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This page was generated on 2025-09-20 12:03 -0400 (Sat, 20 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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 1751/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReUseData 1.9.0  (landing page)
Qian Liu
Snapshot Date: 2025-09-19 13:45 -0400 (Fri, 19 Sep 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: 2025-09-20 03:29:34 -0400 (Sat, 20 Sep 2025)
EndedAt: 2025-09-20 03:32:20 -0400 (Sat, 20 Sep 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 6.077  0.263   6.342
* 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...
23af2fa308552_GRCh38.primary_assembly.genome.fa.1.bt2 added
23af2fdab8c02_GRCh38.primary_assembly.genome.fa.2.bt2 added
23af2f704a1180_GRCh38.primary_assembly.genome.fa.3.bt2 added
23af2f435dbf92_GRCh38.primary_assembly.genome.fa.4.bt2 added
23af2f7455d764_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
23af2f445b78c8_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
23af2f1e515333_outfile.txt added
23af2f220eb99d_GRCh37_to_GRCh38.chain added
23af2f7975a47e_GRCh37_to_NCBI34.chain added
23af2f49417f9c_GRCh37_to_NCBI35.chain added
23af2f6580fabc_GRCh37_to_NCBI36.chain added
23af2f6f83bf3d_GRCh38_to_GRCh37.chain added
23af2f32b57ad7_GRCh38_to_NCBI34.chain added
23af2f5a8bea5c_GRCh38_to_NCBI35.chain added
23af2f7be9fadd_GRCh38_to_NCBI36.chain added
23af2f482dedb_NCBI34_to_GRCh37.chain added
23af2fc7b86fc_NCBI34_to_GRCh38.chain added
23af2f2ae5774c_NCBI35_to_GRCh37.chain added
23af2f5c8605fa_NCBI35_to_GRCh38.chain added
23af2f4475d96a_NCBI36_to_GRCh37.chain added
23af2f7945ab95_NCBI36_to_GRCh38.chain added
23af2f5c3d2f03_GRCm38_to_NCBIM36.chain added
23af2f2496931e_GRCm38_to_NCBIM37.chain added
23af2f752b47c8_NCBIM36_to_GRCm38.chain added
23af2f2ab1f1b5_NCBIM37_to_GRCm38.chain added
23af2f1b64e7a8_1000G_omni2.5.b37.vcf.gz added
23af2f5162615a_1000G_omni2.5.b37.vcf.gz.tbi added
23af2f6d4b9e2e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
23af2f8693448_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
23af2f50a5f0f5_1000G_omni2.5.hg38.vcf.gz added
23af2f7855b95e_1000G_omni2.5.hg38.vcf.gz.tbi added
23af2f1299b99a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
23af2f5e517cf7_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
23af2f689fcade_af-only-gnomad.raw.sites.vcf added
23af2f55f7792c_af-only-gnomad.raw.sites.vcf.idx added
23af2f52a7545b_Mutect2-exome-panel.vcf.idx added
23af2f2cfb43a7_Mutect2-WGS-panel-b37.vcf added
23af2f7448cc5f_Mutect2-WGS-panel-b37.vcf.idx added
23af2f74b60df9_small_exac_common_3.vcf added
23af2f2670e825_small_exac_common_3.vcf.idx added
23af2f3d8a4bfc_1000g_pon.hg38.vcf.gz added
23af2f5a3708b5_1000g_pon.hg38.vcf.gz.tbi added
23af2f15f4a763_af-only-gnomad.hg38.vcf.gz added
23af2f703fc6d3_af-only-gnomad.hg38.vcf.gz.tbi added
23af2f34c2f311_small_exac_common_3.hg38.vcf.gz added
23af2f11dea240_small_exac_common_3.hg38.vcf.gz.tbi added
23af2f74c2a5ae_gencode.v41.annotation.gtf added
23af2f413e7a0e_gencode.v42.annotation.gtf added
23af2f3cc4198c_gencode.vM30.annotation.gtf added
23af2f5148aba9_gencode.vM31.annotation.gtf added
23af2f5b45378_gencode.v41.transcripts.fa added
23af2f3609c521_gencode.v41.transcripts.fa.fai added
23af2f2d85daac_gencode.v42.transcripts.fa added
23af2f2a4ae696_gencode.v42.transcripts.fa.fai added
23af2f2b350ce9_gencode.vM30.pc_transcripts.fa added
23af2f5837cc61_gencode.vM30.pc_transcripts.fa.fai added
23af2f45afce3e_gencode.vM31.pc_transcripts.fa added
23af2f7c976e43_gencode.vM31.pc_transcripts.fa.fai added
