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 11:37:04 -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: /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: 2024-05-04 02:54:19 -0400 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 02:57:19 -0400 (Sat, 04 May 2024) |
EllapsedTime: 179.6 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 beta (2024-04-15 r86425) * 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 6.296 0.459 6.757 * 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 beta (2024-04-15 r86425) -- "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... 345ec93c0f619b_GRCh38.primary_assembly.genome.fa.1.bt2 added 345ec97746a31_GRCh38.primary_assembly.genome.fa.2.bt2 added 345ec956c4c46e_GRCh38.primary_assembly.genome.fa.3.bt2 added 345ec97272d7d5_GRCh38.primary_assembly.genome.fa.4.bt2 added 345ec94cd1b9ca_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added 345ec959569517_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added 345ec938b5fc80_outfile.txt added 345ec94ab82122_GRCh37_to_GRCh38.chain added 345ec926e4c06b_GRCh37_to_NCBI34.chain added 345ec982edfb_GRCh37_to_NCBI35.chain added 345ec94bb9f29a_GRCh37_to_NCBI36.chain added 345ec9785fcb4e_GRCh38_to_GRCh37.chain added 345ec9331c403b_GRCh38_to_NCBI34.chain added 345ec96cc876cb_GRCh38_to_NCBI35.chain added 345ec9306d44f4_GRCh38_to_NCBI36.chain added 345ec96d630de2_NCBI34_to_GRCh37.chain added 345ec9a035f39_NCBI34_to_GRCh38.chain added 345ec958117186_NCBI35_to_GRCh37.chain added 345ec9617a6bea_NCBI35_to_GRCh38.chain added 345ec9cd3db14_NCBI36_to_GRCh37.chain added 345ec939db687d_NCBI36_to_GRCh38.chain added 345ec97161ffa7_GRCm38_to_NCBIM36.chain added 345ec992632c3_GRCm38_to_NCBIM37.chain added 345ec92220dd40_NCBIM36_to_GRCm38.chain added 345ec96de7778_NCBIM37_to_GRCm38.chain added 345ec96a3aef40_1000G_omni2.5.b37.vcf.gz added 345ec96450f3c5_1000G_omni2.5.b37.vcf.gz.tbi added 345ec91dc21733_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added 345ec93015efb3_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added 345ec93cc743ed_1000G_omni2.5.hg38.vcf.gz added 345ec964bb7a52_1000G_omni2.5.hg38.vcf.gz.tbi added 345ec96c25514e_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added 345ec9443bae1f_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added 345ec93b803ec1_af-only-gnomad.raw.sites.vcf added 345ec95e982923_af-only-gnomad.raw.sites.vcf.idx added 345ec9110d67e9_Mutect2-exome-panel.vcf.idx added 345ec914d6d3d8_Mutect2-WGS-panel-b37.vcf added 345ec9174e25a4_Mutect2-WGS-panel-b37.vcf.idx added 345ec95bc5890c_small_exac_common_3.vcf added 345ec93bbb9443_small_exac_common_3.vcf.idx added 345ec917d1139f_1000g_pon.hg38.vcf.gz added 345ec9277f7ba6_1000g_pon.hg38.vcf.gz.tbi added 345ec9341b5f91_af-only-gnomad.hg38.vcf.gz added 345ec94aed53db_af-only-gnomad.hg38.vcf.gz.tbi added 345ec91447f271_small_exac_common_3.hg38.vcf.gz added 345ec96488a485_small_exac_common_3.hg38.vcf.gz.tbi added 345ec9385061bd_gencode.v41.annotation.gtf added 345ec91e4b51aa_gencode.v42.annotation.gtf added 345ec93c9a160c_gencode.vM30.annotation.gtf added 345ec919cacda7_gencode.vM31.annotation.gtf added 345ec92b1f2cbe_gencode.v41.transcripts.fa added 345ec976757e89_gencode.v41.transcripts.fa.fai added 345ec9b2ccd4f_gencode.v42.transcripts.fa added 345ec934455f81_gencode.v42.transcripts.fa.fai added 345ec918965bc9_gencode.vM30.pc_transcripts.fa added 345ec9120b44c7_gencode.vM30.pc_transcripts.fa.fai added 345ec91e804ec2_gencode.vM31.pc_transcripts.fa added 345ec97ce74f8e_gencode.vM31.pc_transcripts.fa.fai added 345ec92fcd5bfa_GRCh38.primary_assembly.genome.fa.1.ht2 added 