Qian Liu
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_21 |
| git_last_commit: 601a107 |
| git_last_commit_date: 2025-04-15 13:01:44 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:39 -0400 (Thu, 16 Oct 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" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 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. |
| Package: ReUseData |
| Version: 1.8.0 |
| 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_1.8.0.tar.gz |
| StartedAt: 2025-10-14 09:04:55 -0400 (Tue, 14 Oct 2025) |
| EndedAt: 2025-10-14 09:09:06 -0400 (Tue, 14 Oct 2025) |
| EllapsedTime: 251.3 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* 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 ‘1.8.0’
* 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 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 12.153 1.261 13.660
getCloudData 4.677 0.214 6.131
* 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’ ... ** 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 version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 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...
91267ca17082_GRCh38.primary_assembly.genome.fa.1.bt2 added
91264ae1a6ba_GRCh38.primary_assembly.genome.fa.2.bt2 added
9126248923be_GRCh38.primary_assembly.genome.fa.3.bt2 added
91262789a1af_GRCh38.primary_assembly.genome.fa.4.bt2 added
91263cd5fc70_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
91264b03c44_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
91264e4496c3_outfile.txt added
912679060459_GRCh37_to_GRCh38.chain added
91267a07ad21_GRCh37_to_NCBI34.chain added
9126df7901e_GRCh37_to_NCBI35.chain added
91267816a8bb_GRCh37_to_NCBI36.chain added
9126179fca95_GRCh38_to_GRCh37.chain added
91267bad0850_GRCh38_to_NCBI34.chain added
91261cfcfb9f_GRCh38_to_NCBI35.chain added
912624eb9297_GRCh38_to_NCBI36.chain added
912665e50a70_NCBI34_to_GRCh37.chain added
912620107353_NCBI34_to_GRCh38.chain added
912618035e97_NCBI35_to_GRCh37.chain added
912653717d2_NCBI35_to_GRCh38.chain added
912663fcdeaa_NCBI36_to_GRCh37.chain added
91266e7e9e2e_NCBI36_to_GRCh38.chain added
91263ac316ae_GRCm38_to_NCBIM36.chain added
91265e0617a5_GRCm38_to_NCBIM37.chain added
912661fa81dc_NCBIM36_to_GRCm38.chain added
9126563c4c5_NCBIM37_to_GRCm38.chain added
9126590b6446_1000G_omni2.5.b37.vcf.gz added
91267ae45d55_1000G_omni2.5.b37.vcf.gz.tbi added
912626abb67b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
912653595912_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
9126ee6d77e_1000G_omni2.5.hg38.vcf.gz added
9126554d98d6_1000G_omni2.5.hg38.vcf.gz.tbi added
9126596d355a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
912610c9d594_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
912632e4f028_af-only-gnomad.raw.sites.vcf added
91265452ec32_af-only-gnomad.raw.sites.vcf.idx added
91261010f1de_Mutect2-exome-panel.vcf.idx added
912648772e0f_Mutect2-WGS-panel-b37.vcf added
9126870fff4_Mutect2-WGS-panel-b37.vcf.idx added
912632b3f080_small_exac_common_3.vcf added
912643727d81_small_exac_common_3.vcf.idx added
9126118dc2bf_1000g_pon.hg38.vcf.gz added
912671ec9299_1000g_pon.hg38.vcf.gz.tbi added
9126628cb53d_af-only-gnomad.hg38.vcf.gz added
91263ceea57_af-only-gnomad.hg38.vcf.gz.tbi added
912657af7b5_small_exac_common_3.hg38.vcf.gz added
91264c1c8ee2_small_exac_common_3.hg38.vcf.gz.tbi added
912666e8be77_gencode.v41.annotation.gtf added
91263a30ab69_gencode.v42.annotation.gtf added
912651459857_gencode.vM30.annotation.gtf added
91263014a170_gencode.vM31.annotation.gtf added
91261a72d8b9_gencode.v41.transcripts.fa added
912669f2673f_gencode.v41.transcripts.fa.fai added
912629588f70_gencode.v42.transcripts.fa added
912675311744_gencode.v42.transcripts.fa.fai added
