Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-11-28 12:17 -0500 (Thu, 28 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
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 1712/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ReUseData 1.7.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | 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: 1.7.0 |
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_1.7.0.tar.gz |
StartedAt: 2024-11-28 01:29:59 -0500 (Thu, 28 Nov 2024) |
EndedAt: 2024-11-28 01:35:36 -0500 (Thu, 28 Nov 2024) |
EllapsedTime: 337.1 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_1.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ReUseData/DESCRIPTION’ ... OK * this is package ‘ReUseData’ version ‘1.7.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 5.515 0.709 6.335 * 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’ ... ** 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) (2024-11-20 r87352) -- "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... 169fd4c6a4745_GRCh38.primary_assembly.genome.fa.1.bt2 added 169fd556d2a34_GRCh38.primary_assembly.genome.fa.2.bt2 added 169fd71ede7bc_GRCh38.primary_assembly.genome.fa.3.bt2 added 169fd3a092213_GRCh38.primary_assembly.genome.fa.4.bt2 added 169fd2d9c2b29_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added 169fd67d5a823_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added 169fd7c11c716_outfile.txt added 169fd7325b4fc_GRCh37_to_GRCh38.chain added 169fd308d4773_GRCh37_to_NCBI34.chain added 169fdb4de7ec_GRCh37_to_NCBI35.chain added 169fd27b53cc0_GRCh37_to_NCBI36.chain added 169fd6ba7759d_GRCh38_to_GRCh37.chain added 169fd3f1acda2_GRCh38_to_NCBI34.chain added 169fd78b2670b_GRCh38_to_NCBI35.chain added 169fd88b4115_GRCh38_to_NCBI36.chain added 169fd6e5dce14_NCBI34_to_GRCh37.chain added 169fd5084bba7_NCBI34_to_GRCh38.chain added 169fd3a3bfa3d_NCBI35_to_GRCh37.chain added 169fd37a9d8a9_NCBI35_to_GRCh38.chain added 169fd6fcf5bcb_NCBI36_to_GRCh37.chain added 169fd1693a5c6_NCBI36_to_GRCh38.chain added 169fd376875be_GRCm38_to_NCBIM36.chain added 169fd2b0a295d_GRCm38_to_NCBIM37.chain added 169fd2821aebe_NCBIM36_to_GRCm38.chain added 169fd3b575087_NCBIM37_to_GRCm38.chain added 169fd6167ed80_1000G_omni2.5.b37.vcf.gz added 169fd6e19a075_1000G_omni2.5.b37.vcf.gz.tbi added 169fd547599cb_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added 169fd74c409be_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added 169fd725bd4d5_1000G_omni2.5.hg38.vcf.gz added 169fd6af2269a_1000G_omni2.5.hg38.vcf.gz.tbi added 169fd3fc47f50_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added 169fd7d827de4_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added 169fd217441c_af-only-gnomad.raw.sites.vcf added 169fd45788b56_af-only-gnomad.raw.sites.vcf.idx added 169fd6d03debb_Mutect2-exome-panel.vcf.idx added 169fd1913fee7_Mutect2-WGS-panel-b37.vcf added 169fd6fc3fc8d_Mutect2-WGS-panel-b37.vcf.idx added 169fd2bf9c64e_small_exac_common_3.vcf added 169fd1b4a4170_small_exac_common_3.vcf.idx added 169fd280e2e0f_1000g_pon.hg38.vcf.gz added 169fd3af1ef54_1000g_pon.hg38.vcf.gz.tbi added 169fd61979207_af-only-gnomad.hg38.vcf.gz added 169fd25f43b9f_af-only-gnomad.hg38.vcf.gz.tbi added 169fd45765730_small_exac_common_3.hg38.vcf.gz added 169fd5c5633f0_small_exac_common_3.hg38.vcf.gz.tbi added 169fd1f6c00ec_gencode.v41.annotation.gtf added 169fd6bb09611_gencode.v42.annotation.gtf added 169fd164c6d53_gencode.vM30.annotation.gtf added 169fd739d6f94_gencode.vM31.annotation.gtf added 169fd650898d8_gencode.v41.transcripts.fa added 169fd176ac0ba_gencode.v41.transcripts.fa.fai added 169fd6192ff58_gencode.v42.transcripts.fa added 169fd79ba1c73_gencode.v42.transcripts.fa.fai added 169fd29a20074_gencode.vM30.pc_transcripts.fa added 