Qian Liu
| Snapshot Date: 2025-08-26 13:45 -0400 (Tue, 26 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) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-27 12:05 -0400 (Wed, 27 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4822 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4612 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4539 |
| 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 1741/2319 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.9.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| 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: 2025-08-26 23:12:42 -0400 (Tue, 26 Aug 2025) |
| EndedAt: 2025-08-26 23:15:09 -0400 (Tue, 26 Aug 2025) |
| EllapsedTime: 146.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dataHub-class 7.789 0.928 8.832
* 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.
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-x86_64/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)
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-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.)
}[1;30mINFO[0m Final process status is success
Updating data record...
outfile.txt added
Updating data record...
17ed735197832_GRCh38.primary_assembly.genome.fa.1.bt2 added
17ed71b2235da_GRCh38.primary_assembly.genome.fa.2.bt2 added
17ed762fd8920_GRCh38.primary_assembly.genome.fa.3.bt2 added
17ed77335c6a5_GRCh38.primary_assembly.genome.fa.4.bt2 added
17ed74f84b5ba_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
17ed711b6ef1f_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
17ed710ce54f_outfile.txt added
17ed775a2a612_GRCh37_to_GRCh38.chain added
17ed79452414_GRCh37_to_NCBI34.chain added
17ed71a43a1cd_GRCh37_to_NCBI35.chain added
17ed74e33a733_GRCh37_to_NCBI36.chain added
17ed721262d61_GRCh38_to_GRCh37.chain added
17ed7516d4c47_GRCh38_to_NCBI34.chain added
17ed75eaaf314_GRCh38_to_NCBI35.chain added
17ed7293cd69a_GRCh38_to_NCBI36.chain added
17ed7592d2d9c_NCBI34_to_GRCh37.chain added
17ed7250d8a81_NCBI34_to_GRCh38.chain added
17ed71c002e28_NCBI35_to_GRCh37.chain added
17ed74fd65274_NCBI35_to_GRCh38.chain added
17ed77fbf669e_NCBI36_to_GRCh37.chain added
17ed76eea5097_NCBI36_to_GRCh38.chain added
17ed759512264_GRCm38_to_NCBIM36.chain added
17ed75da9010b_GRCm38_to_NCBIM37.chain added
17ed7283a937_NCBIM36_to_GRCm38.chain added
17ed711da5b2b_NCBIM37_to_GRCm38.chain added
17ed716976d35_1000G_omni2.5.b37.vcf.gz added
17ed72f82be29_1000G_omni2.5.b37.vcf.gz.tbi added
17ed730928e1d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
17ed765b02ad4_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
17ed710cbf874_1000G_omni2.5.hg38.vcf.gz added
17ed73f249049_1000G_omni2.5.hg38.vcf.gz.tbi added
17ed7797cc901_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
17ed76f709ef6_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
17ed74ad461a2_af-only-gnomad.raw.sites.vcf added
17ed73d55f90f_af-only-gnomad.raw.sites.vcf.idx added
17ed75752673e_Mutect2-exome-panel.vcf.idx added
17ed762f8443b_Mutect2-WGS-panel-b37.vcf added
17ed71947b040_Mutect2-WGS-panel-b37.vcf.idx added
17ed7318446b7_small_exac_common_3.vcf added
17ed7633eb1c6_small_exac_common_3.vcf.idx added
17ed729097111_1000g_pon.hg38.vcf.gz added
17ed72ade2823_1000g_pon.hg38.vcf.gz.tbi added
17ed75f1d27d1_af-only-gnomad.hg38.vcf.gz added
17ed773213b1f_af-only-gnomad.hg38.vcf.gz.tbi added
17ed7ab0ab46_small_exac_common_3.hg38.vcf.gz added
17ed754bc8625_small_exac_common_3.hg38.vcf.gz.tbi added
17ed7250b1299_gencode.v41.annotation.gtf added
17ed779f20dce_gencode.v42.annotation.gtf added
17ed72688dee_gencode.vM30.annotation.gtf added
17ed71e3e057e_gencode.vM31.annotation.gtf added
17ed779daa2b4_gencode.v41.transcripts.fa added
17ed7f015ec_gencode.v41.transcripts.fa.fai added
17ed7122f396f_gencode.v42.transcripts.fa added
17ed75a63afbc_gencode.v42.transcripts.fa.fai added
