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This page was generated on 2025-10-28 12:03 -0400 (Tue, 28 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4901
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4691
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4637
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 1773/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReUseData 1.9.0  (landing page)
Qian Liu
Snapshot Date: 2025-10-27 13:45 -0400 (Mon, 27 Oct 2025)
git_url: https://git.bioconductor.org/packages/ReUseData
git_branch: devel
git_last_commit: c5927b9
git_last_commit_date: 2025-04-15 13:01:44 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for ReUseData on nebbiolo2

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.

raw results


Summary

Package: ReUseData
Version: 1.9.0
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_1.9.0.tar.gz
StartedAt: 2025-10-28 03:16:58 -0400 (Tue, 28 Oct 2025)
EndedAt: 2025-10-28 03:19:40 -0400 (Tue, 28 Oct 2025)
EllapsedTime: 162.2 seconds
RetCode: 0
Status:   OK  
CheckDir: ReUseData.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.9.0’
* 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 5.865   0.23   6.098
* 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.

Installation output

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 ‘1.9.0’
** 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)

Tests output

ReUseData.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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.)

}INFO Final process status is success

Updating data record...
outfile.txt added

Updating data record...
29d57c7f1f205f_GRCh38.primary_assembly.genome.fa.1.bt2 added
29d57c75aa1b8e_GRCh38.primary_assembly.genome.fa.2.bt2 added
29d57c7a6086d4_GRCh38.primary_assembly.genome.fa.3.bt2 added
29d57c2da9825f_GRCh38.primary_assembly.genome.fa.4.bt2 added
29d57c43133735_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
29d57c7827b6c5_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
29d57c409e3548_outfile.txt added
29d57c768ad9ec_GRCh37_to_GRCh38.chain added
29d57c963d500_GRCh37_to_NCBI34.chain added
29d57c53e6a07d_GRCh37_to_NCBI35.chain added
29d57c5699651_GRCh37_to_NCBI36.chain added
29d57c13bfc675_GRCh38_to_GRCh37.chain added
29d57c62a82cd9_GRCh38_to_NCBI34.chain added
29d57c46f7ae66_GRCh38_to_NCBI35.chain added
29d57c210ae8d4_GRCh38_to_NCBI36.chain added
29d57c55b9eda0_NCBI34_to_GRCh37.chain added
29d57c70c959bb_NCBI34_to_GRCh38.chain added
29d57c7f6d88dc_NCBI35_to_GRCh37.chain added
29d57c11e353ae_NCBI35_to_GRCh38.chain added
29d57cb86c85f_NCBI36_to_GRCh37.chain added
29d57c5596bb3f_NCBI36_to_GRCh38.chain added
29d57c2af1051b_GRCm38_to_NCBIM36.chain added
29d57c44375f11_GRCm38_to_NCBIM37.chain added
29d57c48d3f9e7_NCBIM36_to_GRCm38.chain added
29d57c6567e7bd_NCBIM37_to_GRCm38.chain added
29d57c5a890442_1000G_omni2.5.b37.vcf.gz added
29d57cd425996_1000G_omni2.5.b37.vcf.gz.tbi added
29d57c5a6609db_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
29d57c56c38b48_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
29d57c7fc78d2_1000G_omni2.5.hg38.vcf.gz added
29d57c12cfb497_1000G_omni2.5.hg38.vcf.gz.tbi added
29d57c55e2aba7_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
29d57c7da69461_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
29d57cd303b6c_af-only-gnomad.raw.sites.vcf added
29d57c38c2e06_af-only-gnomad.raw.sites.vcf.idx added
29d57c40b9cb96_Mutect2-exome-panel.vcf.idx added
29d57c557f231_Mutect2-WGS-panel-b37.vcf added
29d57c442a634e_Mutect2-WGS-panel-b37.vcf.idx added
29d57c3744a583_small_exac_common_3.vcf added
29d57cebbc731_small_exac_common_3.vcf.idx added
29d57c181103cc_1000g_pon.hg38.vcf.gz added
29d57c3cae3bd4_1000g_pon.hg38.vcf.gz.tbi added
29d57c227b8da6_af-only-gnomad.hg38.vcf.gz added
29d57c7ab930a5_af-only-gnomad.hg38.vcf.gz.tbi added
29d57c3a5ea3b_small_exac_common_3.hg38.vcf.gz added
29d57c4386767a_small_exac_common_3.hg38.vcf.gz.tbi added
29d57c50731e45_gencode.v41.annotation.gtf added
29d57c746f43f6_gencode.v42.annotation.gtf added
29d57c42f3ff56_gencode.vM30.annotation.gtf added
