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 11:41:00 -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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: ReUseData |
Version: 1.4.0 |
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings ReUseData_1.4.0.tar.gz |
StartedAt: 2024-05-04 11:10:52 -0000 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 11:13:44 -0000 (Sat, 04 May 2024) |
EllapsedTime: 171.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ReUseData.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --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: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * 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 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 9.299 0.379 9.716 getCloudData 3.769 0.647 7.172 * 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 ‘/home/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck/00check.log’ for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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: aarch64-unknown-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... 20b78a7a55edea_GRCh38.primary_assembly.genome.fa.1.bt2 added 20b78a40c5e3ea_GRCh38.primary_assembly.genome.fa.2.bt2 added 20b78a730225dc_GRCh38.primary_assembly.genome.fa.3.bt2 added 20b78a77b7e2ee_GRCh38.primary_assembly.genome.fa.4.bt2 added 20b78a289fc7ba_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added 20b78a32ba521f_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added 20b78a27a58cab_outfile.txt added 20b78a3b1a6d18_GRCh37_to_GRCh38.chain added 20b78a662eb6ef_GRCh37_to_NCBI34.chain added 20b78a5d488de3_GRCh37_to_NCBI35.chain added 20b78a59cbdedf_GRCh37_to_NCBI36.chain added 20b78a23f71a7f_GRCh38_to_GRCh37.chain added 20b78a7c581c1c_GRCh38_to_NCBI34.chain added 20b78a2bc2156e_GRCh38_to_NCBI35.chain added 20b78a4d5b3bec_GRCh38_to_NCBI36.chain added 20b78a623d681a_NCBI34_to_GRCh37.chain added 20b78a147ee65f_NCBI34_to_GRCh38.chain added 20b78a3e27dfa7_NCBI35_to_GRCh37.chain added 20b78a701c23a1_NCBI35_to_GRCh38.chain added 20b78a1094ec3f_NCBI36_to_GRCh37.chain added 20b78a630d2572_NCBI36_to_GRCh38.chain added 20b78a5bdfe1cc_GRCm38_to_NCBIM36.chain added 20b78a11444488_GRCm38_to_NCBIM37.chain added 20b78af713391_NCBIM36_to_GRCm38.chain added 20b78a527a0d21_NCBIM37_to_GRCm38.chain added 20b78a3c7075a5_1000G_omni2.5.b37.vcf.gz added 20b78a703400e_1000G_omni2.5.b37.vcf.gz.tbi added 20b78af14560c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added 20b78a4caf611b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added 20b78a13c330bb_1000G_omni2.5.hg38.vcf.gz added 20b78a2f5e9c27_1000G_omni2.5.hg38.vcf.gz.tbi added 20b78a47054f06_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added 20b78a548914a5_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added 20b78a2260c204_af-only-gnomad.raw.sites.vcf added 20b78a3ebd31f4_af-only-gnomad.raw.sites.vcf.idx added 20b78a7d28dc5f_Mutect2-exome-panel.vcf.idx added 20b78a551b1423_Mutect2-WGS-panel-b37.vcf added 20b78a6662be9f_Mutect2-WGS-panel-b37.vcf.idx added 20b78a38434977_small_exac_common_3.vcf added 20b78a3b49cb12_small_exac_common_3.vcf.idx added 20b78a43ab4c82_1000g_pon.hg38.vcf.gz added 20b78a120f2857_1000g_pon.hg38.vcf.gz.tbi added 20b78a5f40e591_af-only-gnomad.hg38.vcf.gz added 20b78a4003689e_af-only-gnomad.hg38.vcf.gz.tbi added 20b78a3dd13dc5_small_exac_common_3.hg38.vcf.gz added 20b78a2c9c217d_small_exac_common_3.hg38.vcf.gz.tbi added 20b78a2240d0b8_gencode.v41.annotation.gtf added 20b78a52502425_gencode.v42.annotation.gtf added 20b78a6ac40124_gencode.vM30.annotation.gtf added 20b78a125cf459_gencode.vM31.annotation.gtf added 20b78a62e51064_gencode.v41.transcripts.fa added 20b78a4dd12696_gencode.v41.transcripts.fa.fai added 20b78a6e3cd625_gencode.v42.transcripts.fa added 20b78a742954ed_gencode.v42.transcripts.fa.fai added 20b78a5d425a28_gencode.vM30.pc_transcripts.fa