Qian Liu
| Snapshot Date: 2025-10-24 13:45 -0400 (Fri, 24 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) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-25 12:05 -0400 (Sat, 25 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 1773/2361 | 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 12.7.6 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 | NA | NA | ||||||||||
|
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: 2025-10-24 23:42:17 -0400 (Fri, 24 Oct 2025) |
| EndedAt: 2025-10-24 23:44:47 -0400 (Fri, 24 Oct 2025) |
| EllapsedTime: 150.2 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 Patched (2025-09-10 r88807)
* 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 7.327 0.886 8.327
getCloudData 2.790 0.165 10.268
* 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 Patched (2025-09-10 r88807) -- "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...
424662c56c0a_GRCh38.primary_assembly.genome.fa.1.bt2 added
4246f38372f_GRCh38.primary_assembly.genome.fa.2.bt2 added
424633aef677_GRCh38.primary_assembly.genome.fa.3.bt2 added
424623b71923_GRCh38.primary_assembly.genome.fa.4.bt2 added
424649d35b26_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
4246530541a7_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
42467e196585_outfile.txt added
424635583f70_GRCh37_to_GRCh38.chain added
424634aced6c_GRCh37_to_NCBI34.chain added
424645176878_GRCh37_to_NCBI35.chain added
42463cbc1b8_GRCh37_to_NCBI36.chain added
4246361b18fa_GRCh38_to_GRCh37.chain added
42462d04e0d6_GRCh38_to_NCBI34.chain added
42461b4518b1_GRCh38_to_NCBI35.chain added
424655581a73_GRCh38_to_NCBI36.chain added
4246b309fcb_NCBI34_to_GRCh37.chain added
4246254ace2a_NCBI34_to_GRCh38.chain added
424652253a86_NCBI35_to_GRCh37.chain added
4246a255d8c_NCBI35_to_GRCh38.chain added
42461b209788_NCBI36_to_GRCh37.chain added
424678bc6fa1_NCBI36_to_GRCh38.chain added
42461b44f0f4_GRCm38_to_NCBIM36.chain added
42464b273128_GRCm38_to_NCBIM37.chain added
42467a0c5fa3_NCBIM36_to_GRCm38.chain added
4246425b04ee_NCBIM37_to_GRCm38.chain added
424665a0c74a_1000G_omni2.5.b37.vcf.gz added
42461e7bff66_1000G_omni2.5.b37.vcf.gz.tbi added
42465ebc912c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
42462ddf104b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
4246fa6c374_1000G_omni2.5.hg38.vcf.gz added
4246d69fcb3_1000G_omni2.5.hg38.vcf.gz.tbi added
4246294d52a6_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
4246136d2579_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
424662b734e5_af-only-gnomad.raw.sites.vcf added
424669f1d904_af-only-gnomad.raw.sites.vcf.idx added
42464decbf3_Mutect2-exome-panel.vcf.idx added
42463f1fc104_Mutect2-WGS-panel-b37.vcf added
42463db90dfc_Mutect2-WGS-panel-b37.vcf.idx added
424640453b0c_small_exac_common_3.vcf added
4246127b1cb_small_exac_common_3.vcf.idx added
424655098704_1000g_pon.hg38.vcf.gz added
4246647f4339_1000g_pon.hg38.vcf.gz.tbi added
42465f1686ba_af-only-gnomad.hg38.vcf.gz added
42463fe74e1b_af-only-gnomad.hg38.vcf.gz.tbi added
42466ab8ef63_small_exac_common_3.hg38.vcf.gz added
4246136c8352_small_exac_common_3.hg38.vcf.gz.tbi added
424639218674_gencode.v41.annotation.gtf added
4246480246f9_gencode.v42.annotation.gtf added
4246d81aa5e_gencode.vM30.annotation.gtf added
42463bd8083f_gencode.vM31.annotation.gtf added
424664057eca_gencode.v41.transcripts.fa added
424624c73313_gencode.v41.transcripts.fa.fai added
424611ea3742_gencode.v42.transcripts.fa added
424627d1d73e_gencode.v42.transcripts.fa.fai added
4246418a3bde_gencode.vM30.pc_transcripts.fa added
42465a608d6f_gencode.vM30.pc_transcripts.fa.fai added