345ec94e963e75_GRCh38.primary_assembly.genome.fa.2.ht2 added 345ec939ae937c_GRCh38.primary_assembly.genome.fa.3.ht2 added 345ec91488d64c_GRCh38.primary_assembly.genome.fa.4.ht2 added 345ec93abb8fc3_GRCh38.primary_assembly.genome.fa.5.ht2 added 345ec97dea419b_GRCh38.primary_assembly.genome.fa.6.ht2 added 345ec95009150d_GRCh38.primary_assembly.genome.fa.7.ht2 added 345ec91953b8e6_GRCh38.primary_assembly.genome.fa.8.ht2 added 345ec9ef7a984_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added 345ec964dfe8e5_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added 345ec930a1de8a_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added 345ec96abd3290_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added 345ec9209b7d28_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added 345ec94872f22a_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added 345ec9123cae36_GRCh38_full_analysis_set_plus_decoy_hla.fa added 345ec954b6dcb9_GRCh38.primary_assembly.genome.fa.fai added 345ec913604605_GRCh38.primary_assembly.genome.fa.amb added 345ec92684a0a7_GRCh38.primary_assembly.genome.fa.ann added 345ec9393f813f_GRCh38.primary_assembly.genome.fa.bwt added 345ec94bb0a7c2_GRCh38.primary_assembly.genome.fa.pac added 345ec944cff252_GRCh38.primary_assembly.genome.fa.sa added 345ec975d9974b_GRCh38.primary_assembly.genome.fa added 345ec9657b756a_hs37d5.fa.fai added 345ec96fef1f10_hs37d5.fa.amb added 345ec96c4f15d4_hs37d5.fa.ann added 345ec970a842b9_hs37d5.fa.bwt added 345ec924347e92_hs37d5.fa.pac added 345ec94e5719d_hs37d5.fa.sa added 345ec92b38780_hs37d5.fa added 345ec942b4cd54_complete_ref_lens.bin added 345ec91ccc12c_ctable.bin added 345ec93280e37a_ctg_offsets.bin added 345ec9114b0bc9_duplicate_clusters.tsv added 345ec93b7b54a8_info.json added 345ec94709b9c6_mphf.bin added 345ec94c069b8c_pos.bin added 345ec939659643_pre_indexing.log added 345ec91712ced4_rank.bin added 345ec9655a5472_ref_indexing.log added 345ec9485d3fc7_refAccumLengths.bin added 345ec97bf2b7b9_reflengths.bin added 345ec915fc32fd_refseq.bin added 345ec9331a7258_seq.bin added 345ec91c8e34e2_versionInfo.json added 345ec95e6f2527_salmon_index added 345ec94557208e_chrLength.txt added 345ec97145119b_chrName.txt added 345ec971cf6b2c_chrNameLength.txt added 345ec96bdbc136_chrStart.txt added 345ec92a8492da_exonGeTrInfo.tab added 345ec93d8012ee_exonInfo.tab added 345ec930abb388_geneInfo.tab added 345ec9205e2a25_Genome added 345ec922fb8858_genomeParameters.txt added 345ec9209ad298_Log.out added 345ec9cad3ff9_SA added 345ec913a3cb11_SAindex added 345ec944cf512a_sjdbInfo.txt added 345ec91192b197_sjdbList.fromGTF.out.tab added 345ec916575291_sjdbList.out.tab added 345ec97841e7e_transcriptInfo.tab added 345ec9135f72c3_GRCh38.GENCODE.v42_100 added 345ec948d8360b_knownGene_hg38.sql added 345ec918cf2a47_knownGene_hg38.txt added 345ec94edac76b_refGene_hg38.sql added 345ec9fe1efd2_refGene_hg38.txt added 345ec964d5c5d3_knownGene_mm39.sql added 345ec98405dae_knownGene_mm39.txt added 345ec926f4bea6_refGene_mm39.sql added 345ec94a301a46_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/Rtmp7pxUAv/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 20.939 1.784 23.048
ReUseData.Rcheck/ReUseData-Ex.timings
name | user | system | elapsed | |
dataHub-class | 6.296 | 0.459 | 6.757 | |
dataSearch | 1.123 | 0.083 | 1.208 | |
dataUpdate | 0.000 | 0.000 | 0.001 | |
getCloudData | 2.915 | 0.188 | 3.616 | |
getData | 0.000 | 0.001 | 0.000 | |
meta_data | 0.000 | 0.001 | 0.001 | |
recipeHub-class | 0.133 | 0.000 | 0.134 | |
recipeLoad | 1.328 | 0.086 | 1.415 | |
recipeMake | 0 | 0 | 0 | |
recipeSearch | 0.547 | 0.015 | 0.562 | |
recipeUpdate | 0.001 | 0.000 | 0.000 | |