17ed746a68e00_gencode.vM30.pc_transcripts.fa added
17ed760b4c63c_gencode.vM30.pc_transcripts.fa.fai added
17ed77c42bebd_gencode.vM31.pc_transcripts.fa added
17ed71f8aa07_gencode.vM31.pc_transcripts.fa.fai added
17ed76c62b293_GRCh38.primary_assembly.genome.fa.1.ht2 added
17ed743ba087c_GRCh38.primary_assembly.genome.fa.2.ht2 added
17ed76a8327a0_GRCh38.primary_assembly.genome.fa.3.ht2 added
17ed7489eb001_GRCh38.primary_assembly.genome.fa.4.ht2 added
17ed72a3536e6_GRCh38.primary_assembly.genome.fa.5.ht2 added
17ed7ba74bb0_GRCh38.primary_assembly.genome.fa.6.ht2 added
17ed7145a15ca_GRCh38.primary_assembly.genome.fa.7.ht2 added
17ed7264c8b36_GRCh38.primary_assembly.genome.fa.8.ht2 added
17ed76b4799de_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
17ed729c6f4d8_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
17ed744f4a655_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
17ed719d439d1_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
17ed73c1fd596_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
17ed74dff89b0_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
17ed743a8a9d1_GRCh38_full_analysis_set_plus_decoy_hla.fa added
17ed77624fb0a_GRCh38.primary_assembly.genome.fa.fai added
17ed775dd8a1e_GRCh38.primary_assembly.genome.fa.amb added
17ed72396f406_GRCh38.primary_assembly.genome.fa.ann added
17ed7b6ec82b_GRCh38.primary_assembly.genome.fa.bwt added
17ed7161784ea_GRCh38.primary_assembly.genome.fa.pac added
17ed7621729fa_GRCh38.primary_assembly.genome.fa.sa added
17ed75ec50e65_GRCh38.primary_assembly.genome.fa added
17ed75b34397e_hs37d5.fa.fai added
17ed741aaadf9_hs37d5.fa.amb added
17ed72c83d81d_hs37d5.fa.ann added
17ed73e16ec0_hs37d5.fa.bwt added
17ed7452e013d_hs37d5.fa.pac added
17ed74f536f46_hs37d5.fa.sa added
17ed76eae8559_hs37d5.fa added
17ed73b4ced4_complete_ref_lens.bin added
17ed75376c232_ctable.bin added
17ed719c78b6d_ctg_offsets.bin added
17ed77b92ae53_duplicate_clusters.tsv added
17ed75af30a86_info.json added
17ed7a381210_mphf.bin added
17ed76729ddad_pos.bin added
17ed76d98bdc4_pre_indexing.log added
17ed746d2c712_rank.bin added
17ed7380b9311_ref_indexing.log added
17ed77fe45dd5_refAccumLengths.bin added
17ed769cc8c8b_reflengths.bin added
17ed7741f2ff0_refseq.bin added
17ed72b84711f_seq.bin added
17ed741ec08b_versionInfo.json added
17ed77ef2e7c9_salmon_index added
17ed77d4f7e3b_chrLength.txt added
17ed76de893c2_chrName.txt added
17ed7403cdded_chrNameLength.txt added
17ed75c0e138d_chrStart.txt added
17ed72025bd32_exonGeTrInfo.tab added
17ed7da82e1b_exonInfo.tab added
17ed71c6af59e_geneInfo.tab added
17ed7322366a5_Genome added
17ed73227f45a_genomeParameters.txt added
17ed75d1b5a6f_Log.out added
17ed72ece5d2a_SA added
17ed76e468867_SAindex added
17ed758a55ac0_sjdbInfo.txt added
17ed74fe920b7_sjdbList.fromGTF.out.tab added
17ed75262f75d_sjdbList.out.tab added
17ed75f5e24ec_transcriptInfo.tab added
17ed71dca32de_GRCh38.GENCODE.v42_100 added
17ed745d19c19_knownGene_hg38.sql added
17ed7445f511e_knownGene_hg38.txt added
17ed74dc6aba3_refGene_hg38.sql added
17ed72e2e8239_refGene_hg38.txt added
17ed76f6783de_knownGene_mm39.sql added
17ed775029cf5_knownGene_mm39.txt added
17ed77e8ed4d6_refGene_mm39.sql added
17ed753376e83_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/RtmpmQzb8v/test_gcpData/outfile.txt
}[1;30mINFO[0m 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
22.358 2.457 25.908
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.789 | 0.928 | 8.832 | |
| dataSearch | 1.388 | 0.064 | 1.468 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.818 | 0.164 | 4.424 | |
| getData | 0.000 | 0.001 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.147 | 0.014 | 0.162 | |
| recipeLoad | 1.588 | 0.099 | 1.701 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.698 | 0.045 | 0.750 | |
| recipeUpdate | 0 | 0 | 0 | |