added 20b78a40b6e347_gencode.vM30.pc_transcripts.fa.fai added 20b78a3099ca92_gencode.vM31.pc_transcripts.fa added 20b78a64459a36_gencode.vM31.pc_transcripts.fa.fai added 20b78a4fcb3953_GRCh38.primary_assembly.genome.fa.1.ht2 added 20b78a7d492bad_GRCh38.primary_assembly.genome.fa.2.ht2 added 20b78a7808caf1_GRCh38.primary_assembly.genome.fa.3.ht2 added 20b78a7f29d57b_GRCh38.primary_assembly.genome.fa.4.ht2 added 20b78a444e7ab3_GRCh38.primary_assembly.genome.fa.5.ht2 added 20b78a4c91df96_GRCh38.primary_assembly.genome.fa.6.ht2 added 20b78a218a977f_GRCh38.primary_assembly.genome.fa.7.ht2 added 20b78a30baca7_GRCh38.primary_assembly.genome.fa.8.ht2 added 20b78a49babbf5_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added 20b78a76a5aba2_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added 20b78a696e6b46_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added 20b78a1fe056c_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added 20b78a31ef76b4_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added 20b78a2d19b7c8_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added 20b78a140d2dc3_GRCh38_full_analysis_set_plus_decoy_hla.fa added 20b78a11305c45_GRCh38.primary_assembly.genome.fa.fai added 20b78a6d1d2067_GRCh38.primary_assembly.genome.fa.amb added 20b78a51de6b89_GRCh38.primary_assembly.genome.fa.ann added 20b78a3dcc7dc2_GRCh38.primary_assembly.genome.fa.bwt added 20b78af5df11f_GRCh38.primary_assembly.genome.fa.pac added 20b78a242e8fae_GRCh38.primary_assembly.genome.fa.sa added 20b78a28907ee6_GRCh38.primary_assembly.genome.fa added 20b78a21bae579_hs37d5.fa.fai added 20b78a713a012_hs37d5.fa.amb added 20b78a7661a57c_hs37d5.fa.ann added 20b78aff7bb9e_hs37d5.fa.bwt added 20b78a7b3cf4ff_hs37d5.fa.pac added 20b78a53a3ffa4_hs37d5.fa.sa added 20b78a50ae9ee5_hs37d5.fa added 20b78a2bd6bf91_complete_ref_lens.bin added 20b78a37e999da_ctable.bin added 20b78a2079d839_ctg_offsets.bin added 20b78a291feb3f_duplicate_clusters.tsv added 20b78a2ff264cb_info.json added 20b78a1fa3adb4_mphf.bin added 20b78a6d6e65f2_pos.bin added 20b78a7c844461_pre_indexing.log added 20b78a412e4533_rank.bin added 20b78a707a129a_ref_indexing.log added 20b78a463f0056_refAccumLengths.bin added 20b78a37d3f0d5_reflengths.bin added 20b78a59e87de0_refseq.bin added 20b78a483d05c3_seq.bin added 20b78a69c36789_versionInfo.json added 20b78a70235a9_salmon_index added 20b78a5c4a3386_chrLength.txt added 20b78a7af3c3ce_chrName.txt added 20b78a741f5610_chrNameLength.txt added 20b78a2e289f0f_chrStart.txt added 20b78a38c04190_exonGeTrInfo.tab added 20b78a37d472f_exonInfo.tab added 20b78a52572ebd_geneInfo.tab added 20b78a6150c076_Genome added 20b78a25382ca8_genomeParameters.txt added 20b78a596aced0_Log.out added 20b78a57b265f2_SA added 20b78a352fe847_SAindex added 20b78a54a7c3cf_sjdbInfo.txt added 20b78a2b566597_sjdbList.fromGTF.out.tab added 20b78a5de872c_sjdbList.out.tab added 20b78a7e8361_transcriptInfo.tab added 20b78a633fff71_GRCh38.GENCODE.v42_100 added 20b78a26585f65_knownGene_hg38.sql added 20b78a299e6ea0_knownGene_hg38.txt added 20b78a1332643d_refGene_hg38.sql added 20b78a45fc0d19_refGene_hg38.txt added 20b78a170cd492_knownGene_mm39.sql added 20b78afb6a89e_knownGene_mm39.txt added 20b78a72a524c_refGene_mm39.sql added 20b78a786e72c_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: /home/biocbuild/tmp/RtmpwjqCS1/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 29.733 2.122 34.396
ReUseData.Rcheck/ReUseData-Ex.timings
name | user | system | elapsed | |
dataHub-class | 9.299 | 0.379 | 9.716 | |
dataSearch | 1.797 | 0.036 | 1.870 | |
dataUpdate | 0.001 | 0.000 | 0.000 | |
getCloudData | 3.769 | 0.647 | 7.172 | |
getData | 0 | 0 | 0 | |
meta_data | 0.001 | 0.000 | 0.001 | |
recipeHub-class | 0.185 | 0.056 | 0.242 | |
recipeLoad | 2.020 | 0.371 | 2.402 | |
recipeMake | 0 | 0 | 0 | |
recipeSearch | 0.864 | 0.036 | 0.902 | |
recipeUpdate | 0 | 0 | 0 | |