169fd4acbd506_gencode.vM30.pc_transcripts.fa.fai added 169fdc0ea347_gencode.vM31.pc_transcripts.fa added 169fd15019080_gencode.vM31.pc_transcripts.fa.fai added 169fd19b5ce46_GRCh38.primary_assembly.genome.fa.1.ht2 added 169fd6ef962d9_GRCh38.primary_assembly.genome.fa.2.ht2 added 169fd36c8cd7a_GRCh38.primary_assembly.genome.fa.3.ht2 added 169fd392a20af_GRCh38.primary_assembly.genome.fa.4.ht2 added 169fd7cc7de7a_GRCh38.primary_assembly.genome.fa.5.ht2 added 169fd25df5b96_GRCh38.primary_assembly.genome.fa.6.ht2 added 169fd6af5e846_GRCh38.primary_assembly.genome.fa.7.ht2 added 169fd36648286_GRCh38.primary_assembly.genome.fa.8.ht2 added 169fdb54750_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added 169fd7d5cd58c_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added 169fd59c81aa0_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added 169fd604c2c6c_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added 169fd28f897d8_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added 169fd58b8faeb_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added 169fd586187ce_GRCh38_full_analysis_set_plus_decoy_hla.fa added 169fd6b1b12b6_GRCh38.primary_assembly.genome.fa.fai added 169fd3e69a1a9_GRCh38.primary_assembly.genome.fa.amb added 169fd8f47e42_GRCh38.primary_assembly.genome.fa.ann added 169fd6b8d23a5_GRCh38.primary_assembly.genome.fa.bwt added 169fd7f1f5ccc_GRCh38.primary_assembly.genome.fa.pac added 169fd64059647_GRCh38.primary_assembly.genome.fa.sa added 169fd2acd429e_GRCh38.primary_assembly.genome.fa added 169fd9d0a906_hs37d5.fa.fai added 169fd6208cdf2_hs37d5.fa.amb added 169fd3008fd26_hs37d5.fa.ann added 169fd1e23e26d_hs37d5.fa.bwt added 169fd45e67190_hs37d5.fa.pac added 169fd1c29c8ca_hs37d5.fa.sa added 169fd7b3d5437_hs37d5.fa added 169fd77642616_complete_ref_lens.bin added 169fd5000ab96_ctable.bin added 169fd5c012de2_ctg_offsets.bin added 169fd516b7f9e_duplicate_clusters.tsv added 169fd688787d4_info.json added 169fd19e6a4e9_mphf.bin added 169fd7554ca47_pos.bin added 169fd11ac377f_pre_indexing.log added 169fd416f7be9_rank.bin added 169fd7e301f8e_ref_indexing.log added 169fd967e45b_refAccumLengths.bin added 169fd3c11730_reflengths.bin added 169fd79d9523c_refseq.bin added 169fd2aa61fa3_seq.bin added 169fd671c35_versionInfo.json added 169fd716cdbc7_salmon_index added 169fd21d11ffe_chrLength.txt added 169fd288b6e0a_chrName.txt added 169fd59e56751_chrNameLength.txt added 169fd63e224f2_chrStart.txt added 169fd13e7bf19_exonGeTrInfo.tab added 169fd53b30c84_exonInfo.tab added 169fdffad90a_geneInfo.tab added 169fd1dbf27b8_Genome added 169fd70c8b049_genomeParameters.txt added 169fd7adc278_Log.out added 169fd20ba5838_SA added 169fd29f5d551_SAindex added 169fd4a87ce5c_sjdbInfo.txt added 169fd19fd203e_sjdbList.fromGTF.out.tab added 169fd394fd3c6_sjdbList.out.tab added 169fd27d8898f_transcriptInfo.tab added 169fd792f1fb8_GRCh38.GENCODE.v42_100 added 169fd4cba730_knownGene_hg38.sql added 169fd564d42c5_knownGene_hg38.txt added 169fd6a5abfc6_refGene_hg38.sql added 169fd6be496b6_refGene_hg38.txt added 169fd6c62be10_knownGene_mm39.sql added 169fd46ac4407_knownGene_mm39.txt added 169fd57a64bd0_refGene_mm39.sql added 169fd66bb71a4_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/RtmpkGDuhU/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 17.578 2.462 21.070
ReUseData.Rcheck/ReUseData-Ex.timings
name | user | system | elapsed | |
dataHub-class | 5.515 | 0.709 | 6.335 | |
dataSearch | 0.970 | 0.044 | 1.020 | |
dataUpdate | 0 | 0 | 0 | |
getCloudData | 2.045 | 0.133 | 3.110 | |
getData | 0 | 0 | 0 | |
meta_data | 0.001 | 0.000 | 0.001 | |
recipeHub-class | 0.109 | 0.010 | 0.120 | |
recipeLoad | 1.065 | 0.072 | 1.145 | |
recipeMake | 0.000 | 0.000 | 0.001 | |
recipeSearch | 0.454 | 0.030 | 0.486 | |
recipeUpdate | 0 | 0 | 0 | |