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This page was generated on 2025-10-16 11:38 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 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 1758/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReUseData 1.8.0  (landing page)
Qian Liu
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/ReUseData
git_branch: RELEASE_3_21
git_last_commit: 601a107
git_last_commit_date: 2025-04-15 13:01:44 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for ReUseData on nebbiolo1

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: 1.8.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ReUseData_1.8.0.tar.gz
StartedAt: 2025-10-16 02:47:21 -0400 (Thu, 16 Oct 2025)
EndedAt: 2025-10-16 02:50:16 -0400 (Thu, 16 Oct 2025)
EllapsedTime: 175.2 seconds
RetCode: 0
Status:   OK  
CheckDir: ReUseData.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ReUseData_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.8.0’
* 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 6.281  0.437   6.722
* 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-3.21-bioc/meat/ReUseData.Rcheck/00check.log’
for details.

Installation output

ReUseData.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL ReUseData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘ReUseData’ ...
** this is package ‘ReUseData’ version ‘1.8.0’
** 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 (2025-06-13) -- "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...
2aa6da1146a060_GRCh38.primary_assembly.genome.fa.1.bt2 added
2aa6da4a3bb318_GRCh38.primary_assembly.genome.fa.2.bt2 added
2aa6da5fc18fb1_GRCh38.primary_assembly.genome.fa.3.bt2 added
2aa6da5302512a_GRCh38.primary_assembly.genome.fa.4.bt2 added
2aa6da766ef692_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2aa6da44b3c1d3_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2aa6da7264349_outfile.txt added
2aa6da3b1cb9a4_GRCh37_to_GRCh38.chain added
2aa6da445c2c6f_GRCh37_to_NCBI34.chain added
2aa6da19fe0a3b_GRCh37_to_NCBI35.chain added
2aa6da76c6c8d4_GRCh37_to_NCBI36.chain added
2aa6da1dcb127a_GRCh38_to_GRCh37.chain added
2aa6da3994317b_GRCh38_to_NCBI34.chain added
2aa6da1a2f68a6_GRCh38_to_NCBI35.chain added
2aa6da2b04a310_GRCh38_to_NCBI36.chain added
2aa6da1b9f2829_NCBI34_to_GRCh37.chain added
2aa6da4c7aab24_NCBI34_to_GRCh38.chain added
2aa6da6e452883_NCBI35_to_GRCh37.chain added
2aa6da351bec43_NCBI35_to_GRCh38.chain added
2aa6da6f14b027_NCBI36_to_GRCh37.chain added
2aa6da6fde44b1_NCBI36_to_GRCh38.chain added
2aa6da54345a49_GRCm38_to_NCBIM36.chain added
2aa6da2d039f30_GRCm38_to_NCBIM37.chain added
2aa6da5d7daad1_NCBIM36_to_GRCm38.chain added
2aa6da4b4b2f65_NCBIM37_to_GRCm38.chain added
2aa6da24d9338b_1000G_omni2.5.b37.vcf.gz added
2aa6da322a075c_1000G_omni2.5.b37.vcf.gz.tbi added
2aa6da1fe366a2_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2aa6da60c719d1_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2aa6da3a8c4dd0_1000G_omni2.5.hg38.vcf.gz added
2aa6da28693932_1000G_omni2.5.hg38.vcf.gz.tbi added
2aa6da720dba31_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2aa6da4c800e9_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2aa6da82ac8e3_af-only-gnomad.raw.sites.vcf added
2aa6da45100b5b_af-only-gnomad.raw.sites.vcf.idx added
2aa6da7b36f77b_Mutect2-exome-panel.vcf.idx added
2aa6da4cde8ab6_Mutect2-WGS-panel-b37.vcf added
2aa6da4c364ea5_Mutect2-WGS-panel-b37.vcf.idx added
2aa6da3653b11f_small_exac_common_3.vcf added
2aa6da113ab725_small_exac_common_3.vcf.idx added
2aa6da663458e0_1000g_pon.hg38.vcf.gz added
2aa6da2d1a79f3_1000g_pon.hg38.vcf.gz.tbi added
2aa6da2f05c9a0_af-only-gnomad.hg38.vcf.gz added
2aa6da1fc88a5b_af-only-gnomad.hg38.vcf.gz.tbi added
2aa6da4749e29a_small_exac_common_3.hg38.vcf.gz added
2aa6da5a0a6cb0_small_exac_common_3.hg38.vcf.gz.tbi added
2aa6da3b67b284_gencode.v41.annotation.gtf added
2aa6da13c48dbe_gencode.v42.annotation.gtf added
2aa6da484f9533_gencode.vM30.annotation.gtf added
