Qian Liu
| Snapshot Date: 2026-04-28 14:14 -0400 (Tue, 28 Apr 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 2026-04-29 10:16 -0400 (Wed, 29 Apr 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" | 4988 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There" | 4694 |
| 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 1812/2415 | 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: 2026-04-28 23:17:44 -0400 (Tue, 28 Apr 2026) |
| EndedAt: 2026-04-28 23:18:35 -0400 (Tue, 28 Apr 2026) |
| EllapsedTime: 51.6 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: 2026-04-29 03:17:44 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...
13bac1261e024_GRCh38.primary_assembly.genome.fa.1.bt2 added
13bac57c264e9_GRCh38.primary_assembly.genome.fa.2.bt2 added
13bac1b6f2a02_GRCh38.primary_assembly.genome.fa.3.bt2 added
13bac1f2ef760_GRCh38.primary_assembly.genome.fa.4.bt2 added
13bac4472cf9e_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
13bac4d9cb12d_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
13bac6a342929_outfile.txt added
13bac67a7938_GRCh37_to_GRCh38.chain added
13bac52ac4eda_GRCh37_to_NCBI34.chain added
13bac2e6cf49d_GRCh37_to_NCBI35.chain added
13bac732f873a_GRCh37_to_NCBI36.chain added
13bac35572bea_GRCh38_to_GRCh37.chain added
13bac6e042b01_GRCh38_to_NCBI34.chain added
13bac53a38714_GRCh38_to_NCBI35.chain added
13bac14f95cf2_GRCh38_to_NCBI36.chain added
13bac7f451e9f_NCBI34_to_GRCh37.chain added
13bac12dd9a00_NCBI34_to_GRCh38.chain added
13bac12a97fad_NCBI35_to_GRCh37.chain added
13bac35fd406d_NCBI35_to_GRCh38.chain added
13bac590cfcc_NCBI36_to_GRCh37.chain added
13bac663a5cee_NCBI36_to_GRCh38.chain added
13bac1ab41b1_GRCm38_to_NCBIM36.chain added
13bac1265cc52_GRCm38_to_NCBIM37.chain added
13bac594924ed_NCBIM36_to_GRCm38.chain added
13bac51177166_NCBIM37_to_GRCm38.chain added
13bac5a160921_1000G_omni2.5.b37.vcf.gz added
13bac5cb183bb_1000G_omni2.5.b37.vcf.gz.tbi added
13baca3f9988_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
13bac5578b4f9_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
13bac67b17345_1000G_omni2.5.hg38.vcf.gz added
13bac3306ec32_1000G_omni2.5.hg38.vcf.gz.tbi added
13bacb7ce0ca_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
13bac3389f3aa_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
13bac25dc3855_af-only-gnomad.raw.sites.vcf added
13bac1cf667de_af-only-gnomad.raw.sites.vcf.idx added
13bac751d2eac_Mutect2-exome-panel.vcf.idx added
13bac4ee35a45_Mutect2-WGS-panel-b37.vcf added
13bac303b9079_Mutect2-WGS-panel-b37.vcf.idx added
13bac168a10ac_small_exac_common_3.vcf added
13bac424c97c3_small_exac_common_3.vcf.idx added
13bac327fa536_1000g_pon.hg38.vcf.gz added
13bac5a379620_1000g_pon.hg38.vcf.gz.tbi added
13bac77613d25_af-only-gnomad.hg38.vcf.gz added
13bac10f5855e_af-only-gnomad.hg38.vcf.gz.tbi added
13bac6706e704_small_exac_common_3.hg38.vcf.gz added
13bac7628ec73_small_exac_common_3.hg38.vcf.gz.tbi added
13bac78bbae9f_gencode.v41.annotation.gtf added
13bac69c586a5_gencode.v42.annotation.gtf added
13bac270af0e3_gencode.vM30.annotation.gtf added
13bac3f4cdb1b_gencode.vM31.annotation.gtf added
13bac4ec4ea14_gencode.v41.transcripts.fa added
13bac61e3ef72_gencode.v41.transcripts.fa.fai added
13bac3b7d5793_gencode.v42.transcripts.fa added
13bac22009268_gencode.v42.transcripts.fa.fai added
13bac538bfb48_gencode.vM30.pc_transcripts.fa added
13bacb1e5ed2_gencode.vM30.pc_transcripts.fa.fai added
13bac76e332b1_gencode.vM31.pc_transcripts.fa added
13bac3e153f71_gencode.vM31.pc_transcripts.fa.fai added
