Qian Liu
| Snapshot Date: 2026-05-06 13:40 -0400 (Wed, 06 May 2026) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_23 |
| git_last_commit: bb3489b |
| git_last_commit_date: 2026-04-28 08:59:39 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-07 11:36 -0400 (Thu, 07 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4990 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There" | 4723 |
| 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 1815/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.12.0 (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: 1.12.0 |
| 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_1.12.0.tar.gz |
| StartedAt: 2026-05-06 22:09:13 -0400 (Wed, 06 May 2026) |
| EndedAt: 2026-05-06 22:10:05 -0400 (Wed, 06 May 2026) |
| EllapsedTime: 52.6 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R version 4.6.0 Patched (2026-04-24 r89963)
* 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: 2026-05-07 02:09:13 UTC
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.12.0’
* 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 ‘1.12.0’ ** 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 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There"
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...
25f14e29adaa_GRCh38.primary_assembly.genome.fa.1.bt2 added
25f112489bfd_GRCh38.primary_assembly.genome.fa.2.bt2 added
25f15cf9086b_GRCh38.primary_assembly.genome.fa.3.bt2 added
25f16197d87c_GRCh38.primary_assembly.genome.fa.4.bt2 added
25f13805e6f2_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
25f1b7d369a_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
25f1498bbe5a_outfile.txt added
25f1757e2c6e_GRCh37_to_GRCh38.chain added
25f12e972605_GRCh37_to_NCBI34.chain added
25f145412a28_GRCh37_to_NCBI35.chain added
25f13936cb9d_GRCh37_to_NCBI36.chain added
25f13c71cdc3_GRCh38_to_GRCh37.chain added
25f1537bdc35_GRCh38_to_NCBI34.chain added
25f168b64664_GRCh38_to_NCBI35.chain added
25f116c784f1_GRCh38_to_NCBI36.chain added
25f14e8f5e6_NCBI34_to_GRCh37.chain added
25f15a67d18e_NCBI34_to_GRCh38.chain added
25f155eef000_NCBI35_to_GRCh37.chain added
25f139cebc13_NCBI35_to_GRCh38.chain added
25f1339da10b_NCBI36_to_GRCh37.chain added
25f131b7f3a6_NCBI36_to_GRCh38.chain added
25f123dd30ca_GRCm38_to_NCBIM36.chain added
25f1eae302b_GRCm38_to_NCBIM37.chain added
25f14ddc5e94_NCBIM36_to_GRCm38.chain added
25f13ec56e7b_NCBIM37_to_GRCm38.chain added
25f113d86d6f_1000G_omni2.5.b37.vcf.gz added
25f165f89c96_1000G_omni2.5.b37.vcf.gz.tbi added
25f124f07027_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
25f125532363_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
25f175384bb9_1000G_omni2.5.hg38.vcf.gz added
25f142f39ace_1000G_omni2.5.hg38.vcf.gz.tbi added
25f17386cb9_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
25f1969e963_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
25f18596769_af-only-gnomad.raw.sites.vcf added
25f1259422c7_af-only-gnomad.raw.sites.vcf.idx added
25f120774a17_Mutect2-exome-panel.vcf.idx added
25f177a13ca7_Mutect2-WGS-panel-b37.vcf added
25f17a95354c_Mutect2-WGS-panel-b37.vcf.idx added
25f159de4f73_small_exac_common_3.vcf added
25f11232351d_small_exac_common_3.vcf.idx added
25f11e3d0c40_1000g_pon.hg38.vcf.gz added
25f139ef4d42_1000g_pon.hg38.vcf.gz.tbi added
25f1db945c5_af-only-gnomad.hg38.vcf.gz added
25f17e938f8c_af-only-gnomad.hg38.vcf.gz.tbi added
25f19b57140_small_exac_common_3.hg38.vcf.gz added
25f1671e25ba_small_exac_common_3.hg38.vcf.gz.tbi added
25f16c3f0b39_gencode.v41.annotation.gtf added
25f11efa02b4_gencode.v42.annotation.gtf added
25f12fc7874f_gencode.vM30.annotation.gtf added
25f154846c0a_gencode.vM31.annotation.gtf added
25f141d12fdf_gencode.v41.transcripts.fa added
25f1c9dfb3b_gencode.v41.transcripts.fa.fai added
25f157d8e4f5_gencode.v42.transcripts.fa added
25f1609fbde1_gencode.v42.transcripts.fa.fai added
25f1176b3056_gencode.vM30.pc_transcripts.fa added
25f17e326a1c_gencode.vM30.pc_transcripts.fa.fai added
25f11fd494fe_gencode.vM31.pc_transcripts.fa added
25f13d81c005_gencode.vM31.pc_transcripts.fa.fai added
25f11165a7cf_GRCh38.primary_assembly.genome.fa.1.ht2 added
25f128ec0ff5_GRCh38.primary_assembly.genome.fa.2.ht2 added
25f1220bb2d0_GRCh38.primary_assembly.genome.fa.3.ht2 added
25f12e088726_GRCh38.primary_assembly.genome.fa.4.ht2 added
25f131e0e766_GRCh38.primary_assembly.genome.fa.5.ht2 added
25f12477f31f_GRCh38.primary_assembly.genome.fa.6.ht2 added
25f13efa8aed_GRCh38.primary_assembly.genome.fa.7.ht2 added
25f132b6ede8_GRCh38.primary_assembly.genome.fa.8.ht2 added
25f17bd345b_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
25f116b84655_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
25f11c11821a_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
25f14174875b_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
25f1496288ef_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
25f1640c288c_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
25f15a3a32a4_GRCh38_full_analysis_set_plus_decoy_hla.fa added
25f122d2db43_GRCh38.primary_assembly.genome.fa.fai added
25f141391d91_GRCh38.primary_assembly.genome.fa.amb added
25f1cc43c0b_GRCh38.primary_assembly.genome.fa.ann added
25f12741fcb9_GRCh38.primary_assembly.genome.fa.bwt added
25f15d36e9d1_GRCh38.primary_assembly.genome.fa.pac added
25f14030c826_GRCh38.primary_assembly.genome.fa.sa added
25f142a457b6_GRCh38.primary_assembly.genome.fa added
25f1337a8fe8_hs37d5.fa.fai added
25f1337de2bf_hs37d5.fa.amb added
25f1db18402_hs37d5.fa.ann added
25f1151a654_hs37d5.fa.bwt added
25f1177ed579_hs37d5.fa.pac added
25f17f106fc_hs37d5.fa.sa added
25f161018e76_hs37d5.fa added
25f12d3016bb_complete_ref_lens.bin added
25f13024662a_ctable.bin added
25f125af6817_ctg_offsets.bin added
25f11edad155_duplicate_clusters.tsv added
25f12fe53346_info.json added
25f17089513a_mphf.bin added
25f14733f08e_pos.bin added
25f122f61f27_pre_indexing.log added
25f14c774b5f_rank.bin added
25f12bf57131_ref_indexing.log added
25f17eda5e82_refAccumLengths.bin added
25f13272e9de_reflengths.bin added
25f1165807b2_refseq.bin added
25f16d614293_seq.bin added
25f1c59f8ff_versionInfo.json added
25f166ea33ae_salmon_index added
25f119e7194b_chrLength.txt added
25f1132d9836_chrName.txt added
25f116640b10_chrNameLength.txt added
25f121252ec_chrStart.txt added
25f11020504_exonGeTrInfo.tab added
25f12b974a20_exonInfo.tab added
25f15983913b_geneInfo.tab added
25f14cb3e666_Genome added
25f136db59e1_genomeParameters.txt added
25f17ae9dee9_Log.out added
25f11029d20a_SA added
25f1299c96d0_SAindex added
25f167714707_sjdbInfo.txt added
25f13dee519f_sjdbList.fromGTF.out.tab added
25f16930bd7c_sjdbList.out.tab added
25f17ee84dd7_transcriptInfo.tab added
25f1454e9f58_GRCh38.GENCODE.v42_100 added
25f12cbf6df4_knownGene_hg38.sql added
25f14bcbc51f_knownGene_hg38.txt added
25f12efa9d19_refGene_hg38.sql added
25f1475fec67_refGene_hg38.txt added
25f16a9982cc_knownGene_mm39.sql added
25f145a55c1_knownGene_mm39.txt added
25f146b3f422_refGene_mm39.sql added
25f150610871_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//RtmpD7Rrth/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
6.894 0.840 8.513
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.022 | 0.272 | 2.317 | |
| dataSearch | 0.373 | 0.019 | 0.391 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.809 | 0.052 | 1.732 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.039 | 0.004 | 0.043 | |
| recipeLoad | 0.415 | 0.030 | 0.452 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.155 | 0.012 | 0.167 | |
| recipeUpdate | 0 | 0 | 0 | |