424678e5a0c3_gencode.vM31.pc_transcripts.fa added
42462b9da037_gencode.vM31.pc_transcripts.fa.fai added
42467981913f_GRCh38.primary_assembly.genome.fa.1.ht2 added
42462966fd6b_GRCh38.primary_assembly.genome.fa.2.ht2 added
424628879109_GRCh38.primary_assembly.genome.fa.3.ht2 added
42465c42faa8_GRCh38.primary_assembly.genome.fa.4.ht2 added
424631565aea_GRCh38.primary_assembly.genome.fa.5.ht2 added
42461c6ad1f4_GRCh38.primary_assembly.genome.fa.6.ht2 added
424628fdf8bf_GRCh38.primary_assembly.genome.fa.7.ht2 added
424639d5d89f_GRCh38.primary_assembly.genome.fa.8.ht2 added
4246680cc63_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
424671ea7aea_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
4246592bd313_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
42464c2eb221_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
4246db0bb9a_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
42464dec827b_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
4246626a8134_GRCh38_full_analysis_set_plus_decoy_hla.fa added
42463e48af66_GRCh38.primary_assembly.genome.fa.fai added
424615f3717c_GRCh38.primary_assembly.genome.fa.amb added
4246219f8f26_GRCh38.primary_assembly.genome.fa.ann added
4246726f1908_GRCh38.primary_assembly.genome.fa.bwt added
42465bd496e9_GRCh38.primary_assembly.genome.fa.pac added
424661ffca18_GRCh38.primary_assembly.genome.fa.sa added
4246602d1feb_GRCh38.primary_assembly.genome.fa added
4246328aaea1_hs37d5.fa.fai added
42462ecee5f3_hs37d5.fa.amb added
4246115acc87_hs37d5.fa.ann added
42466029bbf7_hs37d5.fa.bwt added
424653f38673_hs37d5.fa.pac added
424619001314_hs37d5.fa.sa added
424653e492de_hs37d5.fa added
4246436657d9_complete_ref_lens.bin added
424674118a20_ctable.bin added
42462b837668_ctg_offsets.bin added
424643d2bc29_duplicate_clusters.tsv added
4246403f4a88_info.json added
42467b3647ab_mphf.bin added
4246289b6abf_pos.bin added
4246737d366c_pre_indexing.log added
4246218027b0_rank.bin added
424664ada4fe_ref_indexing.log added
4246442b5355_refAccumLengths.bin added
4246786c1469_reflengths.bin added
42467fb03742_refseq.bin added
42469fc0f8c_seq.bin added
4246360b573_versionInfo.json added
4246422892c0_salmon_index added
424675ba9d2e_chrLength.txt added
42462ea57364_chrName.txt added
4246703ac228_chrNameLength.txt added
424621a109a8_chrStart.txt added
4246538105d7_exonGeTrInfo.tab added
42463ba69115_exonInfo.tab added
4246347f184b_geneInfo.tab added
4246413feda_Genome added
42463cc09c4d_genomeParameters.txt added
4246955a264_Log.out added
424655185805_SA added
4246313adbe8_SAindex added
4246f3b7598_sjdbInfo.txt added
42468a555f8_sjdbList.fromGTF.out.tab added
42461eaf1137_sjdbList.out.tab added
42467793419d_transcriptInfo.tab added
424664b8e7bf_GRCh38.GENCODE.v42_100 added
42462776e042_knownGene_hg38.sql added
42466d7d214b_knownGene_hg38.txt added
42463214fb15_refGene_hg38.sql added
42467f703962_refGene_hg38.txt added
424620c7924b_knownGene_mm39.sql added
4246e558abd_knownGene_mm39.txt added
4246120785a5_refGene_mm39.sql added
42462bd71ce2_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/RtmpRd8jxm/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
21.301 2.395 24.662
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.327 | 0.886 | 8.327 | |
| dataSearch | 1.328 | 0.057 | 1.393 | |
| dataUpdate | 0.000 | 0.001 | 0.001 | |
| getCloudData | 2.790 | 0.165 | 10.268 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.150 | 0.014 | 0.167 | |
| recipeLoad | 1.496 | 0.099 | 1.609 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.629 | 0.039 | 0.673 | |
| recipeUpdate | 0 | 0 | 0 | |