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This page was generated on 2025-10-09 12:06 -0400 (Thu, 09 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4854
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4642
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4587
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4584
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 1757/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReUseData 1.9.0  (landing page)
Qian Liu
Snapshot Date: 2025-10-08 14:17 -0400 (Wed, 08 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 kjohnson3

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReUseData_1.9.0.tar.gz
StartedAt: 2025-10-08 21:25:31 -0400 (Wed, 08 Oct 2025)
EndedAt: 2025-10-08 21:26:20 -0400 (Wed, 08 Oct 2025)
EllapsedTime: 48.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ReUseData.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReUseData_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck/00check.log’
for details.


Installation output

ReUseData.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ReUseData
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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 (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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...
2f0229b325c8_GRCh38.primary_assembly.genome.fa.1.bt2 added
2f02307582db_GRCh38.primary_assembly.genome.fa.2.bt2 added
2f0272e210b7_GRCh38.primary_assembly.genome.fa.3.bt2 added
2f0257b7994d_GRCh38.primary_assembly.genome.fa.4.bt2 added
2f0256b1bb38_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2f022e7a85ff_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2f026df3402f_outfile.txt added
2f027cfb060d_GRCh37_to_GRCh38.chain added
2f02444a7f95_GRCh37_to_NCBI34.chain added
2f0276fe3239_GRCh37_to_NCBI35.chain added
2f022a937937_GRCh37_to_NCBI36.chain added
2f0237fb1fb7_GRCh38_to_GRCh37.chain added
2f0247df4417_GRCh38_to_NCBI34.chain added
2f0212ef66de_GRCh38_to_NCBI35.chain added
2f02234a8288_GRCh38_to_NCBI36.chain added
2f0270bfc0d1_NCBI34_to_GRCh37.chain added
2f023d0c132b_NCBI34_to_GRCh38.chain added
2f0263be8b5c_NCBI35_to_GRCh37.chain added
2f0272af782c_NCBI35_to_GRCh38.chain added
2f025dfacb86_NCBI36_to_GRCh37.chain added
2f027c47fa9d_NCBI36_to_GRCh38.chain added
2f0259969929_GRCm38_to_NCBIM36.chain added
2f022e2180b2_GRCm38_to_NCBIM37.chain added
2f0219883dc7_NCBIM36_to_GRCm38.chain added
2f023f8fe0e9_NCBIM37_to_GRCm38.chain added
2f027ef70198_1000G_omni2.5.b37.vcf.gz added
2f02a89e347_1000G_omni2.5.b37.vcf.gz.tbi added
2f0262a84fb8_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2f021809eba2_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2f02334ce502_1000G_omni2.5.hg38.vcf.gz added
2f027d4f009d_1000G_omni2.5.hg38.vcf.gz.tbi added
2f024db183b0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2f02413cbfa9_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2f027b4b11b4_af-only-gnomad.raw.sites.vcf added
2f027d777fa8_af-only-gnomad.raw.sites.vcf.idx added
2f02305e2ef2_Mutect2-exome-panel.vcf.idx added
2f02775c2aac_Mutect2-WGS-panel-b37.vcf added
2f0243f5bf6c_Mutect2-WGS-panel-b37.vcf.idx added
2f023aea6e4f_small_exac_common_3.vcf added
2f0274f022c0_small_exac_common_3.vcf.idx added
2f024179a73a_1000g_pon.hg38.vcf.gz added
2f0219d1f26b_1000g_pon.hg38.vcf.gz.tbi added
2f0226825c0b_af-only-gnomad.hg38.vcf.gz added
2f023868e9ed_af-only-gnomad.hg38.vcf.gz.tbi added
2f026fd5e389_small_exac_common_3.hg38.vcf.gz added
2f02434d70bb_small_exac_common_3.hg38.vcf.gz.tbi added
2f0211242782_gencode.v41.annotation.gtf added
2f025c9dd098_gencode.v42.annotation.gtf added
2f027ce9daa8_gencode.vM30.annotation.gtf added
2f025d128ba9_gencode.vM31.annotation.gtf added
2f026c8f33fb_gencode.v41.transcripts.fa added
