Qian Liu
| Snapshot Date: 2026-05-21 13:40 -0400 (Thu, 21 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 Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-22 11:33 -0400 (Fri, 22 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" | 4995 |
| 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 | | ||||||||
| 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: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ReUseData_1.12.0.tar.gz |
| StartedAt: 2026-05-22 05:16:33 -0400 (Fri, 22 May 2026) |
| EndedAt: 2026-05-22 05:19:18 -0400 (Fri, 22 May 2026) |
| EllapsedTime: 165.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ReUseData_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-22 09:16:33 UTC
* 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 loading without being on the library search path ... 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 6.202 0.421 6.625
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-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 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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...
3010691ad92579_GRCh38.primary_assembly.genome.fa.1.bt2 added
301069446b6644_GRCh38.primary_assembly.genome.fa.2.bt2 added
30106917b98ca3_GRCh38.primary_assembly.genome.fa.3.bt2 added
3010695e7d9a54_GRCh38.primary_assembly.genome.fa.4.bt2 added
30106994d455d_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
30106953aa7f2b_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3010693b273c5a_outfile.txt added
3010697cc7793b_GRCh37_to_GRCh38.chain added
30106945e9ff85_GRCh37_to_NCBI34.chain added
3010695cbd8f25_GRCh37_to_NCBI35.chain added
301069130f93f5_GRCh37_to_NCBI36.chain added
30106941d72b1b_GRCh38_to_GRCh37.chain added
301069feae758_GRCh38_to_NCBI34.chain added
30106966775bef_GRCh38_to_NCBI35.chain added
3010697adcb683_GRCh38_to_NCBI36.chain added
301069b530fa5_NCBI34_to_GRCh37.chain added
3010694797952f_NCBI34_to_GRCh38.chain added
30106915cd2a81_NCBI35_to_GRCh37.chain added
30106971999c56_NCBI35_to_GRCh38.chain added
30106971fd3bd8_NCBI36_to_GRCh37.chain added
30106968717fab_NCBI36_to_GRCh38.chain added
30106923bc7572_GRCm38_to_NCBIM36.chain added
30106979272623_GRCm38_to_NCBIM37.chain added
30106962c87f66_NCBIM36_to_GRCm38.chain added
3010692dd337df_NCBIM37_to_GRCm38.chain added
30106975840822_1000G_omni2.5.b37.vcf.gz added
301069799fb0d3_1000G_omni2.5.b37.vcf.gz.tbi added
301069319abcbc_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
301069594f670f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3010692cea085e_1000G_omni2.5.hg38.vcf.gz added
3010695279223f_1000G_omni2.5.hg38.vcf.gz.tbi added
30106974288c88_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
30106971556ea2_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3010696a32aee2_af-only-gnomad.raw.sites.vcf added
30106952a626dc_af-only-gnomad.raw.sites.vcf.idx added
3010697aa2b3ff_Mutect2-exome-panel.vcf.idx added
3010693ddd2e0d_Mutect2-WGS-panel-b37.vcf added
301069dcd6337_Mutect2-WGS-panel-b37.vcf.idx added
301069776a2d3a_small_exac_common_3.vcf added
3010693c72d92_small_exac_common_3.vcf.idx added
3010696a8af25c_1000g_pon.hg38.vcf.gz added
301069a79c12f_1000g_pon.hg38.vcf.gz.tbi added
301069459e58ae_af-only-gnomad.hg38.vcf.gz added
3010697a75d9b4_af-only-gnomad.hg38.vcf.gz.tbi added
30106970f11d1f_small_exac_common_3.hg38.vcf.gz added
301069407b0f31_small_exac_common_3.hg38.vcf.gz.tbi added
3010695c8e959_gencode.v41.annotation.gtf added
3010693888b24e_gencode.v42.annotation.gtf added
301069564839b2_gencode.vM30.annotation.gtf added
301069776285af_gencode.vM31.annotation.gtf added
3010692a85ee26_gencode.v41.transcripts.fa added
3010693eb9b95e_gencode.v41.transcripts.fa.fai added
3010691b1efb21_gencode.v42.transcripts.fa added
30106923ad1449_gencode.v42.transcripts.fa.fai added
