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This page was generated on 2025-10-11 12:03 -0400 (Sat, 11 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4864
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4652
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4597
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4586
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 1762/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReUseData 1.9.0  (landing page)
Qian Liu
Snapshot Date: 2025-10-10 13:45 -0400 (Fri, 10 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 12.7.1 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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

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: 2025-10-11 03:40:43 -0400 (Sat, 11 Oct 2025)
EndedAt: 2025-10-11 03:43:29 -0400 (Sat, 11 Oct 2025)
EllapsedTime: 165.2 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 5.844  0.226   6.072
* 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...
1c499d683745bf_GRCh38.primary_assembly.genome.fa.1.bt2 added
1c499d58cd5969_GRCh38.primary_assembly.genome.fa.2.bt2 added
1c499d58fae831_GRCh38.primary_assembly.genome.fa.3.bt2 added
1c499db98cace_GRCh38.primary_assembly.genome.fa.4.bt2 added
1c499d212727ea_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1c499d112626f2_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1c499d649d123_outfile.txt added
1c499d775ca742_GRCh37_to_GRCh38.chain added
1c499d6ce5e4ca_GRCh37_to_NCBI34.chain added
1c499dc64bce3_GRCh37_to_NCBI35.chain added
1c499d184fa2ed_GRCh37_to_NCBI36.chain added
1c499ddb6b09d_GRCh38_to_GRCh37.chain added
1c499d78b08262_GRCh38_to_NCBI34.chain added
1c499d6866e69_GRCh38_to_NCBI35.chain added
1c499d4161422e_GRCh38_to_NCBI36.chain added
1c499da8120fe_NCBI34_to_GRCh37.chain added
1c499d282b3103_NCBI34_to_GRCh38.chain added
1c499d4a1277da_NCBI35_to_GRCh37.chain added
1c499d4d49b157_NCBI35_to_GRCh38.chain added
1c499d52531866_NCBI36_to_GRCh37.chain added
1c499d66e2ac7a_NCBI36_to_GRCh38.chain added
1c499d527ae818_GRCm38_to_NCBIM36.chain added
1c499d1d79b357_GRCm38_to_NCBIM37.chain added
1c499d65045809_NCBIM36_to_GRCm38.chain added
1c499d348abf_NCBIM37_to_GRCm38.chain added
1c499d45d5fd4_1000G_omni2.5.b37.vcf.gz added
1c499d36d35042_1000G_omni2.5.b37.vcf.gz.tbi added
1c499d3a4c2bdc_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1c499d1b87d5b1_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1c499d76c1b668_1000G_omni2.5.hg38.vcf.gz added
1c499d3bd7dbae_1000G_omni2.5.hg38.vcf.gz.tbi added
1c499d3bf1b70_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1c499d4f8f0fd1_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1c499d14d2c3df_af-only-gnomad.raw.sites.vcf added
1c499df57e63f_af-only-gnomad.raw.sites.vcf.idx added
1c499d70b637bb_Mutect2-exome-panel.vcf.idx added
1c499d25f8ead1_Mutect2-WGS-panel-b37.vcf added
1c499d15a1b762_Mutect2-WGS-panel-b37.vcf.idx added
1c499d6812defd_small_exac_common_3.vcf added
1c499d12decf9b_small_exac_common_3.vcf.idx added
1c499d22067446_1000g_pon.hg38.vcf.gz added
1c499d6281ea_1000g_pon.hg38.vcf.gz.tbi added
1c499d20958038_af-only-gnomad.hg38.vcf.gz added
1c499d1ab6f6a8_af-only-gnomad.hg38.vcf.gz.tbi added
1c499d6e8f053_small_exac_common_3.hg38.vcf.gz added
1c499d61f6c266_small_exac_common_3.hg38.vcf.gz.tbi added
1c499d253817a6_gencode.v41.annotation.gtf added
1c499d2f142156_gencode.v42.annotation.gtf added
1c499d2c093a40_gencode.vM30.annotation.gtf added
1c499d7281c8fd_gencode.vM31.annotation.gtf added
1c499d16739bc_gencode.v41.transcripts.fa added
1c499d12ebe6bb_gencode.v41.transcripts.fa.fai added
1c499d44fcb115_gencode.v42.transcripts.fa added
1c499d1ee0ed13_gencode.v42.transcripts.fa.fai added
