Qian Liu
| Snapshot Date: 2026-04-08 13:40 -0400 (Wed, 08 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: 4a5d06b |
| git_last_commit_date: 2025-10-29 11:20:44 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-09 11:36 -0400 (Thu, 09 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4912 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-26 r89717) -- "Unsuffered Consequences" | 4623 |
| 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 1791/2388 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.11.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| See other builds for ReUseData in R Universe. | ||||||||||||||
|
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: 1.11.0 |
| 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_1.11.0.tar.gz |
| StartedAt: 2026-04-08 21:45:59 -0400 (Wed, 08 Apr 2026) |
| EndedAt: 2026-04-08 21:46:52 -0400 (Wed, 08 Apr 2026) |
| EllapsedTime: 53.6 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_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2026-03-26 r89717)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-09 01:45:59 UTC
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.11.0’
* 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
* 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-3.23-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/4.6/Resources/library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.11.0’ ** 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) (2026-03-26 r89717) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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...
164706b66a5e1_GRCh38.primary_assembly.genome.fa.1.bt2 added
1647020148ddd_GRCh38.primary_assembly.genome.fa.2.bt2 added
16470256db89f_GRCh38.primary_assembly.genome.fa.3.bt2 added
164704673e1eb_GRCh38.primary_assembly.genome.fa.4.bt2 added
1647061f52f6f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1647027fd52a7_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
16470683d6673_outfile.txt added
1647017113d7c_GRCh37_to_GRCh38.chain added
164706cdba3b8_GRCh37_to_NCBI34.chain added
1647047d9bcdd_GRCh37_to_NCBI35.chain added
1647027fe7605_GRCh37_to_NCBI36.chain added
1647032f656c6_GRCh38_to_GRCh37.chain added
164704abafb4d_GRCh38_to_NCBI34.chain added
1647039c8a28f_GRCh38_to_NCBI35.chain added
16470232877ec_GRCh38_to_NCBI36.chain added
1647035d938fc_NCBI34_to_GRCh37.chain added
16470482c4402_NCBI34_to_GRCh38.chain added
1647052250452_NCBI35_to_GRCh37.chain added
164707c3ecd9f_NCBI35_to_GRCh38.chain added
164707f2dc172_NCBI36_to_GRCh37.chain added
1647014f76499_NCBI36_to_GRCh38.chain added
164707ded838f_GRCm38_to_NCBIM36.chain added
16470745861df_GRCm38_to_NCBIM37.chain added
164705681b325_NCBIM36_to_GRCm38.chain added
164705d186e81_NCBIM37_to_GRCm38.chain added
164706eff06e6_1000G_omni2.5.b37.vcf.gz added
16470291e1ef8_1000G_omni2.5.b37.vcf.gz.tbi added
16470788340de_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
164707117eca1_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1647059b07808_1000G_omni2.5.hg38.vcf.gz added
1647050988338_1000G_omni2.5.hg38.vcf.gz.tbi added
164704ccefade_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1647028b82c37_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
16470535ee3c3_af-only-gnomad.raw.sites.vcf added
164707abb41f7_af-only-gnomad.raw.sites.vcf.idx added
164701be7fe14_Mutect2-exome-panel.vcf.idx added
164701bd9e15c_Mutect2-WGS-panel-b37.vcf added
164707d5a6d4c_Mutect2-WGS-panel-b37.vcf.idx added
164703bbdd8df_small_exac_common_3.vcf added
164702ce9371d_small_exac_common_3.vcf.idx added
1647032167f4_1000g_pon.hg38.vcf.gz added
1647062fc5c7_1000g_pon.hg38.vcf.gz.tbi added
164702a618efd_af-only-gnomad.hg38.vcf.gz added
164706af299c7_af-only-gnomad.hg38.vcf.gz.tbi added
164705d4e0eab_small_exac_common_3.hg38.vcf.gz added
164702fa52c68_small_exac_common_3.hg38.vcf.gz.tbi added
164705067848_gencode.v41.annotation.gtf added
164706bc2c18b_gencode.v42.annotation.gtf added
164703f30c3f2_gencode.vM30.annotation.gtf added
164701a906547_gencode.vM31.annotation.gtf added
164707de925f0_gencode.v41.transcripts.fa added