912669eead77_gencode.vM30.pc_transcripts.fa added
912634be95f6_gencode.vM30.pc_transcripts.fa.fai added
91264c676487_gencode.vM31.pc_transcripts.fa added
912617f90241_gencode.vM31.pc_transcripts.fa.fai added
91265d0305b2_GRCh38.primary_assembly.genome.fa.1.ht2 added
9126716b18d2_GRCh38.primary_assembly.genome.fa.2.ht2 added
91262e2abd2a_GRCh38.primary_assembly.genome.fa.3.ht2 added
912677e92813_GRCh38.primary_assembly.genome.fa.4.ht2 added
91266c4634e5_GRCh38.primary_assembly.genome.fa.5.ht2 added
9126753addeb_GRCh38.primary_assembly.genome.fa.6.ht2 added
91266bbfab6d_GRCh38.primary_assembly.genome.fa.7.ht2 added
9126748fb85e_GRCh38.primary_assembly.genome.fa.8.ht2 added
91267915f1b_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
912658fae97e_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
912640f77cd5_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
91263824a545_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
91266dde71ce_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
91262701c3bc_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
912664d97fa5_GRCh38_full_analysis_set_plus_decoy_hla.fa added
912634b5d5d_GRCh38.primary_assembly.genome.fa.fai added
912648de865b_GRCh38.primary_assembly.genome.fa.amb added
9126946e5bd_GRCh38.primary_assembly.genome.fa.ann added
9126d94e00d_GRCh38.primary_assembly.genome.fa.bwt added
912629017c72_GRCh38.primary_assembly.genome.fa.pac added
912620913566_GRCh38.primary_assembly.genome.fa.sa added
91261d48cc3e_GRCh38.primary_assembly.genome.fa added
912616590977_hs37d5.fa.fai added
91262f7c6f17_hs37d5.fa.amb added
91261261675c_hs37d5.fa.ann added
912638c8d271_hs37d5.fa.bwt added
912687015d7_hs37d5.fa.pac added
912676a9da94_hs37d5.fa.sa added
912694d6769_hs37d5.fa added
912638c02344_complete_ref_lens.bin added
91264e4b6277_ctable.bin added
9126372d9ac9_ctg_offsets.bin added
9126130d1e6c_duplicate_clusters.tsv added
912642484e39_info.json added
91261907a22e_mphf.bin added
9126442886d8_pos.bin added
912640acf1dd_pre_indexing.log added
91261a3b0557_rank.bin added
912618dba035_ref_indexing.log added
91267af30452_refAccumLengths.bin added
912668a0e28d_reflengths.bin added
91261a79cca5_refseq.bin added
9126326a7237_seq.bin added
91266a7092bc_versionInfo.json added
91264b1ab3c_salmon_index added
91262c60f28c_chrLength.txt added
912610d3dc17_chrName.txt added
9126451672a2_chrNameLength.txt added
912644c00d1d_chrStart.txt added
91261c9d0e2e_exonGeTrInfo.tab added
9126b0dfcaf_exonInfo.tab added
912643484ad4_geneInfo.tab added
91263f28c6ce_Genome added
9126e141ec7_genomeParameters.txt added
91264af0a209_Log.out added
91267c1e234e_SA added
91261ea0158b_SAindex added
91261fe66862_sjdbInfo.txt added
91264fcf0a4a_sjdbList.fromGTF.out.tab added
912621aca935_sjdbList.out.tab added
91264e98e7d8_transcriptInfo.tab added
9126189d3e38_GRCh38.GENCODE.v42_100 added
91267b5fdb27_knownGene_hg38.sql added
9126522d1cb8_knownGene_hg38.txt added
9126fb89e2e_refGene_hg38.sql added
91262198e612_refGene_hg38.txt added
91263d28b8f9_knownGene_mm39.sql added
91263c8802cd_knownGene_mm39.txt added
912656fffc7_refGene_mm39.sql added
91267c01649a_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/RtmpJf0WxQ/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
41.536 5.082 47.776
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 12.153 | 1.261 | 13.660 | |
| dataSearch | 2.461 | 0.080 | 2.602 | |
| dataUpdate | 0.000 | 0.001 | 0.002 | |
| getCloudData | 4.677 | 0.214 | 6.131 | |
| getData | 0.001 | 0.002 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.002 | |
| recipeHub-class | 0.254 | 0.023 | 0.278 | |
| recipeLoad | 2.812 | 0.141 | 2.978 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 1.159 | 0.053 | 1.215 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |