Qian Liu
| Snapshot Date: 2026-05-04 13:40 -0400 (Mon, 04 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 2026-05-05 11:38 -0400 (Tue, 05 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" | 4989 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There" | 4719 |
| 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: 2026-05-04 21:33:26 -0400 (Mon, 04 May 2026) |
| EndedAt: 2026-05-04 21:34:17 -0400 (Mon, 04 May 2026) |
| EllapsedTime: 51.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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: 2026-05-05 01:33:26 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...
a2c43bbb9c0_GRCh38.primary_assembly.genome.fa.1.bt2 added
a2c4199fee2a_GRCh38.primary_assembly.genome.fa.2.bt2 added
a2c452cd148a_GRCh38.primary_assembly.genome.fa.3.bt2 added
a2c415ff9a7e_GRCh38.primary_assembly.genome.fa.4.bt2 added
a2c43ff7d17a_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
a2c426d9c165_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
a2c42227e1d0_outfile.txt added
a2c4685a3034_GRCh37_to_GRCh38.chain added
a2c47912db71_GRCh37_to_NCBI34.chain added
a2c4450515d0_GRCh37_to_NCBI35.chain added
a2c450db2e16_GRCh37_to_NCBI36.chain added
a2c465aecfd2_GRCh38_to_GRCh37.chain added
a2c437ce1825_GRCh38_to_NCBI34.chain added
a2c43b9341c2_GRCh38_to_NCBI35.chain added
a2c440c2461c_GRCh38_to_NCBI36.chain added
a2c41288f97b_NCBI34_to_GRCh37.chain added
a2c45eb303be_NCBI34_to_GRCh38.chain added
a2c43abadf84_NCBI35_to_GRCh37.chain added
a2c442a8713b_NCBI35_to_GRCh38.chain added
a2c440a1faad_NCBI36_to_GRCh37.chain added
a2c44a509501_NCBI36_to_GRCh38.chain added
a2c470669ac4_GRCm38_to_NCBIM36.chain added
a2c4603af382_GRCm38_to_NCBIM37.chain added
a2c43e490d29_NCBIM36_to_GRCm38.chain added
a2c42dff1eb1_NCBIM37_to_GRCm38.chain added
a2c448380e0e_1000G_omni2.5.b37.vcf.gz added
a2c45822de2c_1000G_omni2.5.b37.vcf.gz.tbi added
a2c4592847e8_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
a2c46388fe12_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
a2c436e082cb_1000G_omni2.5.hg38.vcf.gz added
a2c44daaf992_1000G_omni2.5.hg38.vcf.gz.tbi added
a2c413e70814_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
a2c424c36341_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
a2c417a95342_af-only-gnomad.raw.sites.vcf added
a2c46d991e30_af-only-gnomad.raw.sites.vcf.idx added
a2c45f8d1986_Mutect2-exome-panel.vcf.idx added
a2c42886dd6c_Mutect2-WGS-panel-b37.vcf added
a2c42e32f23d_Mutect2-WGS-panel-b37.vcf.idx added
a2c412bd9a7d_small_exac_common_3.vcf added
a2c45de98e27_small_exac_common_3.vcf.idx added
a2c41073d29c_1000g_pon.hg38.vcf.gz added
a2c424080834_1000g_pon.hg38.vcf.gz.tbi added
a2c4b52a067_af-only-gnomad.hg38.vcf.gz added
a2c45da0cfff_af-only-gnomad.hg38.vcf.gz.tbi added
a2c468b79e5e_small_exac_common_3.hg38.vcf.gz added
a2c46efe6307_small_exac_common_3.hg38.vcf.gz.tbi added
a2c47f17997e_gencode.v41.annotation.gtf added
a2c4665e6061_gencode.v42.annotation.gtf added
a2c43e09b4c8_gencode.vM30.annotation.gtf added
a2c46f3bd649_gencode.vM31.annotation.gtf added
a2c441718bac_gencode.v41.transcripts.fa added
a2c4588eac5_gencode.v41.transcripts.fa.fai added
a2c45fed2e59_gencode.v42.transcripts.fa added
a2c44c7e0642_gencode.v42.transcripts.fa.fai added
a2c465ccfe49_gencode.vM30.pc_transcripts.fa added
a2c4754a9ed5_gencode.vM30.pc_transcripts.fa.fai added
a2c47601ee1b_gencode.vM31.pc_transcripts.fa added
a2c478b76b23_gencode.vM31.pc_transcripts.fa.fai added
