Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-31 05:44:42 -0000 (Wed, 31 May 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
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 |
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
Package 1665/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ReUseData 1.1.0 (landing page) Qian Liu
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: ReUseData |
Version: 1.1.0 |
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings ReUseData_1.1.0.tar.gz |
StartedAt: 2023-05-30 16:49:38 -0000 (Tue, 30 May 2023) |
EndedAt: 2023-05-30 16:53:01 -0000 (Tue, 30 May 2023) |
EllapsedTime: 202.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: ReUseData.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings ReUseData_1.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ReUseData.Rcheck’ * using R version 4.3.0 (2023-04-21) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.2 LTS * using session charset: UTF-8 * checking for file ‘ReUseData/DESCRIPTION’ ... OK * this is package ‘ReUseData’ version ‘1.1.0’ * 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 R 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 dataUpdate 16.082 1.219 17.300 getCloudData 10.719 0.616 14.994 dataHub-class 8.726 0.551 9.283 getData 4.837 0.342 5.173 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘ReUseData_data.Rmd’ using ‘UTF-8’... OK ‘ReUseData_quickStart.Rmd’ using ‘UTF-8’... OK ‘ReUseData_recipe.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘ReUseData_data.Rmd’ using rmarkdown Error: processing vignette 'ReUseData_data.Rmd' failed with diagnostics: there is no package called ‘BiocStyle’ --- failed re-building ‘ReUseData_data.Rmd’ --- re-building ‘ReUseData_quickStart.Rmd’ using rmarkdown Error: processing vignette 'ReUseData_quickStart.Rmd' failed with diagnostics: there is no package called ‘BiocStyle’ --- failed re-building ‘ReUseData_quickStart.Rmd’ --- re-building ‘ReUseData_recipe.Rmd’ using rmarkdown Error: processing vignette 'ReUseData_recipe.Rmd' failed with diagnostics: there is no package called ‘BiocStyle’ --- failed re-building ‘ReUseData_recipe.Rmd’ SUMMARY: processing the following files failed: ‘ReUseData_data.Rmd’ ‘ReUseData_quickStart.Rmd’ ‘ReUseData_recipe.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.18-bioc/meat/ReUseData.Rcheck/00check.log’ for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/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 4.3.0 (2023-04-21) -- "Already Tomorrow" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (64-bit) 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... 2cb14b3f3e9a90_GRCh38.primary_assembly.genome.fa.1.bt2 added 2cb14b4acef023_GRCh38.primary_assembly.genome.fa.2.bt2 added 2cb14b44b0d5d9_GRCh38.primary_assembly.genome.fa.3.bt2 added 2cb14b383a314b_GRCh38.primary_assembly.genome.fa.4.bt2 added 2cb14b6d565ad9_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added 2cb14b73030d88_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added 2cb14b21f1330f_outfile.txt added 2cb14b1e4209b1_GRCh37_to_GRCh38.chain added 2cb14b78c457ea_GRCh37_to_NCBI34.chain added 2cb14b76c56ad2_GRCh37_to_NCBI35.chain added 2cb14b41ad4a81_GRCh37_to_NCBI36.chain added 2cb14b7e9bfc69_GRCh38_to_GRCh37.chain added 2cb14b4343010a_GRCh38_to_NCBI34.chain added 2cb14b3759e0b5_GRCh38_to_NCBI35.chain added 2cb14b3b08db53_GRCh38_to_NCBI36.chain added 2cb14b79b05f17_NCBI34_to_GRCh37.chain added 2cb14b7eb6ce6b_NCBI34_to_GRCh38.chain added 2cb14b6695a59c_NCBI35_to_GRCh37.chain added 2cb14b2b92bb4_NCBI35_to_GRCh38.chain added 2cb14b4d75fd8f_NCBI36_to_GRCh37.chain added 2cb14b5bc3416a_NCBI36_to_GRCh38.chain added 2cb14b42a66ec2_GRCm38_to_NCBIM36.chain added 2cb14b4de8e201_GRCm38_to_NCBIM37.chain added 2cb14b634a45c5_NCBIM36_to_GRCm38.chain added 2cb14b75406247_NCBIM37_to_GRCm38.chain added 2cb14b3b7033a6_1000G_omni2.5.b37.vcf.gz added 2cb14b4ebfa019_1000G_omni2.5.b37.vcf.gz.tbi added 2cb14b4b59ff2c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added 2cb14b4844378a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added 2cb14b254ad5f6_1000G_omni2.5.hg38.vcf.gz added 2cb14b3af86ec7_1000G_omni2.5.hg38.vcf.gz.tbi added 2cb14b782d21a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added 2cb14b7019c619_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added 2cb14b7fa944a0_af-only-gnomad.raw.sites.vcf added 2cb14b3fbd0366_af-only-gnomad.raw.sites.vcf.idx added 2cb14b5d7020f2_Mutect2-exome-panel.vcf.idx added 2cb14b72ac5229_Mutect2-WGS-panel-b37.vcf added 2cb14b61ae3675_Mutect2-WGS-panel-b37.vcf.idx added 2cb14b7bb22aa4_small_exac_common_3.vcf added 2cb14b6b70aa13_small_exac_common_3.vcf.idx added 2cb14b5873a148_1000g_pon.hg38.vcf.gz added 2cb14b3d5f7525_1000g_pon.hg38.vcf.gz.tbi added 2cb14b6a0ca67c_af-only-gnomad.hg38.vcf.gz added 2cb14b1bb6a252_af-only-gnomad.hg38.vcf.gz.tbi added 2cb14b74b955db_small_exac_common_3.hg38.vcf.gz added 2cb14b251581cf_small_exac_common_3.hg38.vcf.gz.tbi added 2cb14b15670169_gencode.v41.annotation.gtf added 2cb14b73702446_gencode.v42.annotation.gtf added 2cb14bbab276c_gencode.vM30.annotation.gtf added 2cb14b18202d1e_gencode.vM31.annotation.gtf added 2cb14b40e621d6_gencode.v41.transcripts.fa added 2cb14b676e68d6_gencode.v41.transcripts.fa.fai added 2cb14b5ac69be0_gencode.v42.transcripts.fa added 2cb14becf03d7_gencode.v42.transcripts.fa.fai added 2cb14b4ab8ae9b_gencode.vM30.pc_transcripts.fa added 2cb14b5006fe28_gencode.vM30.pc_transcripts.fa.fai added 2cb14b4a3f377d_gencode.vM31.pc_transcripts.fa added 2cb14b19784eb5_gencode.vM31.pc_transcripts.fa.fai added 2cb14b1b60fd54_GRCh38.primary_assembly.genome.fa.1.ht2 added 2cb14b12836f07_GRCh38.primary_assembly.genome.fa.2.ht2 added 2cb14b3ec324ab_GRCh38.primary_assembly.genome.fa.3.ht2 added 2cb14b56596c1b_GRCh38.primary_assembly.genome.fa.4.ht2 added 2cb14b1a064121_GRCh38.primary_assembly.genome.fa.5.ht2 added 2cb14b2edceac4_GRCh38.primary_assembly.genome.fa.6.ht2 added 2cb14b5602b0bc_GRCh38.primary_assembly.genome.fa.7.ht2 added 2cb14b59c34487_GRCh38.primary_assembly.genome.fa.8.ht2 added 2cb14bc4d0bb6_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added 2cb14b48af02e5_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added 