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This page was generated on 2025-09-01 11:39 -0400 (Mon, 01 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4606
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4547
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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: 2025-08-28 13:40 -0400 (Thu, 28 Aug 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 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 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: 2025-09-01 02:02:24 -0400 (Mon, 01 Sep 2025)
EndedAt: 2025-09-01 02:05:24 -0400 (Mon, 01 Sep 2025)
EllapsedTime: 179.3 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 6.198  0.427   6.627
* 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...
2f3aad2ff67765_GRCh38.primary_assembly.genome.fa.1.bt2 added
2f3aad4ec34dfe_GRCh38.primary_assembly.genome.fa.2.bt2 added
2f3aad736b4592_GRCh38.primary_assembly.genome.fa.3.bt2 added
2f3aad12b9f64c_GRCh38.primary_assembly.genome.fa.4.bt2 added
2f3aad7095c6c1_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2f3aad6695234d_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2f3aad18e5af5a_outfile.txt added
2f3aad529557a5_GRCh37_to_GRCh38.chain added
2f3aad357ed2b1_GRCh37_to_NCBI34.chain added
2f3aad653cb0a5_GRCh37_to_NCBI35.chain added
2f3aad337fff66_GRCh37_to_NCBI36.chain added
2f3aad1caa0afe_GRCh38_to_GRCh37.chain added
2f3aad63877e25_GRCh38_to_NCBI34.chain added
2f3aad6c7c2dd8_GRCh38_to_NCBI35.chain added
2f3aad5e19221f_GRCh38_to_NCBI36.chain added
2f3aad4d394272_NCBI34_to_GRCh37.chain added
2f3aad12966832_NCBI34_to_GRCh38.chain added
2f3aad531bc1e9_NCBI35_to_GRCh37.chain added
2f3aad7e98c1bf_NCBI35_to_GRCh38.chain added
2f3aad338c7ef0_NCBI36_to_GRCh37.chain added
2f3aad3e0d0037_NCBI36_to_GRCh38.chain added
2f3aadced3317_GRCm38_to_NCBIM36.chain added
2f3aad6da3c07a_GRCm38_to_NCBIM37.chain added
2f3aad48cbe165_NCBIM36_to_GRCm38.chain added
2f3aad3729b94e_NCBIM37_to_GRCm38.chain added
2f3aad77cd44f0_1000G_omni2.5.b37.vcf.gz added
2f3aad7848d06a_1000G_omni2.5.b37.vcf.gz.tbi added
2f3aad726110f3_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2f3aad3f8c91f2_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2f3aad3ab806d4_1000G_omni2.5.hg38.vcf.gz added
2f3aad4b78743f_1000G_omni2.5.hg38.vcf.gz.tbi added
2f3aad6f830957_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2f3aad97b54d2_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2f3aad3ee3b9d1_af-only-gnomad.raw.sites.vcf added
2f3aad23cffa4_af-only-gnomad.raw.sites.vcf.idx added
2f3aad7a111b93_Mutect2-exome-panel.vcf.idx added
2f3aad2578dd1e_Mutect2-WGS-panel-b37.vcf added
2f3aad1b22aefe_Mutect2-WGS-panel-b37.vcf.idx added
2f3aad4ca67338_small_exac_common_3.vcf added
2f3aad5af7afcf_small_exac_common_3.vcf.idx added
2f3aad5f5fa3_1000g_pon.hg38.vcf.gz added
2f3aad26729f_1000g_pon.hg38.vcf.gz.tbi added
2f3aad77a1bace_af-only-gnomad.hg38.vcf.gz added
2f3aad63e6ddc9_af-only-gnomad.hg38.vcf.gz.tbi added
2f3aad6ca2a077_small_exac_common_3.hg38.vcf.gz added
2f3aad55badced_small_exac_common_3.hg38.vcf.gz.tbi added
2f3aad3120203b_gencode.v41.annotation.gtf added
2f3aad7f3908a9_gencode.v42.annotation.gtf added
2f3aad28d69ed6_gencode.vM30.annotation.gtf added
2f3aad2fb8e1fa_gencode.vM31.annotation.gtf added
2f3aad32c58799_gencode.v41.transcripts.fa added
2f3aad66e39f0e_gencode.v41.transcripts.fa.fai added
2f3aad3ca61511_gencode.v42.transcripts.fa added
2f3aad20694813_gencode.v42.transcripts.fa.fai added
2f3aad2faf8073_gencode.vM30.pc_transcripts.fa added
2f3aad73cfce60_gencode.vM30.pc_transcripts.fa.fai added
2f3aad18368d03_gencode.vM31.pc_transcripts.fa added
2f3aad27f850de_gencode.vM31.pc_transcripts.fa.fai added
2f3aad6630df53_GRCh38.primary_assembly.genome.fa.1.ht2 added
2f3aad57c31ef5_GRCh38.primary_assembly.genome.fa.2.ht2 added
2f3aad62b057b2_GRCh38.primary_assembly.genome.fa.3.ht2 added
2f3aad31a95392_GRCh38.primary_assembly.genome.fa.4.ht2 added
2f3aad4746284d_GRCh38.primary_assembly.genome.fa.5.ht2 added
2f3aad6c2bac84_GRCh38.primary_assembly.genome.fa.6.ht2 added
2f3aad708d0d63_GRCh38.primary_assembly.genome.fa.7.ht2 added
2f3aad498327f1_GRCh38.primary_assembly.genome.fa.8.ht2 added
2f3aad663cc817_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2f3aad1605ea81_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2f3aad64a5d6ef_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2f3aad32e33b4f_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2f3aad70fd9a51_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2f3aad65053692_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2f3aad3309adee_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2f3aad689f551f_GRCh38.primary_assembly.genome.fa.fai added
2f3aad48ec145b_GRCh38.primary_assembly.genome.fa.amb added
2f3aad1fac4e65_GRCh38.primary_assembly.genome.fa.ann added
2f3aad3e5a320c_GRCh38.primary_assembly.genome.fa.bwt added
2f3aad7a0c3497_GRCh38.primary_assembly.genome.fa.pac added
2f3aad1ee5570e_GRCh38.primary_assembly.genome.fa.sa added
2f3aad6730d0e3_GRCh38.primary_assembly.genome.fa added
2f3aad29c51691_hs37d5.fa.fai added
2f3aad51aadea7_hs37d5.fa.amb added
2f3aad4e146ff1_hs37d5.fa.ann added
2f3aad666b2ba3_hs37d5.fa.bwt added
2f3aad721426bb_hs37d5.fa.pac added
2f3aad7dc3f064_hs37d5.fa.sa added
2f3aad5a3afa03_hs37d5.fa added
2f3aada4ab3be_complete_ref_lens.bin added
2f3aad25bc4142_ctable.bin added
2f3aad406bd956_ctg_offsets.bin added
2f3aad620dd2b4_duplicate_clusters.tsv added
2f3aad86c98f4_info.json added
2f3aad72152ce9_mphf.bin added
2f3aad2953fb01_pos.bin added
2f3aad74984578_pre_indexing.log added
2f3aad62a23a4c_rank.bin added
2f3aad72d722f2_ref_indexing.log added
2f3aad5ad50d8f_refAccumLengths.bin added
2f3aad78a824ce_reflengths.bin added
2f3aad577cf9e1_refseq.bin added
2f3aaddb848df_seq.bin added
2f3aad69a5bf1f_versionInfo.json added
2f3aad3c823073_salmon_index added
2f3aad40c1f6cd_chrLength.txt added
2f3aad5245143e_chrName.txt added
2f3aad56e44cf_chrNameLength.txt added
2f3aad606e4533_chrStart.txt added
2f3aad109f464a_exonGeTrInfo.tab added
2f3aad7f7a7966_exonInfo.tab added
2f3aad7f539c41_geneInfo.tab added
2f3aad77d0172d_Genome added
2f3aad293f8ff7_genomeParameters.txt added
2f3aad50fe7ae9_Log.out added
2f3aad45e4871e_SA added
2f3aadfaabb9a_SAindex added
2f3aad4312a1a4_sjdbInfo.txt added
2f3aad43a87783_sjdbList.fromGTF.out.tab added
2f3aad69e5b59d_sjdbList.out.tab added
2f3aad4d5d5562_transcriptInfo.tab added
2f3aad6964b8c5_GRCh38.GENCODE.v42_100 added
2f3aad2a518ef4_knownGene_hg38.sql added
2f3aad2f6b2816_knownGene_hg38.txt added
2f3aad71d151ba_refGene_hg38.sql added
2f3aad1c66bbdd_refGene_hg38.txt added
2f3aad58bf2317_knownGene_mm39.sql added
2f3aad66699732_knownGene_mm39.txt added
2f3aad7f08f629_refGene_mm39.sql added
2f3aad4b964609_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/RtmpaLEY4G/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 
 20.875   1.948  23.093

Example timings

ReUseData.Rcheck/ReUseData-Ex.timings

nameusersystemelapsed
dataHub-class6.1980.4276.627
dataSearch1.170.051.22
dataUpdate0.0000.0010.001
getCloudData2.8020.1273.911
getData0.0000.0000.001
meta_data0.0010.0000.001
recipeHub-class0.1260.0000.127
recipeLoad1.2510.0231.275
recipeMake000
recipeSearch0.5660.0070.573
recipeUpdate000