Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-28 11:43 -0400 (Thu, 28 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 1758/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ReUseData 1.8.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: ReUseData |
Version: 1.8.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ReUseData_1.8.0.tar.gz |
StartedAt: 2025-08-26 13:50:38 -0000 (Tue, 26 Aug 2025) |
EndedAt: 2025-08-26 13:53:34 -0000 (Tue, 26 Aug 2025) |
EllapsedTime: 176.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ReUseData.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ReUseData_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ReUseData/DESCRIPTION’ ... OK * this is package ‘ReUseData’ version ‘1.8.0’ * 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 9.161 0.427 9.628 getCloudData 3.452 0.291 5.422 * 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-3.21-bioc/meat/ReUseData.Rcheck/00check.log’ for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.8.0’ ** 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) (2025-02-19 r87757) -- "Unsuffered Consequences" Copyright (C) 2025 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... 1da830654e99b4_GRCh38.primary_assembly.genome.fa.1.bt2 added 1da830598e10ad_GRCh38.primary_assembly.genome.fa.2.bt2 added 1da8304dc39ac6_GRCh38.primary_assembly.genome.fa.3.bt2 added 1da8302919cb8_GRCh38.primary_assembly.genome.fa.4.bt2 added 1da8301c1944af_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added 1da83067e56284_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added 1da830507fae6a_outfile.txt added 1da83022e235af_GRCh37_to_GRCh38.chain added 1da8302c22fb31_GRCh37_to_NCBI34.chain added 1da8308e36aad_GRCh37_to_NCBI35.chain added 1da8307d70bf78_GRCh37_to_NCBI36.chain added 1da83033f33a3d_GRCh38_to_GRCh37.chain added 1da83036958834_GRCh38_to_NCBI34.chain added 1da8302a5cc8dc_GRCh38_to_NCBI35.chain added 1da8301b5c7b59_GRCh38_to_NCBI36.chain added 1da830367ef62_NCBI34_to_GRCh37.chain added 1da83065b68b39_NCBI34_to_GRCh38.chain added 1da83051f2740a_NCBI35_to_GRCh37.chain added 1da8301a6258d9_NCBI35_to_GRCh38.chain added 1da83060643265_NCBI36_to_GRCh37.chain added 1da83039f986a8_NCBI36_to_GRCh38.chain added 1da83077b1f2e7_GRCm38_to_NCBIM36.chain added 1da830f8c76bb_GRCm38_to_NCBIM37.chain added 1da83013b5d74d_NCBIM36_to_GRCm38.chain added 1da830715bfcae_NCBIM37_to_GRCm38.chain added 1da83035685f10_1000G_omni2.5.b37.vcf.gz added 1da8301ec218ae_1000G_omni2.5.b37.vcf.gz.tbi added 1da8303cab02b9_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added 1da8304ccb531b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added 1da83057162b0b_1000G_omni2.5.hg38.vcf.gz added 1da8304bb78dad_1000G_omni2.5.hg38.vcf.gz.tbi added 1da8303219eccf_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added 1da83030a43bb8_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added 1da830197b2874_af-only-gnomad.raw.sites.vcf added 1da83034ab8987_af-only-gnomad.raw.sites.vcf.idx added 1da8304cbd8067_Mutect2-exome-panel.vcf.idx added 1da8301608af8_Mutect2-WGS-panel-b37.vcf added 1da83052b37f1_Mutect2-WGS-panel-b37.vcf.idx added 1da8306f9fb616_small_exac_common_3.vcf added 1da8302d838629_small_exac_common_3.vcf.idx added 1da830e0ea29e_1000g_pon.hg38.vcf.gz added 1da8306d10758f_1000g_pon.hg38.vcf.gz.tbi added 1da8306176c066_af-only-gnomad.hg38.vcf.gz added 1da83044a42ad3_af-only-gnomad.hg38.vcf.gz.tbi added 1da830176d3e6b_small_exac_common_3.hg38.vcf.gz added 1da8307cd33bbf_small_exac_common_3.hg38.vcf.gz.tbi added 1da830480c1a35_gencode.v41.annotation.gtf added 1da8307d23c9a4_gencode.v42.annotation.gtf added 1da8304ec5afc9_gencode.vM30.annotation.gtf added 1da830626e730e_gencode.vM31.annotation.gtf added 1da8305d87fc0a_gencode.v41.transcripts.fa added 1da8308bf3671_gencode.v41.transcripts.fa.fai added 1da8305a2065f5_gencode.v42.transcripts.fa added 1da8306d1472c5_gencode.v42.transcripts.fa.fai