2cb14b3b717afd_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added 2cb14b7ff365a_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added 2cb14b341facf8_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added 2cb14b13e51c45_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added 2cb14b455eab80_GRCh38_full_analysis_set_plus_decoy_hla.fa added 2cb14b1e2c5375_GRCh38.primary_assembly.genome.fa.fai added 2cb14b2f9bbe97_GRCh38.primary_assembly.genome.fa.amb added 2cb14b3a18015b_GRCh38.primary_assembly.genome.fa.ann added 2cb14b4341d544_GRCh38.primary_assembly.genome.fa.bwt added 2cb14b4502c000_GRCh38.primary_assembly.genome.fa.pac added 2cb14b2d8825a1_GRCh38.primary_assembly.genome.fa.sa added 2cb14b4eecfcb0_GRCh38.primary_assembly.genome.fa added 2cb14b5d22ed1e_hs37d5.fa.fai added 2cb14b6e6e4777_hs37d5.fa.amb added 2cb14b365b6587_hs37d5.fa.ann added 2cb14b37e988ff_hs37d5.fa.bwt added 2cb14b7d3d4b4e_hs37d5.fa.pac added 2cb14b1141422_hs37d5.fa.sa added 2cb14b7f08727_hs37d5.fa added 2cb14b477c82cb_complete_ref_lens.bin added 2cb14b1a8c62d7_ctable.bin added 2cb14b2351847b_ctg_offsets.bin added 2cb14b59fff1d2_duplicate_clusters.tsv added 2cb14b594f8782_info.json added 2cb14b79aaf096_mphf.bin added 2cb14b740632f4_pos.bin added 2cb14b82c7246_pre_indexing.log added 2cb14b4fada152_rank.bin added 2cb14b4dc9777b_ref_indexing.log added 2cb14b14797dfd_refAccumLengths.bin added 2cb14b185ca437_reflengths.bin added 2cb14b93af278_refseq.bin added 2cb14b1c78b457_seq.bin added 2cb14b4c7c5130_versionInfo.json added 2cb14b1d200ebd_salmon_index added 2cb14b61d75fd7_chrLength.txt added 2cb14b6aa8a4a5_chrName.txt added 2cb14b4cbbcd54_chrNameLength.txt added 2cb14b1bef6132_chrStart.txt added 2cb14b2dea79e9_exonGeTrInfo.tab added 2cb14b11be8d55_exonInfo.tab added 2cb14b497786d4_geneInfo.tab added 2cb14b7cd7769a_Genome added 2cb14b6ee17a73_genomeParameters.txt added 2cb14b37e5ce4b_Log.out added 2cb14b3332dc21_SA added 2cb14b26cb0372_SAindex added 2cb14b3523199a_sjdbInfo.txt added 2cb14b3446f043_sjdbList.fromGTF.out.tab added 2cb14b2ebb8a99_sjdbList.out.tab added 2cb14b7c9f9c65_transcriptInfo.tab added 2cb14b4ed3531b_GRCh38.GENCODE.v42_100 added 2cb14b520d0f14_knownGene_hg38.sql added 2cb14b569f8e38_knownGene_hg38.txt added 2cb14b2822da9d_refGene_hg38.sql added 2cb14b4bb7ffab_refGene_hg38.txt added 2cb14b4aa5c12c_knownGene_mm39.sql added 2cb14b304f4ce4_knownGene_mm39.txt added 2cb14b1b65a0fd_refGene_mm39.sql added 2cb14b186f38a7_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/RtmphXM5jv/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 ] > > proc.time() user system elapsed 32.164 2.433 36.213
ReUseData.Rcheck/ReUseData-Ex.timings
name | user | system | elapsed | |
dataHub-class | 8.726 | 0.551 | 9.283 | |
dataSearch | 1.394 | 0.059 | 1.454 | |
dataUpdate | 16.082 | 1.219 | 17.300 | |
getCloudData | 10.719 | 0.616 | 14.994 | |
getData | 4.837 | 0.342 | 5.173 | |
meta_data | 0.012 | 0.001 | 0.013 | |
recipeHub-class | 0.266 | 0.024 | 0.290 | |
recipeLoad | 1.578 | 0.092 | 1.673 | |
recipeMake | 4.557 | 0.255 | 4.808 | |
recipeSearch | 0.745 | 0.004 | 0.748 | |
recipeUpdate | 0.002 | 0.000 | 0.002 | |