301069218238c4_gencode.vM30.pc_transcripts.fa added
30106948f23301_gencode.vM30.pc_transcripts.fa.fai added
30106919311c6c_gencode.vM31.pc_transcripts.fa added
3010691b21e998_gencode.vM31.pc_transcripts.fa.fai added
3010697a8cefbd_GRCh38.primary_assembly.genome.fa.1.ht2 added
3010697280837b_GRCh38.primary_assembly.genome.fa.2.ht2 added
301069480bf1f6_GRCh38.primary_assembly.genome.fa.3.ht2 added
3010694d0611fc_GRCh38.primary_assembly.genome.fa.4.ht2 added
30106966a91004_GRCh38.primary_assembly.genome.fa.5.ht2 added
30106939616099_GRCh38.primary_assembly.genome.fa.6.ht2 added
3010693738c0de_GRCh38.primary_assembly.genome.fa.7.ht2 added
301069394f36e0_GRCh38.primary_assembly.genome.fa.8.ht2 added
30106934041498_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3010697515eeec_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
301069471c9a17_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3010692b6e41d3_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
30106978dd1c7e_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
30106931a78c73_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
30106935e80302_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3010693e7b752c_GRCh38.primary_assembly.genome.fa.fai added
3010692c1d6627_GRCh38.primary_assembly.genome.fa.amb added
30106926d92021_GRCh38.primary_assembly.genome.fa.ann added
3010697ef6845d_GRCh38.primary_assembly.genome.fa.bwt added
30106931e64f81_GRCh38.primary_assembly.genome.fa.pac added
3010695f61d26f_GRCh38.primary_assembly.genome.fa.sa added
301069553ebe10_GRCh38.primary_assembly.genome.fa added
3010692948d530_hs37d5.fa.fai added
3010699e7c095_hs37d5.fa.amb added
30106913f8776e_hs37d5.fa.ann added
3010694467d052_hs37d5.fa.bwt added
3010692d94d4df_hs37d5.fa.pac added
301069357ab032_hs37d5.fa.sa added
301069d5a0353_hs37d5.fa added
30106946c5f14b_complete_ref_lens.bin added
301069509c99ca_ctable.bin added
3010697e6f310_ctg_offsets.bin added
301069394674c6_duplicate_clusters.tsv added
30106918a88bc1_info.json added
30106954ed050c_mphf.bin added
3010691fef84ca_pos.bin added
3010695209ec5a_pre_indexing.log added
301069c25c5ea_rank.bin added
301069593ebbab_ref_indexing.log added
30106960e00f2_refAccumLengths.bin added
30106913bb4d6_reflengths.bin added
301069205b55c2_refseq.bin added
301069317c42c5_seq.bin added
3010697a18d155_versionInfo.json added
3010695202e236_salmon_index added
301069676445c8_chrLength.txt added
30106938944681_chrName.txt added
3010697e20485d_chrNameLength.txt added
301069e3d65e9_chrStart.txt added
301069378acadf_exonGeTrInfo.tab added
301069300697de_exonInfo.tab added
3010696d9f3859_geneInfo.tab added
301069cc988ef_Genome added
301069594f6d0f_genomeParameters.txt added
3010697786f8ee_Log.out added
30106920c2005d_SA added
3010691db73d61_SAindex added
301069251bcdcd_sjdbInfo.txt added
301069563cb08f_sjdbList.fromGTF.out.tab added
3010692b1140b4_sjdbList.out.tab added
3010696be1bf18_transcriptInfo.tab added
30106926d94a5a_GRCh38.GENCODE.v42_100 added
30106932f833c4_knownGene_hg38.sql added
301069252833df_knownGene_hg38.txt added
3010693f81d61b_refGene_hg38.sql added
3010697e538d0_refGene_hg38.txt added
3010694517b8a9_knownGene_mm39.sql added
301069118bc275_knownGene_mm39.txt added
301069140afeba_refGene_mm39.sql added
3010691e567454_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/RtmpuUpahT/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
18.639 1.353 20.356
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.202 | 0.421 | 6.625 | |
| dataSearch | 1.163 | 0.040 | 1.202 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.679 | 0.104 | 3.234 | |
| getData | 0.001 | 0.000 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.126 | 0.008 | 0.135 | |
| recipeLoad | 1.310 | 0.022 | 1.335 | |
| recipeMake | 0.001 | 0.000 | 0.001 | |
| recipeSearch | 0.527 | 0.009 | 0.537 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |