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This page was generated on 2025-08-04 12:11 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4536
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4517
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 1737/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReUseData 1.9.0  (landing page)
Qian Liu
Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 Aug 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 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: 2025-08-03 21:12:21 -0400 (Sun, 03 Aug 2025)
EndedAt: 2025-08-03 21:13:11 -0400 (Sun, 03 Aug 2025)
EllapsedTime: 49.6 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 (2025-06-14 r88325)
* 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 13.7.1
* 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 (2025-06-14 r88325) -- "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...
99024148d80c_GRCh38.primary_assembly.genome.fa.1.bt2 added
990215601d50_GRCh38.primary_assembly.genome.fa.2.bt2 added
990259247a26_GRCh38.primary_assembly.genome.fa.3.bt2 added
990269cf8282_GRCh38.primary_assembly.genome.fa.4.bt2 added
990236815b13_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
990266825859_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
990277766fa2_outfile.txt added
99029b31f4_GRCh37_to_GRCh38.chain added
99024cec8a7b_GRCh37_to_NCBI34.chain added
99023d77b8b1_GRCh37_to_NCBI35.chain added
99027efe8bfd_GRCh37_to_NCBI36.chain added
99027998d02d_GRCh38_to_GRCh37.chain added
99021f8b78b9_GRCh38_to_NCBI34.chain added
99027da2c9dc_GRCh38_to_NCBI35.chain added
99024a72caf4_GRCh38_to_NCBI36.chain added
9902366a7f5b_NCBI34_to_GRCh37.chain added
99029cf4b46_NCBI34_to_GRCh38.chain added
9902856e5b2_NCBI35_to_GRCh37.chain added
99021020d65_NCBI35_to_GRCh38.chain added
99022dbd6267_NCBI36_to_GRCh37.chain added
99026c876fa6_NCBI36_to_GRCh38.chain added
99022fb332f4_GRCm38_to_NCBIM36.chain added
99021dd649a3_GRCm38_to_NCBIM37.chain added
99025f7c7ba2_NCBIM36_to_GRCm38.chain added
99026598f9a7_NCBIM37_to_GRCm38.chain added
99021e2e770d_1000G_omni2.5.b37.vcf.gz added
99027c8a05f5_1000G_omni2.5.b37.vcf.gz.tbi added
9902498d57b3_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
99025e78ce7e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
99024d3ce2a6_1000G_omni2.5.hg38.vcf.gz added
9902584427e7_1000G_omni2.5.hg38.vcf.gz.tbi added
99026297dbf6_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
99025fea260b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
9902567cd5f_af-only-gnomad.raw.sites.vcf added
990261dc1abe_af-only-gnomad.raw.sites.vcf.idx added
9902395fe223_Mutect2-exome-panel.vcf.idx added
990245f78542_Mutect2-WGS-panel-b37.vcf added
99027d4dd3f0_Mutect2-WGS-panel-b37.vcf.idx added
99029571d5_small_exac_common_3.vcf added
99025364573f_small_exac_common_3.vcf.idx added
9902609c13de_1000g_pon.hg38.vcf.gz added
990226dc855f_1000g_pon.hg38.vcf.gz.tbi added
990257b833e7_af-only-gnomad.hg38.vcf.gz added
99027e57afae_af-only-gnomad.hg38.vcf.gz.tbi added
99022ecf094f_small_exac_common_3.hg38.vcf.gz added
99021a6c398b_small_exac_common_3.hg38.vcf.gz.tbi added
99023735e23a_gencode.v41.annotation.gtf added
990232976a27_gencode.v42.annotation.gtf added
990272ba4063_gencode.vM30.annotation.gtf added
990221d95e6d_gencode.vM31.annotation.gtf added
990245c65777_gencode.v41.transcripts.fa added
99026098696a_gencode.v41.transcripts.fa.fai added
99023630dfb1_gencode.v42.transcripts.fa added
990242adf942_gencode.v42.transcripts.fa.fai added
99022bc77e41_gencode.vM30.pc_transcripts.fa added