2aa6da70839ec7_gencode.vM31.annotation.gtf added
2aa6da2d93de6_gencode.v41.transcripts.fa added
2aa6da382dd9e4_gencode.v41.transcripts.fa.fai added
2aa6da44b7f911_gencode.v42.transcripts.fa added
2aa6da2fdcdd16_gencode.v42.transcripts.fa.fai added
2aa6da15ab84b6_gencode.vM30.pc_transcripts.fa added
2aa6da10032876_gencode.vM30.pc_transcripts.fa.fai added
2aa6da54b610a1_gencode.vM31.pc_transcripts.fa added
2aa6da47d58c12_gencode.vM31.pc_transcripts.fa.fai added
2aa6da2fe68f18_GRCh38.primary_assembly.genome.fa.1.ht2 added
2aa6da357d2a72_GRCh38.primary_assembly.genome.fa.2.ht2 added
2aa6da261d9e3_GRCh38.primary_assembly.genome.fa.3.ht2 added
2aa6da584fc84a_GRCh38.primary_assembly.genome.fa.4.ht2 added
2aa6da278ae4a3_GRCh38.primary_assembly.genome.fa.5.ht2 added
2aa6da729dacc_GRCh38.primary_assembly.genome.fa.6.ht2 added
2aa6da607a912d_GRCh38.primary_assembly.genome.fa.7.ht2 added
2aa6da6c9aefff_GRCh38.primary_assembly.genome.fa.8.ht2 added
2aa6da260d247_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2aa6da2d591be3_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2aa6da38d13ea4_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2aa6da38b48366_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2aa6da3e93d309_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2aa6da1f059784_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2aa6da65cefd59_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2aa6da6d999ca9_GRCh38.primary_assembly.genome.fa.fai added
2aa6da3ece21df_GRCh38.primary_assembly.genome.fa.amb added
2aa6da2d18dff3_GRCh38.primary_assembly.genome.fa.ann added
2aa6da47a40959_GRCh38.primary_assembly.genome.fa.bwt added
2aa6da7a35d464_GRCh38.primary_assembly.genome.fa.pac added
2aa6da40dd6db2_GRCh38.primary_assembly.genome.fa.sa added
2aa6daff39e8c_GRCh38.primary_assembly.genome.fa added
2aa6da6ab9732b_hs37d5.fa.fai added
2aa6da43b6ab98_hs37d5.fa.amb added
2aa6da48217870_hs37d5.fa.ann added
2aa6da2f716c3c_hs37d5.fa.bwt added
2aa6da739388ae_hs37d5.fa.pac added
2aa6da5dccfd26_hs37d5.fa.sa added
2aa6da3f7494b2_hs37d5.fa added
2aa6da4849994f_complete_ref_lens.bin added
2aa6da25a28939_ctable.bin added
2aa6da6f5b23ca_ctg_offsets.bin added
2aa6da7dc6c3c2_duplicate_clusters.tsv added
2aa6da2804631c_info.json added
2aa6da47aaec14_mphf.bin added
2aa6da2551a865_pos.bin added
2aa6da2f2e3de8_pre_indexing.log added
2aa6da28257d41_rank.bin added
2aa6da11ec9864_ref_indexing.log added
2aa6da318f102f_refAccumLengths.bin added
2aa6da557e9925_reflengths.bin added
2aa6da4abdd708_refseq.bin added
2aa6da6a439395_seq.bin added
2aa6da14126c2e_versionInfo.json added
2aa6da69c36e8c_salmon_index added
2aa6da501290ee_chrLength.txt added
2aa6da1ac08d7_chrName.txt added
2aa6da2891906c_chrNameLength.txt added
2aa6da7d2b70e2_chrStart.txt added
2aa6da49501230_exonGeTrInfo.tab added
2aa6da22c764d0_exonInfo.tab added
2aa6da3e08de94_geneInfo.tab added
2aa6da5943b0bc_Genome added
2aa6dad80d7fb_genomeParameters.txt added
2aa6da1bf8a2c_Log.out added
2aa6da2165292c_SA added
2aa6da3cf24438_SAindex added
2aa6da755312da_sjdbInfo.txt added
2aa6da7f322653_sjdbList.fromGTF.out.tab added
2aa6da7c66d8ea_sjdbList.out.tab added
2aa6da3d9cac29_transcriptInfo.tab added
2aa6da24d4af8c_GRCh38.GENCODE.v42_100 added
2aa6da6bc1fcb5_knownGene_hg38.sql added
2aa6da3b636feb_knownGene_hg38.txt added
2aa6da4cd912a8_refGene_hg38.sql added
2aa6da336ce8c9_refGene_hg38.txt added
2aa6da60b51851_knownGene_mm39.sql added
2aa6da7c075090_knownGene_mm39.txt added
2aa6da5b92660b_refGene_mm39.sql added
2aa6da72a1b0b5_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/RtmpvnJiob/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 
 21.112   1.653  23.081

Example timings

ReUseData.Rcheck/ReUseData-Ex.timings

nameusersystemelapsed
dataHub-class6.2810.4376.722
dataSearch1.1570.0581.216
dataUpdate000
getCloudData2.7190.1453.709
getData000
meta_data0.0010.0000.001
recipeHub-class0.1300.0030.134
recipeLoad1.2710.0671.339
recipeMake0.0010.0000.001
recipeSearch0.5420.0110.554
recipeUpdate000