a2c451db04bf_GRCh38.primary_assembly.genome.fa.1.ht2 added
a2c4214c195_GRCh38.primary_assembly.genome.fa.2.ht2 added
a2c420b11e44_GRCh38.primary_assembly.genome.fa.3.ht2 added
a2c44c3a1320_GRCh38.primary_assembly.genome.fa.4.ht2 added
a2c478bdc0f8_GRCh38.primary_assembly.genome.fa.5.ht2 added
a2c471c817b5_GRCh38.primary_assembly.genome.fa.6.ht2 added
a2c478ca66f_GRCh38.primary_assembly.genome.fa.7.ht2 added
a2c42302c548_GRCh38.primary_assembly.genome.fa.8.ht2 added
a2c4ae60bed_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
a2c4518fa32_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
a2c42ad1eb3b_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
a2c43baa8473_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
a2c437ddb89f_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
a2c43d83eb60_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
a2c41fd20b2d_GRCh38_full_analysis_set_plus_decoy_hla.fa added
a2c416dbc7ad_GRCh38.primary_assembly.genome.fa.fai added
a2c437123a94_GRCh38.primary_assembly.genome.fa.amb added
a2c4dc3e6cb_GRCh38.primary_assembly.genome.fa.ann added
a2c43865207c_GRCh38.primary_assembly.genome.fa.bwt added
a2c47737c9d0_GRCh38.primary_assembly.genome.fa.pac added
a2c46fa2b3d5_GRCh38.primary_assembly.genome.fa.sa added
a2c422cc9e35_GRCh38.primary_assembly.genome.fa added
a2c427a6bb6c_hs37d5.fa.fai added
a2c4335ac3ca_hs37d5.fa.amb added
a2c4bec1d1d_hs37d5.fa.ann added
a2c43a6b6108_hs37d5.fa.bwt added
a2c45faf722e_hs37d5.fa.pac added
a2c477715b15_hs37d5.fa.sa added
a2c43312fcf6_hs37d5.fa added
a2c4239d94ac_complete_ref_lens.bin added
a2c43e8bba78_ctable.bin added
a2c4477f3c5c_ctg_offsets.bin added
a2c47253e0af_duplicate_clusters.tsv added
a2c460c43bcc_info.json added
a2c47331ffb5_mphf.bin added
a2c4578aff28_pos.bin added
a2c46675c7fe_pre_indexing.log added
a2c43e9d293f_rank.bin added
a2c43fff0736_ref_indexing.log added
a2c4328b0d_refAccumLengths.bin added
a2c476470294_reflengths.bin added
a2c42ffa7f36_refseq.bin added
a2c466b5cad5_seq.bin added
a2c429179aa1_versionInfo.json added
a2c44ca8d51a_salmon_index added
a2c4603ec547_chrLength.txt added
a2c43909e9ae_chrName.txt added
a2c439ccbbc3_chrNameLength.txt added
a2c4303b1cda_chrStart.txt added
a2c478e344f2_exonGeTrInfo.tab added
a2c410c3a9df_exonInfo.tab added
a2c41dc57812_geneInfo.tab added
a2c4f4df503_Genome added
a2c447109fce_genomeParameters.txt added
a2c4146bb1d5_Log.out added
a2c42a68216c_SA added
a2c41a6a4f34_SAindex added
a2c43975ec78_sjdbInfo.txt added
a2c46cf7d7c0_sjdbList.fromGTF.out.tab added
a2c4375b624_sjdbList.out.tab added
a2c42508f742_transcriptInfo.tab added
a2c46fa1210c_GRCh38.GENCODE.v42_100 added
a2c43b80d415_knownGene_hg38.sql added
a2c46e3cd38_knownGene_hg38.txt added
a2c455b61b10_refGene_hg38.sql added
a2c426aae366_refGene_hg38.txt added
a2c41d37515f_knownGene_mm39.sql added
a2c41abf42f5_knownGene_mm39.txt added
a2c42c4f08b_refGene_mm39.sql added
a2c44f8c3718_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//RtmpvjYJrQ/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
6.795 0.825 8.400
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.045 | 0.277 | 2.329 | |
| dataSearch | 0.358 | 0.017 | 0.376 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.879 | 0.055 | 1.678 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.041 | 0.003 | 0.045 | |
| recipeLoad | 0.418 | 0.029 | 0.452 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.152 | 0.010 | 0.162 | |
| recipeUpdate | 0 | 0 | 0 | |