1647055b9f024_gencode.v41.transcripts.fa.fai added
164702244f774_gencode.v42.transcripts.fa added
164705dd1f23f_gencode.v42.transcripts.fa.fai added
164702773638_gencode.vM30.pc_transcripts.fa added
16470608897cb_gencode.vM30.pc_transcripts.fa.fai added
1647027a5c1f0_gencode.vM31.pc_transcripts.fa added
16470735f87e5_gencode.vM31.pc_transcripts.fa.fai added
164704d30690_GRCh38.primary_assembly.genome.fa.1.ht2 added
164703a53da69_GRCh38.primary_assembly.genome.fa.2.ht2 added
1647057284169_GRCh38.primary_assembly.genome.fa.3.ht2 added
1647013de8133_GRCh38.primary_assembly.genome.fa.4.ht2 added
1647074f44575_GRCh38.primary_assembly.genome.fa.5.ht2 added
1647050fc404f_GRCh38.primary_assembly.genome.fa.6.ht2 added
1647060e22c12_GRCh38.primary_assembly.genome.fa.7.ht2 added
1647020bb836f_GRCh38.primary_assembly.genome.fa.8.ht2 added
1647076b1fd32_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
164701f661a7f_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
16470685597f3_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
164704b6b0808_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
164705fdc6be6_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
164702ffa35_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
164704dd3adab_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1647042edd78_GRCh38.primary_assembly.genome.fa.fai added
1647020cdf36d_GRCh38.primary_assembly.genome.fa.amb added
16470312889ee_GRCh38.primary_assembly.genome.fa.ann added
164705c778178_GRCh38.primary_assembly.genome.fa.bwt added
1647029d51cb5_GRCh38.primary_assembly.genome.fa.pac added
16470664fc487_GRCh38.primary_assembly.genome.fa.sa added
164707eefaf8a_GRCh38.primary_assembly.genome.fa added
1647029edce21_hs37d5.fa.fai added
164703b77ee08_hs37d5.fa.amb added
164703eac6db8_hs37d5.fa.ann added
164702a576b2d_hs37d5.fa.bwt added
16470513d6d12_hs37d5.fa.pac added
1647017c3e269_hs37d5.fa.sa added
164703d4567af_hs37d5.fa added
16470179a3196_complete_ref_lens.bin added
16470c2d7af5_ctable.bin added
164707de37111_ctg_offsets.bin added
164705f1453a8_duplicate_clusters.tsv added
164702f806b5c_info.json added
1647018087d61_mphf.bin added
16470555f779a_pos.bin added
164706ea54b3f_pre_indexing.log added
1647025ef4dd9_rank.bin added
164701dff504_ref_indexing.log added
16470164eda92_refAccumLengths.bin added
1647012efb2af_reflengths.bin added
1647036bc08df_refseq.bin added
1647072ea848b_seq.bin added
164702a3fc9e_versionInfo.json added
164705c1dea6c_salmon_index added
16470300987b3_chrLength.txt added
1647041ac1168_chrName.txt added
164707aae487_chrNameLength.txt added
1647064815eff_chrStart.txt added
164706983eae5_exonGeTrInfo.tab added
1647053b29681_exonInfo.tab added
1647071b71a14_geneInfo.tab added
164702c11515f_Genome added
1647024f54a93_genomeParameters.txt added
1647063f30bd9_Log.out added
16470698f06d2_SA added
164702d08fb22_SAindex added
16470289f8c47_sjdbInfo.txt added
164702b29e27_sjdbList.fromGTF.out.tab added
164701cad13d3_sjdbList.out.tab added
1647026f0905a_transcriptInfo.tab added
164707b9518ae_GRCh38.GENCODE.v42_100 added
16470798786e4_knownGene_hg38.sql added
1647030a92111_knownGene_hg38.txt added
164702fb9fc0c_refGene_hg38.sql added
164705b52904e_refGene_hg38.txt added
164709801fb9_knownGene_mm39.sql added
164703aa2af8e_knownGene_mm39.txt added
16470eb3b1b5_refGene_mm39.sql added
164703757e99d_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:
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTZlJNK/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 1 | SKIP 0 | PASS 44 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 44 ]
> Sys.setenv(cachePath = file.path(tempdir(), "cache"))
>
>
>
> proc.time()
user system elapsed
6.849 0.874 8.454
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.037 | 0.287 | 2.362 | |
| dataSearch | 0.339 | 0.018 | 0.358 | |
| dataUpdate | 0.000 | 0.001 | 0.000 | |
| getCloudData | 0.844 | 0.055 | 1.645 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.037 | 0.003 | 0.040 | |
| recipeLoad | 0.410 | 0.029 | 0.445 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.161 | 0.012 | 0.172 | |
| recipeUpdate | 0 | 0 | 0 | |