Qian Liu
| Snapshot Date: 2026-04-07 13:45 -0400 (Tue, 07 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_22 |
| git_last_commit: 2d4066b |
| git_last_commit_date: 2025-10-29 11:20:44 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-04-08 11:58 -0400 (Wed, 08 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4897 |
| 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 1773/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.10.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.3 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: 1.10.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReUseData_1.10.0.tar.gz |
| StartedAt: 2026-04-08 03:09:04 -0400 (Wed, 08 Apr 2026) |
| EndedAt: 2026-04-08 03:11:50 -0400 (Wed, 08 Apr 2026) |
| EllapsedTime: 165.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReUseData_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.10.0’
* 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 5.949 0.271 6.227
* 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-3.22-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.10.0’ ** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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...
2b1fe041e9580a_GRCh38.primary_assembly.genome.fa.1.bt2 added
2b1fe069d00baf_GRCh38.primary_assembly.genome.fa.2.bt2 added
2b1fe0523fe8d0_GRCh38.primary_assembly.genome.fa.3.bt2 added
2b1fe02358605d_GRCh38.primary_assembly.genome.fa.4.bt2 added
2b1fe068ea201f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2b1fe05b5ee1b0_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2b1fe011e48f2e_outfile.txt added
2b1fe02e31bbd0_GRCh37_to_GRCh38.chain added
2b1fe05dd30798_GRCh37_to_NCBI34.chain added
2b1fe039ce23ea_GRCh37_to_NCBI35.chain added
2b1fe02f5b7034_GRCh37_to_NCBI36.chain added
2b1fe01664bb60_GRCh38_to_GRCh37.chain added
2b1fe019c8c45d_GRCh38_to_NCBI34.chain added
2b1fe0b9f5e47_GRCh38_to_NCBI35.chain added
2b1fe0eaf4149_GRCh38_to_NCBI36.chain added
2b1fe01ba55e74_NCBI34_to_GRCh37.chain added
2b1fe064666f2b_NCBI34_to_GRCh38.chain added
2b1fe02d58275b_NCBI35_to_GRCh37.chain added
2b1fe030e7b1de_NCBI35_to_GRCh38.chain added
2b1fe07243bbfb_NCBI36_to_GRCh37.chain added
2b1fe05b5982f5_NCBI36_to_GRCh38.chain added
2b1fe07c3bf4e6_GRCm38_to_NCBIM36.chain added
2b1fe06b5f502d_GRCm38_to_NCBIM37.chain added
2b1fe0309c1d34_NCBIM36_to_GRCm38.chain added
2b1fe035389070_NCBIM37_to_GRCm38.chain added
2b1fe07519834d_1000G_omni2.5.b37.vcf.gz added
2b1fe02af7574_1000G_omni2.5.b37.vcf.gz.tbi added
2b1fe059dc081c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2b1fe07538eb3b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2b1fe076e0b25a_1000G_omni2.5.hg38.vcf.gz added
2b1fe0789c297d_1000G_omni2.5.hg38.vcf.gz.tbi added
2b1fe037224345_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2b1fe060b0be0a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2b1fe04adc124d_af-only-gnomad.raw.sites.vcf added
2b1fe05a7aa3a2_af-only-gnomad.raw.sites.vcf.idx added
2b1fe0499ade29_Mutect2-exome-panel.vcf.idx added
2b1fe0263af3fd_Mutect2-WGS-panel-b37.vcf added
2b1fe06c5f32d0_Mutect2-WGS-panel-b37.vcf.idx added
2b1fe077cc99f9_small_exac_common_3.vcf added
2b1fe040dfb96_small_exac_common_3.vcf.idx added
2b1fe0262d56bb_1000g_pon.hg38.vcf.gz added
2b1fe027280a2e_1000g_pon.hg38.vcf.gz.tbi added
2b1fe01a72b6f6_af-only-gnomad.hg38.vcf.gz added
2b1fe03ff61b18_af-only-gnomad.hg38.vcf.gz.tbi added
2b1fe032c76875_small_exac_common_3.hg38.vcf.gz added
2b1fe02921f83f_small_exac_common_3.hg38.vcf.gz.tbi added
2b1fe05b9b798c_gencode.v41.annotation.gtf added
2b1fe0172dd7a0_gencode.v42.annotation.gtf added
2b1fe0567a1f9a_gencode.vM30.annotation.gtf added
2b1fe0c832b6a_gencode.vM31.annotation.gtf added
2b1fe0971939b_gencode.v41.transcripts.fa added
2b1fe031d3a290_gencode.v41.transcripts.fa.fai added
2b1fe08bf2051_gencode.v42.transcripts.fa added