23af2f45836a8f_GRCh38.primary_assembly.genome.fa.1.ht2 added
23af2f4e190286_GRCh38.primary_assembly.genome.fa.2.ht2 added
23af2f4d3d5f38_GRCh38.primary_assembly.genome.fa.3.ht2 added
23af2f3dd923ee_GRCh38.primary_assembly.genome.fa.4.ht2 added
23af2f60b2bc21_GRCh38.primary_assembly.genome.fa.5.ht2 added
23af2f2b8edc30_GRCh38.primary_assembly.genome.fa.6.ht2 added
23af2f2678eecc_GRCh38.primary_assembly.genome.fa.7.ht2 added
23af2f36aa354d_GRCh38.primary_assembly.genome.fa.8.ht2 added
23af2f7e36308b_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
23af2f53743273_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
23af2f2af301ad_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
23af2f72ec3e84_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
23af2f79e51a99_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
23af2f687d4da9_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
23af2f4d23473a_GRCh38_full_analysis_set_plus_decoy_hla.fa added
23af2ffd9c1fc_GRCh38.primary_assembly.genome.fa.fai added
23af2f58bd147c_GRCh38.primary_assembly.genome.fa.amb added
23af2f1e63a4b_GRCh38.primary_assembly.genome.fa.ann added
23af2f21b8643c_GRCh38.primary_assembly.genome.fa.bwt added
23af2f4d7fba2a_GRCh38.primary_assembly.genome.fa.pac added
23af2f4324b459_GRCh38.primary_assembly.genome.fa.sa added
23af2f5e7c7dc9_GRCh38.primary_assembly.genome.fa added
23af2f1ec865d3_hs37d5.fa.fai added
23af2f48d907d1_hs37d5.fa.amb added
23af2f148642ea_hs37d5.fa.ann added
23af2f4c4e4080_hs37d5.fa.bwt added
23af2f7323ee68_hs37d5.fa.pac added
23af2f3fbb4fd4_hs37d5.fa.sa added
23af2f24860ce1_hs37d5.fa added
23af2f38d3bca6_complete_ref_lens.bin added
23af2f3c52be17_ctable.bin added
23af2f6a097771_ctg_offsets.bin added
23af2f6ecbf2d_duplicate_clusters.tsv added
23af2f9901d50_info.json added
23af2f27e29b5f_mphf.bin added
23af2f679f7b4e_pos.bin added
23af2f351ef980_pre_indexing.log added
23af2f4e5b8a2b_rank.bin added
23af2f1e49b09b_ref_indexing.log added
23af2f33552a0b_refAccumLengths.bin added
23af2f21cfbc9f_reflengths.bin added
23af2f493cb248_refseq.bin added
23af2f26416890_seq.bin added
23af2f1bb4d738_versionInfo.json added
23af2f31b9fff1_salmon_index added
23af2f7364afca_chrLength.txt added
23af2f2b8e9934_chrName.txt added
23af2fa77146d_chrNameLength.txt added
23af2f754aea15_chrStart.txt added
23af2f4d46fd70_exonGeTrInfo.tab added
23af2f57f6ce98_exonInfo.tab added
23af2f386f9e6f_geneInfo.tab added
23af2f2bc37b39_Genome added
23af2f76bf346b_genomeParameters.txt added
23af2f148a640_Log.out added
23af2f4049be24_SA added
23af2f430d74eb_SAindex added
23af2f746c94a8_sjdbInfo.txt added
23af2f50df8_sjdbList.fromGTF.out.tab added
23af2f679381cd_sjdbList.out.tab added
23af2f2d40514f_transcriptInfo.tab added
23af2f3c57cc0f_GRCh38.GENCODE.v42_100 added
23af2f519cf93e_knownGene_hg38.sql added
23af2f342d107c_knownGene_hg38.txt added
23af2f45e7e95f_refGene_hg38.sql added
23af2f797f949d_refGene_hg38.txt added
23af2f1bcc8bca_knownGene_mm39.sql added
23af2f7b06e2df_knownGene_mm39.txt added
23af2f47db1ec8_refGene_mm39.sql added
23af2f3a163c65_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/RtmpErpshc/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 
 17.783   1.032  19.270

Example timings

ReUseData.Rcheck/ReUseData-Ex.timings

nameusersystemelapsed
dataHub-class6.0770.2636.342
dataSearch1.1320.0091.141
dataUpdate0.0000.0000.001
getCloudData2.6740.1493.848
getData000
meta_data0.0010.0000.001
recipeHub-class0.1170.0010.121
recipeLoad1.2330.0611.295
recipeMake000
recipeSearch0.5160.0030.518
recipeUpdate000