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This page was generated on 2025-10-04 12:04 -0400 (Sat, 04 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4853
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4640
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4585
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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: 2025-10-03 13:45 -0400 (Fri, 03 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 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: 2025-10-04 03:24:21 -0400 (Sat, 04 Oct 2025)
EndedAt: 2025-10-04 03:27:06 -0400 (Sat, 04 Oct 2025)
EllapsedTime: 164.2 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 6.042   0.26   6.303
* 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...
eef6b514aae62_GRCh38.primary_assembly.genome.fa.1.bt2 added
eef6b5ebfd3e6_GRCh38.primary_assembly.genome.fa.2.bt2 added
eef6b39e6aea3_GRCh38.primary_assembly.genome.fa.3.bt2 added
eef6b506ffd2f_GRCh38.primary_assembly.genome.fa.4.bt2 added
eef6b4cdb9e8d_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
eef6b4c2dd899_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
eef6b1a015366_outfile.txt added
eef6b6e0d67bf_GRCh37_to_GRCh38.chain added
eef6b3e5f9a9b_GRCh37_to_NCBI34.chain added
eef6b13a4f64a_GRCh37_to_NCBI35.chain added
eef6b51aa2c9a_GRCh37_to_NCBI36.chain added
eef6b3357195b_GRCh38_to_GRCh37.chain added
eef6b18466415_GRCh38_to_NCBI34.chain added
eef6b7ac27433_GRCh38_to_NCBI35.chain added
eef6b17205fa9_GRCh38_to_NCBI36.chain added
eef6b3e4426aa_NCBI34_to_GRCh37.chain added
eef6b1b32a01d_NCBI34_to_GRCh38.chain added
eef6b3ab465cc_NCBI35_to_GRCh37.chain added
eef6b7dca6ff3_NCBI35_to_GRCh38.chain added
eef6b7691acf3_NCBI36_to_GRCh37.chain added
eef6b5c507c7d_NCBI36_to_GRCh38.chain added
eef6b311b1b3f_GRCm38_to_NCBIM36.chain added
eef6b4a90d19_GRCm38_to_NCBIM37.chain added
eef6b5b6108c5_NCBIM36_to_GRCm38.chain added
eef6b61fc25b8_NCBIM37_to_GRCm38.chain added
eef6b4fa3262f_1000G_omni2.5.b37.vcf.gz added
eef6b22b673ea_1000G_omni2.5.b37.vcf.gz.tbi added
eef6b202b1a24_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
eef6b61d56a4f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
eef6b129626b5_1000G_omni2.5.hg38.vcf.gz added
eef6b4fd440a1_1000G_omni2.5.hg38.vcf.gz.tbi added
eef6b332018b2_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
eef6b7155fa9b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
eef6b9baef44_af-only-gnomad.raw.sites.vcf added
eef6b39015e1_af-only-gnomad.raw.sites.vcf.idx added
eef6b3e319928_Mutect2-exome-panel.vcf.idx added
eef6b55e8c7dd_Mutect2-WGS-panel-b37.vcf added
eef6b1d916947_Mutect2-WGS-panel-b37.vcf.idx added
eef6b2c3f00e7_small_exac_common_3.vcf added
eef6b14486279_small_exac_common_3.vcf.idx added
eef6b31365f91_1000g_pon.hg38.vcf.gz added
eef6b7de92d82_1000g_pon.hg38.vcf.gz.tbi added
eef6b479f7bd4_af-only-gnomad.hg38.vcf.gz added
eef6b497cc3a6_af-only-gnomad.hg38.vcf.gz.tbi added
eef6b78aba1b5_small_exac_common_3.hg38.vcf.gz added
eef6b5ebfdb7d_small_exac_common_3.hg38.vcf.gz.tbi added
eef6b7c0ea50_gencode.v41.annotation.gtf added
eef6b13de41d2_gencode.v42.annotation.gtf added
eef6b1974414a_gencode.vM30.annotation.gtf added
eef6b58b5a44_gencode.vM31.annotation.gtf added
eef6ba6feec5_gencode.v41.transcripts.fa added
eef6b75c4bdc7_gencode.v41.transcripts.fa.fai added
eef6b36a67583_gencode.v42.transcripts.fa added
eef6bf18fbde_gencode.v42.transcripts.fa.fai added
eef6b5125c68c_gencode.vM30.pc_transcripts.fa added
eef6b18a29b3b_gencode.vM30.pc_transcripts.fa.fai added
