | |
recipeLoad | 1.713 | 0.113 | 1.848 | |
recipeMake | 0.001 | 0.001 | 0.001 | |
recipeSearch | 0.725 | 0.048 | 0.781 | |
recipeUpdate | 0.000 | 0.001 | 0.001 | |