99023631f3db_gencode.vM30.pc_transcripts.fa.fai added
9902980caa9_gencode.vM31.pc_transcripts.fa added
99026679221e_gencode.vM31.pc_transcripts.fa.fai added
99021aaf1421_GRCh38.primary_assembly.genome.fa.1.ht2 added
99025c529036_GRCh38.primary_assembly.genome.fa.2.ht2 added
99023079f894_GRCh38.primary_assembly.genome.fa.3.ht2 added
990217aed569_GRCh38.primary_assembly.genome.fa.4.ht2 added
9902573ceca4_GRCh38.primary_assembly.genome.fa.5.ht2 added
990260d42fba_GRCh38.primary_assembly.genome.fa.6.ht2 added
9902a898e00_GRCh38.primary_assembly.genome.fa.7.ht2 added
99024cc9a767_GRCh38.primary_assembly.genome.fa.8.ht2 added
99024b0d8293_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
990263f7a763_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
9902180e87db_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
990261f94733_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
990234b19785_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
99027752b7c9_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
990257a02a52_GRCh38_full_analysis_set_plus_decoy_hla.fa added
9902543a9a6f_GRCh38.primary_assembly.genome.fa.fai added
99025371189c_GRCh38.primary_assembly.genome.fa.amb added
99022606d490_GRCh38.primary_assembly.genome.fa.ann added
9902a6d4d71_GRCh38.primary_assembly.genome.fa.bwt added
9902df73b10_GRCh38.primary_assembly.genome.fa.pac added
990262469e99_GRCh38.primary_assembly.genome.fa.sa added
9902a568137_GRCh38.primary_assembly.genome.fa added
9902353d472e_hs37d5.fa.fai added
99024a0c3850_hs37d5.fa.amb added
99026845322a_hs37d5.fa.ann added
990216e098e1_hs37d5.fa.bwt added
99027354e782_hs37d5.fa.pac added
99024b2b42f5_hs37d5.fa.sa added
99025390961_hs37d5.fa added
99026396c1f4_complete_ref_lens.bin added
99023e97ad40_ctable.bin added
990257ef64da_ctg_offsets.bin added
990225c65150_duplicate_clusters.tsv added
99027f046e8f_info.json added
99027bf6af6e_mphf.bin added
9902779e57_pos.bin added
99022d3c61fe_pre_indexing.log added
9902574581e5_rank.bin added
990214530e26_ref_indexing.log added
990258c5eb36_refAccumLengths.bin added
990229d553c2_reflengths.bin added
9902746dfb02_refseq.bin added
9902607a7c05_seq.bin added
99029645dbf_versionInfo.json added
99021c46ab6a_salmon_index added
9902639fcaa6_chrLength.txt added
9902fb18b63_chrName.txt added
9902513618a1_chrNameLength.txt added
9902368b1bae_chrStart.txt added
990266c6587b_exonGeTrInfo.tab added
990267db27f3_exonInfo.tab added
9902651bf7c9_geneInfo.tab added
9902f28e0fb_Genome added
990244ca8683_genomeParameters.txt added
99024c4525bd_Log.out added
99024fb0c269_SA added
99025daba45e_SAindex added
99022fb4475d_sjdbInfo.txt added
990264b94322_sjdbList.fromGTF.out.tab added
99023ee6a0d7_sjdbList.out.tab added
99021749a384_transcriptInfo.tab added
9902638e3b0d_GRCh38.GENCODE.v42_100 added
9902ec7058b_knownGene_hg38.sql added
99022c3cf041_knownGene_hg38.txt added
990254c15217_refGene_hg38.sql added
99025ff48f79_refGene_hg38.txt added
990230f78226_knownGene_mm39.sql added
99024981a5e7_knownGene_mm39.txt added
99025eb30664_refGene_mm39.sql added
99023b68bfce_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//Rtmp25NhNn/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 
  6.340   0.714   7.835 

Example timings

ReUseData.Rcheck/ReUseData-Ex.timings

nameusersystemelapsed
dataHub-class1.9920.2462.246
dataSearch0.3490.0180.369
dataUpdate000
getCloudData0.9170.0621.961
getData000
meta_data000
recipeHub-class0.0380.0050.043
recipeLoad0.3990.0280.430
recipeMake000
recipeSearch0.1670.0120.178
recipeUpdate000