29d57c625671f4_gencode.vM31.annotation.gtf added
29d57c7ff60c55_gencode.v41.transcripts.fa added
29d57c188aba96_gencode.v41.transcripts.fa.fai added
29d57cd47770f_gencode.v42.transcripts.fa added
29d57c442d6b66_gencode.v42.transcripts.fa.fai added
29d57c615eb47d_gencode.vM30.pc_transcripts.fa added
29d57c72af5ecc_gencode.vM30.pc_transcripts.fa.fai added
29d57c1eb66fa9_gencode.vM31.pc_transcripts.fa added
29d57c6ea10e13_gencode.vM31.pc_transcripts.fa.fai added
29d57c4d1568a8_GRCh38.primary_assembly.genome.fa.1.ht2 added
29d57c7579faf1_GRCh38.primary_assembly.genome.fa.2.ht2 added
29d57c769d86e6_GRCh38.primary_assembly.genome.fa.3.ht2 added
29d57c5fe51d3f_GRCh38.primary_assembly.genome.fa.4.ht2 added
29d57c4b5ca698_GRCh38.primary_assembly.genome.fa.5.ht2 added
29d57c74441b47_GRCh38.primary_assembly.genome.fa.6.ht2 added
29d57c6d1558ab_GRCh38.primary_assembly.genome.fa.7.ht2 added
29d57c4ee8d49f_GRCh38.primary_assembly.genome.fa.8.ht2 added
29d57c34fde6dd_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
29d57c726d4adc_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
29d57c131337ed_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
29d57c6c428c60_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
29d57c129120d_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
29d57c2b243bb9_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
29d57c28f0c835_GRCh38_full_analysis_set_plus_decoy_hla.fa added
29d57c23a49fb3_GRCh38.primary_assembly.genome.fa.fai added
29d57c25dd6c5f_GRCh38.primary_assembly.genome.fa.amb added
29d57c2c96b270_GRCh38.primary_assembly.genome.fa.ann added
29d57c672b162d_GRCh38.primary_assembly.genome.fa.bwt added
29d57c76508aa4_GRCh38.primary_assembly.genome.fa.pac added
29d57c2105f666_GRCh38.primary_assembly.genome.fa.sa added
29d57c2a1f1584_GRCh38.primary_assembly.genome.fa added
29d57c58a6fc98_hs37d5.fa.fai added
29d57c20fc02bb_hs37d5.fa.amb added
29d57c42a9d01a_hs37d5.fa.ann added
29d57c65ee73a8_hs37d5.fa.bwt added
29d57c65296e21_hs37d5.fa.pac added
29d57c24088497_hs37d5.fa.sa added
29d57c589dd274_hs37d5.fa added
29d57c3dfddca_complete_ref_lens.bin added
29d57c12a992ab_ctable.bin added
29d57c25b33b1c_ctg_offsets.bin added
29d57c7959d8bb_duplicate_clusters.tsv added
29d57c9471991_info.json added
29d57c598585c_mphf.bin added
29d57c44b67f54_pos.bin added
29d57c7d8b34d8_pre_indexing.log added
29d57c72adb107_rank.bin added
29d57c139f53f3_ref_indexing.log added
29d57c32891bb5_refAccumLengths.bin added
29d57c651afbe4_reflengths.bin added
29d57c26b28be0_refseq.bin added
29d57c1ecba816_seq.bin added
29d57c66440df1_versionInfo.json added
29d57c51d6c79a_salmon_index added
29d57c47bc704b_chrLength.txt added
29d57c9e8ada5_chrName.txt added
29d57c77b433f9_chrNameLength.txt added
29d57c745322bb_chrStart.txt added
29d57c7113c3d2_exonGeTrInfo.tab added
29d57c6e04be9d_exonInfo.tab added
29d57c15591921_geneInfo.tab added
29d57c1b32d956_Genome added
29d57c46abbb36_genomeParameters.txt added
29d57c36551bdc_Log.out added
29d57c5ddca970_SA added
29d57c2c9a2ede_SAindex added
29d57c1b7e89fd_sjdbInfo.txt added
29d57c1e52e08_sjdbList.fromGTF.out.tab added
29d57c5380152_sjdbList.out.tab added
29d57c1f5e67c8_transcriptInfo.tab added
29d57c148ec0b3_GRCh38.GENCODE.v42_100 added
29d57c2aeb3c6f_knownGene_hg38.sql added
29d57c18b84083_knownGene_hg38.txt added
29d57c1dd5da44_refGene_hg38.sql added
29d57c308394cb_refGene_hg38.txt added
29d57c5d6ebfd7_knownGene_mm39.sql added
29d57c1b610f1c_knownGene_mm39.txt added
29d57c233145d2_refGene_mm39.sql added
29d57c710e13ca_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/RtmpnK8nD4/test_gcpData/outfile.txt
}INFO 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 0 | SKIP 0 | PASS 44 ]
> Sys.setenv(cachePath = file.path(tempdir(), "cache"))
> 
> 
> 
> proc.time()
   user  system elapsed 
 17.843   0.885  19.125

Example timings

ReUseData.Rcheck/ReUseData-Ex.timings

nameusersystemelapsed
dataHub-class5.8650.2306.098
dataSearch1.0930.0081.101
dataUpdate0.0010.0000.000
getCloudData2.8230.1794.237
getData000
meta_data0.0000.0000.001
recipeHub-class0.1240.0080.133
recipeLoad1.2200.0321.252
recipeMake000
recipeSearch0.5500.0050.556
recipeUpdate000