2f022d9ddb6b_gencode.v41.transcripts.fa.fai added
2f0256b06532_gencode.v42.transcripts.fa added
2f0256c3e214_gencode.v42.transcripts.fa.fai added
2f02562fbb8c_gencode.vM30.pc_transcripts.fa added
2f0257c21088_gencode.vM30.pc_transcripts.fa.fai added
2f025cb7dbb_gencode.vM31.pc_transcripts.fa added
2f0272ab82f5_gencode.vM31.pc_transcripts.fa.fai added
2f025a22dda3_GRCh38.primary_assembly.genome.fa.1.ht2 added
2f0227052690_GRCh38.primary_assembly.genome.fa.2.ht2 added
2f024326cbf3_GRCh38.primary_assembly.genome.fa.3.ht2 added
2f022817e0f6_GRCh38.primary_assembly.genome.fa.4.ht2 added
2f0237b24b0a_GRCh38.primary_assembly.genome.fa.5.ht2 added
2f021a5c9a17_GRCh38.primary_assembly.genome.fa.6.ht2 added
2f0235886986_GRCh38.primary_assembly.genome.fa.7.ht2 added
2f02ec7f7df_GRCh38.primary_assembly.genome.fa.8.ht2 added
2f026a62590d_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2f025ec49b0b_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2f023d9f1fc8_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2f0219dfa313_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2f02294b41aa_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2f02bc41514_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2f027643da14_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2f0260a293b4_GRCh38.primary_assembly.genome.fa.fai added
2f02518f3ffc_GRCh38.primary_assembly.genome.fa.amb added
2f0213b1e339_GRCh38.primary_assembly.genome.fa.ann added
2f023bcbd49_GRCh38.primary_assembly.genome.fa.bwt added
2f025c2f0589_GRCh38.primary_assembly.genome.fa.pac added
2f02131494a7_GRCh38.primary_assembly.genome.fa.sa added
2f022c2b69ba_GRCh38.primary_assembly.genome.fa added
2f02562a48fd_hs37d5.fa.fai added
2f02721e063c_hs37d5.fa.amb added
2f02112b87ac_hs37d5.fa.ann added
2f0240d83602_hs37d5.fa.bwt added
2f0232c1de90_hs37d5.fa.pac added
2f0255fad9f8_hs37d5.fa.sa added
2f0247fc54e1_hs37d5.fa added
2f02728a4b3_complete_ref_lens.bin added
2f027d54e770_ctable.bin added
2f025126aa58_ctg_offsets.bin added
2f024179a107_duplicate_clusters.tsv added
2f02183af426_info.json added
2f024672f737_mphf.bin added
2f0225c46003_pos.bin added
2f027f7b7853_pre_indexing.log added
2f02318d288_rank.bin added
2f0252a5e04e_ref_indexing.log added
2f028294b46_refAccumLengths.bin added
2f024f0ce4d9_reflengths.bin added
2f0257848b1a_refseq.bin added
2f023ec884d9_seq.bin added
2f025e89e2c2_versionInfo.json added
2f022e865f0b_salmon_index added
2f0277c9e309_chrLength.txt added
2f026758a14f_chrName.txt added
2f026bc67e8a_chrNameLength.txt added
2f02349dcd4d_chrStart.txt added
2f0264119537_exonGeTrInfo.tab added
2f023e5b8134_exonInfo.tab added
2f02697f9ce7_geneInfo.tab added
2f02391637cd_Genome added
2f0261a99102_genomeParameters.txt added
2f02436f4c65_Log.out added
2f0240009d79_SA added
2f02686293c2_SAindex added
2f021fd2db18_sjdbInfo.txt added
2f024c2e14fa_sjdbList.fromGTF.out.tab added
2f0265635028_sjdbList.out.tab added
2f025b23a618_transcriptInfo.tab added
2f0216da067_GRCh38.GENCODE.v42_100 added
2f02443dcaec_knownGene_hg38.sql added
2f0234d56ef4_knownGene_hg38.txt added
2f0228677045_refGene_hg38.sql added
2f021efbd6bc_refGene_hg38.txt added
2f0227cee088_knownGene_mm39.sql added
2f027ef71522_knownGene_mm39.txt added
2f02f8cac4d_refGene_mm39.sql added
2f025c83fb34_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: 
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpADtQPb/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 
  6.318   0.659   7.669 

Example timings

ReUseData.Rcheck/ReUseData-Ex.timings

nameusersystemelapsed
dataHub-class1.8230.1982.025
dataSearch0.3180.0130.332
dataUpdate000
getCloudData0.8740.0531.931
getData000
meta_data000
recipeHub-class0.0380.0050.043
recipeLoad0.3960.0260.424
recipeMake0.0000.0000.001
recipeSearch0.1640.0110.174
recipeUpdate000