1c499d77f03ec4_gencode.vM30.pc_transcripts.fa added
1c499d45313bd5_gencode.vM30.pc_transcripts.fa.fai added
1c499d233e4ce8_gencode.vM31.pc_transcripts.fa added
1c499d2ec38f06_gencode.vM31.pc_transcripts.fa.fai added
1c499d7f7d67b1_GRCh38.primary_assembly.genome.fa.1.ht2 added
1c499d3ec62299_GRCh38.primary_assembly.genome.fa.2.ht2 added
1c499d2585456e_GRCh38.primary_assembly.genome.fa.3.ht2 added
1c499d3b55435f_GRCh38.primary_assembly.genome.fa.4.ht2 added
1c499d42853e09_GRCh38.primary_assembly.genome.fa.5.ht2 added
1c499d7514553f_GRCh38.primary_assembly.genome.fa.6.ht2 added
1c499d5028073e_GRCh38.primary_assembly.genome.fa.7.ht2 added
1c499d51dd2448_GRCh38.primary_assembly.genome.fa.8.ht2 added
1c499d65ca8cfa_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1c499d7620f20f_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1c499d677edbab_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1c499d4ddd6bf8_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1c499d8ffc1aa_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1c499d9854ff1_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1c499d4e3fede2_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1c499d299541e2_GRCh38.primary_assembly.genome.fa.fai added
1c499d243c4699_GRCh38.primary_assembly.genome.fa.amb added
1c499d5528de36_GRCh38.primary_assembly.genome.fa.ann added
1c499db8c0448_GRCh38.primary_assembly.genome.fa.bwt added
1c499d49745e3f_GRCh38.primary_assembly.genome.fa.pac added
1c499d43cff8c_GRCh38.primary_assembly.genome.fa.sa added
1c499d37953e89_GRCh38.primary_assembly.genome.fa added
1c499d3bf6273d_hs37d5.fa.fai added
1c499d5a43949_hs37d5.fa.amb added
1c499d4a812544_hs37d5.fa.ann added
1c499df2d852_hs37d5.fa.bwt added
1c499d2485265c_hs37d5.fa.pac added
1c499d42716408_hs37d5.fa.sa added
1c499d46241427_hs37d5.fa added
1c499d47c37344_complete_ref_lens.bin added
1c499d7134f30f_ctable.bin added
1c499d45a17bd8_ctg_offsets.bin added
1c499d68995dd_duplicate_clusters.tsv added
1c499d16ba387d_info.json added
1c499df6bf37_mphf.bin added
1c499d490ed3e7_pos.bin added
1c499dbce8dbd_pre_indexing.log added
1c499d511ec675_rank.bin added
1c499d1aebf82f_ref_indexing.log added
1c499d71991ab7_refAccumLengths.bin added
1c499d473fb884_reflengths.bin added
1c499d26ad3da_refseq.bin added
1c499d3f7686af_seq.bin added
1c499d503f7a2e_versionInfo.json added
1c499dbf023cb_salmon_index added
1c499ddb67492_chrLength.txt added
1c499d79d4bc10_chrName.txt added
1c499d302c6a64_chrNameLength.txt added
1c499d62df52c8_chrStart.txt added
1c499d560c059_exonGeTrInfo.tab added
1c499d79a0c8a4_exonInfo.tab added
1c499d671c5254_geneInfo.tab added
1c499d3cf5fee2_Genome added
1c499d3596efe1_genomeParameters.txt added
1c499d6cc08b9d_Log.out added
1c499d7772426_SA added
1c499d3689c833_SAindex added
1c499d1145b1fa_sjdbInfo.txt added
1c499d49e8882e_sjdbList.fromGTF.out.tab added
1c499d7caddc5b_sjdbList.out.tab added
1c499d5909253e_transcriptInfo.tab added
1c499d3b1d7b3d_GRCh38.GENCODE.v42_100 added
1c499d424f5833_knownGene_hg38.sql added
1c499d5f92bb1c_knownGene_hg38.txt added
1c499d51d7b3bb_refGene_hg38.sql added
1c499d4346176b_refGene_hg38.txt added
1c499d28a18f03_knownGene_mm39.sql added
1c499d5da64178_knownGene_mm39.txt added
1c499d1464dde0_refGene_mm39.sql added
1c499d438d8732_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/RtmpXbAs6c/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 
 18.090   1.182  19.756

Example timings

ReUseData.Rcheck/ReUseData-Ex.timings

nameusersystemelapsed
dataHub-class5.8440.2266.072
dataSearch1.1190.0111.130
dataUpdate000
getCloudData2.6280.1043.635
getData000
meta_data0.0010.0000.000
recipeHub-class0.1270.0010.128
recipeLoad1.2920.0811.374
recipeMake000
recipeSearch0.5450.0260.572
recipeUpdate000