eef6b5ebc220d_gencode.vM31.pc_transcripts.fa added
eef6b73dc3a76_gencode.vM31.pc_transcripts.fa.fai added
eef6b38cdb55f_GRCh38.primary_assembly.genome.fa.1.ht2 added
eef6b40918c5d_GRCh38.primary_assembly.genome.fa.2.ht2 added
eef6b672612b_GRCh38.primary_assembly.genome.fa.3.ht2 added
eef6b8a1f600_GRCh38.primary_assembly.genome.fa.4.ht2 added
eef6b73b1a50f_GRCh38.primary_assembly.genome.fa.5.ht2 added
eef6b77c85bc6_GRCh38.primary_assembly.genome.fa.6.ht2 added
eef6b125ce544_GRCh38.primary_assembly.genome.fa.7.ht2 added
eef6b7741baf0_GRCh38.primary_assembly.genome.fa.8.ht2 added
eef6b35f9f4ee_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
eef6b6845ad22_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
eef6b14d32437_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
eef6b6238f5d6_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
eef6b7c8e0f9b_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
eef6b460983c8_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
eef6b60222358_GRCh38_full_analysis_set_plus_decoy_hla.fa added
eef6b442d8b6f_GRCh38.primary_assembly.genome.fa.fai added
eef6bf86476e_GRCh38.primary_assembly.genome.fa.amb added
eef6b58cdc50d_GRCh38.primary_assembly.genome.fa.ann added
eef6b22ed66ed_GRCh38.primary_assembly.genome.fa.bwt added
eef6b174731bf_GRCh38.primary_assembly.genome.fa.pac added
eef6b6cac06df_GRCh38.primary_assembly.genome.fa.sa added
eef6b3c61a837_GRCh38.primary_assembly.genome.fa added
eef6b1cd28c03_hs37d5.fa.fai added
eef6b771bf5a4_hs37d5.fa.amb added
eef6b322665fe_hs37d5.fa.ann added
eef6b53790186_hs37d5.fa.bwt added
eef6b634f183_hs37d5.fa.pac added
eef6b34c2c8a_hs37d5.fa.sa added
eef6b6c1b9cc1_hs37d5.fa added
eef6b64f11390_complete_ref_lens.bin added
eef6b77286700_ctable.bin added
eef6b24e95220_ctg_offsets.bin added
eef6b25829fed_duplicate_clusters.tsv added
eef6b7d9ac82b_info.json added
eef6b2d8b4821_mphf.bin added
eef6b193444fc_pos.bin added
eef6b756323f1_pre_indexing.log added
eef6b3fe82d65_rank.bin added
eef6b1075ffec_ref_indexing.log added
eef6b2b5d18df_refAccumLengths.bin added
eef6b282dda87_reflengths.bin added
eef6b25492423_refseq.bin added
eef6bd960eb5_seq.bin added
eef6b24bbea22_versionInfo.json added
eef6b6b52a7eb_salmon_index added
eef6b6db8320d_chrLength.txt added
eef6b68e97592_chrName.txt added
eef6b7ad8ef5a_chrNameLength.txt added
eef6b4685f71a_chrStart.txt added
eef6bbd6dc7f_exonGeTrInfo.tab added
eef6b12202119_exonInfo.tab added
eef6b3331fdf9_geneInfo.tab added
eef6b483884b6_Genome added
eef6b2ef2ad1c_genomeParameters.txt added
eef6b2a4df39e_Log.out added
eef6b7a5eeab4_SA added
eef6b26baea2_SAindex added
eef6b3082e521_sjdbInfo.txt added
eef6b7dab173e_sjdbList.fromGTF.out.tab added
eef6b6e874b63_sjdbList.out.tab added
eef6b1573f8b1_transcriptInfo.tab added
eef6b74d37e3e_GRCh38.GENCODE.v42_100 added
eef6b13709d83_knownGene_hg38.sql added
eef6b3af6989f_knownGene_hg38.txt added
eef6b726e4669_refGene_hg38.sql added
eef6b40fbe5a4_refGene_hg38.txt added
eef6b542add9b_knownGene_mm39.sql added
eef6b67d16a5a_knownGene_mm39.txt added
eef6be4130a_refGene_mm39.sql added
eef6b64a0dd88_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/RtmpVfmNv0/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 
 17.991   1.028  19.488 

Example timings

ReUseData.Rcheck/ReUseData-Ex.timings

nameusersystemelapsed
dataHub-class6.0420.2606.303
dataSearch1.0830.0091.093
dataUpdate000
getCloudData2.6880.1353.826
getData000
meta_data0.0010.0000.000
recipeHub-class0.1240.0000.124
recipeLoad1.2340.0501.284
recipeMake000
recipeSearch0.5360.0090.546
recipeUpdate000