2b1fe074d0e3c8_gencode.v42.transcripts.fa.fai added
2b1fe0626fbfc4_gencode.vM30.pc_transcripts.fa added
2b1fe03df7b0c1_gencode.vM30.pc_transcripts.fa.fai added
2b1fe069ea6716_gencode.vM31.pc_transcripts.fa added
2b1fe0651f3538_gencode.vM31.pc_transcripts.fa.fai added
2b1fe017d3b8dd_GRCh38.primary_assembly.genome.fa.1.ht2 added
2b1fe05f235251_GRCh38.primary_assembly.genome.fa.2.ht2 added
2b1fe05bffe793_GRCh38.primary_assembly.genome.fa.3.ht2 added
2b1fe0106fe25a_GRCh38.primary_assembly.genome.fa.4.ht2 added
2b1fe016459596_GRCh38.primary_assembly.genome.fa.5.ht2 added
2b1fe03cb0a59d_GRCh38.primary_assembly.genome.fa.6.ht2 added
2b1fe05b4bf4a7_GRCh38.primary_assembly.genome.fa.7.ht2 added
2b1fe070c03938_GRCh38.primary_assembly.genome.fa.8.ht2 added
2b1fe064b83c6_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2b1fe0186e8a5_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2b1fe05d1f6c09_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2b1fe07e181dbf_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2b1fe0594e43b_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2b1fe034cc2c4_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2b1fe0254027ed_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2b1fe020079b31_GRCh38.primary_assembly.genome.fa.fai added
2b1fe04342dddc_GRCh38.primary_assembly.genome.fa.amb added
2b1fe058079062_GRCh38.primary_assembly.genome.fa.ann added
2b1fe049299371_GRCh38.primary_assembly.genome.fa.bwt added
2b1fe01ede5769_GRCh38.primary_assembly.genome.fa.pac added
2b1fe06f356802_GRCh38.primary_assembly.genome.fa.sa added
2b1fe01fa3b30b_GRCh38.primary_assembly.genome.fa added
2b1fe02b6182d3_hs37d5.fa.fai added
2b1fe078a6fb9d_hs37d5.fa.amb added
2b1fe05177559b_hs37d5.fa.ann added
2b1fe03420a324_hs37d5.fa.bwt added
2b1fe06d77df66_hs37d5.fa.pac added
2b1fe033e71560_hs37d5.fa.sa added
2b1fe0721853e5_hs37d5.fa added
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2b1fe019064a98_ctable.bin added
2b1fe09ec0cc3_ctg_offsets.bin added
2b1fe0368598cd_duplicate_clusters.tsv added
2b1fe07506322b_info.json added
2b1fe01a5bef1d_mphf.bin added
2b1fe04ccb2e63_pos.bin added
2b1fe031b6d7c8_pre_indexing.log added
2b1fe075a7e3c5_rank.bin added
2b1fe03d8b679b_ref_indexing.log added
2b1fe038025b8e_refAccumLengths.bin added
2b1fe0772ecc6a_reflengths.bin added
2b1fe01aaad3a4_refseq.bin added
2b1fe0361a794e_seq.bin added
2b1fe07cc3b0a5_versionInfo.json added
2b1fe01df79668_salmon_index added
2b1fe05b5aa13b_chrLength.txt added
2b1fe01ccb4bd6_chrName.txt added
2b1fe0613a7445_chrNameLength.txt added
2b1fe03362319e_chrStart.txt added
2b1fe065f4df47_exonGeTrInfo.tab added
2b1fe018cbae_exonInfo.tab added
2b1fe0229799a0_geneInfo.tab added
2b1fe05989253_Genome added
2b1fe02b7a4e81_genomeParameters.txt added
2b1fe01b3e953e_Log.out added
2b1fe0570fe7ee_SA added
2b1fe05f9af1a6_SAindex added
2b1fe08b674a4_sjdbInfo.txt added
2b1fe0af6fd4e_sjdbList.fromGTF.out.tab added
2b1fe051b3458b_sjdbList.out.tab added
2b1fe06018bb20_transcriptInfo.tab added
2b1fe023fd47e7_GRCh38.GENCODE.v42_100 added
2b1fe05b9f524e_knownGene_hg38.sql added
2b1fe0169e53ed_knownGene_hg38.txt added
2b1fe019037a12_refGene_hg38.sql added
2b1fe075fb416c_refGene_hg38.txt added
2b1fe063698250_knownGene_mm39.sql added
2b1fe04aba51db_knownGene_mm39.txt added
2b1fe06ba32531_refGene_mm39.sql added
2b1fe020f4e9eb_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/Rtmp7eK18N/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
18.311 1.004 19.938
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.949 | 0.271 | 6.227 | |
| dataSearch | 1.187 | 0.029 | 1.217 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.790 | 0.126 | 3.840 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.133 | 0.006 | 0.140 | |
| recipeLoad | 1.261 | 0.027 | 1.289 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.560 | 0.003 | 0.563 | |
| recipeUpdate | 0 | 0 | 0 | |