13bac64f8338e_GRCh38.primary_assembly.genome.fa.1.ht2 added
13bac6300e36b_GRCh38.primary_assembly.genome.fa.2.ht2 added
13bac4f52b894_GRCh38.primary_assembly.genome.fa.3.ht2 added
13bac3fd4253b_GRCh38.primary_assembly.genome.fa.4.ht2 added
13bacd8653a_GRCh38.primary_assembly.genome.fa.5.ht2 added
13bac7eddc344_GRCh38.primary_assembly.genome.fa.6.ht2 added
13bac113ee66e_GRCh38.primary_assembly.genome.fa.7.ht2 added
13bac388a489a_GRCh38.primary_assembly.genome.fa.8.ht2 added
13bac7ea49375_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
13bac66cd2747_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
13bac26cddb0b_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
13bac14e7c314_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
13bac7bb860c4_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
13bac5d92351_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
13bac729d9dd6_GRCh38_full_analysis_set_plus_decoy_hla.fa added
13bac49e58763_GRCh38.primary_assembly.genome.fa.fai added
13bac7c1b9a7b_GRCh38.primary_assembly.genome.fa.amb added
13bac783b40e4_GRCh38.primary_assembly.genome.fa.ann added
13bac7a217666_GRCh38.primary_assembly.genome.fa.bwt added
13bac2ae4612e_GRCh38.primary_assembly.genome.fa.pac added
13bac77a82901_GRCh38.primary_assembly.genome.fa.sa added
13bac411c3e06_GRCh38.primary_assembly.genome.fa added
13bac252c1d4f_hs37d5.fa.fai added
13bac73384099_hs37d5.fa.amb added
13bac721937e7_hs37d5.fa.ann added
13bac55a55936_hs37d5.fa.bwt added
13bac5a841427_hs37d5.fa.pac added
13bac15473ade_hs37d5.fa.sa added
13bac7769cfbb_hs37d5.fa added
13bac43c53b3c_complete_ref_lens.bin added
13bac49b402e6_ctable.bin added
13bac492a6fd7_ctg_offsets.bin added
13bac114b1c8_duplicate_clusters.tsv added
13bac75a3c205_info.json added
13bac52171299_mphf.bin added
13bac68c624e9_pos.bin added
13bac28a172bc_pre_indexing.log added
13bac7f73a97a_rank.bin added
13bac27bc9f5_ref_indexing.log added
13bacd07f519_refAccumLengths.bin added
13bac56c42fe_reflengths.bin added
13bac6a2347a_refseq.bin added
13bac32338fd_seq.bin added
13bac7d726ba6_versionInfo.json added
13bac62f99fa1_salmon_index added
13bac725f35ca_chrLength.txt added
13bac48c49b6f_chrName.txt added
13bac63b8b9bb_chrNameLength.txt added
13bac74a9d722_chrStart.txt added
13bac3a6b3504_exonGeTrInfo.tab added
13bac5465b792_exonInfo.tab added
13bac61f6fd87_geneInfo.tab added
13bac1e7edc50_Genome added
13bac1ab217d4_genomeParameters.txt added
13bac223a6cfd_Log.out added
13bac29c96799_SA added
13bac65b0833d_SAindex added
13bac27784df3_sjdbInfo.txt added
13bac4b45a0c3_sjdbList.fromGTF.out.tab added
13bac483d88d0_sjdbList.out.tab added
13bac3fe134bd_transcriptInfo.tab added
13bac5a4d850e_GRCh38.GENCODE.v42_100 added
13bac175a8873_knownGene_hg38.sql added
13bac38b441ff_knownGene_hg38.txt added
13bac4258e96e_refGene_hg38.sql added
13bac5b4556c9_refGene_hg38.txt added
13bac2544d4ef_knownGene_mm39.sql added
13bac49f7aa06_knownGene_mm39.txt added
13bac22bb95da_refGene_mm39.sql added
13bac496b2d06_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//RtmpagL89X/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
6.608 0.821 8.536
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.076 | 0.265 | 2.352 | |
| dataSearch | 0.352 | 0.018 | 0.369 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.861 | 0.054 | 1.685 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.040 | 0.004 | 0.044 | |
| recipeLoad | 0.412 | 0.029 | 0.443 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.167 | 0.013 | 0.181 | |
| recipeUpdate | 0 | 0 | 0 | |