added 1da8301c750dbe_gencode.vM30.pc_transcripts.fa added 1da8304b7c62a3_gencode.vM30.pc_transcripts.fa.fai added 1da830227cd1d5_gencode.vM31.pc_transcripts.fa added 1da8303b37266d_gencode.vM31.pc_transcripts.fa.fai added 1da830827655c_GRCh38.primary_assembly.genome.fa.1.ht2 added 1da8306f4824f0_GRCh38.primary_assembly.genome.fa.2.ht2 added 1da830124d5178_GRCh38.primary_assembly.genome.fa.3.ht2 added 1da83053def30a_GRCh38.primary_assembly.genome.fa.4.ht2 added 1da830216211bf_GRCh38.primary_assembly.genome.fa.5.ht2 added 1da83042f18d30_GRCh38.primary_assembly.genome.fa.6.ht2 added 1da8306d5a1b7e_GRCh38.primary_assembly.genome.fa.7.ht2 added 1da830560d9b46_GRCh38.primary_assembly.genome.fa.8.ht2 added 1da830faf0d98_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added 1da8306ebaa676_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added 1da8305b38d338_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added 1da8307f4ec3ae_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added 1da8301c3e2c9f_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added 1da830694775d6_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added 1da8306c5f393d_GRCh38_full_analysis_set_plus_decoy_hla.fa added 1da8307db4ed06_GRCh38.primary_assembly.genome.fa.fai added 1da8302deba0a9_GRCh38.primary_assembly.genome.fa.amb added 1da8303cc77a8_GRCh38.primary_assembly.genome.fa.ann added 1da8307a8828c5_GRCh38.primary_assembly.genome.fa.bwt added 1da83075f7bade_GRCh38.primary_assembly.genome.fa.pac added 1da830f0414d_GRCh38.primary_assembly.genome.fa.sa added 1da830494dd88f_GRCh38.primary_assembly.genome.fa added 1da83058662ded_hs37d5.fa.fai added 1da8305e783d57_hs37d5.fa.amb added 1da830520d0f00_hs37d5.fa.ann added 1da830328693e2_hs37d5.fa.bwt added 1da8304b8cb01c_hs37d5.fa.pac added 1da8306e821cbf_hs37d5.fa.sa added 1da8307e02f686_hs37d5.fa added 1da8306e0981f1_complete_ref_lens.bin added 1da83029b9432c_ctable.bin added 1da83062a5be2_ctg_offsets.bin added 1da8305d51a6e1_duplicate_clusters.tsv added 1da8303c0694a4_info.json added 1da8305a094eec_mphf.bin added 1da8307eb3b8a0_pos.bin added 1da8307ef821d4_pre_indexing.log added 1da83047636a6a_rank.bin added 1da83054c153e6_ref_indexing.log added 1da830ea72f6c_refAccumLengths.bin added 1da830361e10e0_reflengths.bin added 1da8302ffa271e_refseq.bin added 1da830df5f31b_seq.bin added 1da830525c3d80_versionInfo.json added 1da83019419cf5_salmon_index added 1da8307a552c58_chrLength.txt added 1da83050112a86_chrName.txt added 1da830472d3d9e_chrNameLength.txt added 1da8307e21a401_chrStart.txt added 1da8304a99534b_exonGeTrInfo.tab added 1da8303d24f87d_exonInfo.tab added 1da8307f11e54e_geneInfo.tab added 1da83013e72bda_Genome added 1da830158b266a_genomeParameters.txt added 1da8305d8a22a5_Log.out added 1da83065f43adb_SA added 1da8304811ba4c_SAindex added 1da8302916d2c1_sjdbInfo.txt added 1da8305476579a_sjdbList.fromGTF.out.tab added 1da8304614b0d2_sjdbList.out.tab added 1da830172054b2_transcriptInfo.tab added 1da8307e2f9ac6_GRCh38.GENCODE.v42_100 added 1da8304c3f0cb5_knownGene_hg38.sql added 1da8307471fb93_knownGene_hg38.txt added 1da8303a362f6a_refGene_hg38.sql added 1da83026485ba1_refGene_hg38.txt added 1da8307325b433_knownGene_mm39.sql added 1da830392e513e_knownGene_mm39.txt added 1da8306dabc60c_refGene_mm39.sql added 1da83047e70819_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/RtmpJrn8q0/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 31.041 1.990 35.655
ReUseData.Rcheck/ReUseData-Ex.timings
name | user | system | elapsed | |
dataHub-class | 9.161 | 0.427 | 9.628 | |
dataSearch | 1.641 | 0.003 | 1.649 | |
dataUpdate | 0 | 0 | 0 | |
getCloudData | 3.452 | 0.291 | 5.422 | |
getData | 0 | 0 | 0 | |
meta_data | 0.000 | 0.001 | 0.001 | |
recipeHub-class | 0.180 | 0.006 | 0.187 | |
recipeLoad | 1.922 | 0.120 | 2.049 | |
recipeMake | 0 | 0 | 0 | |
recipeSearch | 0.827 | 0.023 | 0.853 | |
recipeUpdate | 0 | 0 | 0 | |