Qian Liu
| Snapshot Date: 2025-10-19 13:45 -0400 (Sun, 19 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 2025-10-20 12:05 -0400 (Mon, 20 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" | 4887 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4632 |
| 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 1765/2353 | 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 | 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: 2025-10-20 01:05:40 -0400 (Mon, 20 Oct 2025) |
| EndedAt: 2025-10-20 01:08:13 -0400 (Mon, 20 Oct 2025) |
| EllapsedTime: 152.7 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 7.604 0.922 8.665
getCloudData 2.733 0.156 7.047
* 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...
8b33236f6de2_GRCh38.primary_assembly.genome.fa.1.bt2 added
8b336897229a_GRCh38.primary_assembly.genome.fa.2.bt2 added
8b331a60e21b_GRCh38.primary_assembly.genome.fa.3.bt2 added
8b334e9c6824_GRCh38.primary_assembly.genome.fa.4.bt2 added
8b337e793bcd_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
8b3349455099_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
8b3365ae9263_outfile.txt added
8b33280cd5bc_GRCh37_to_GRCh38.chain added
8b3362a43e2e_GRCh37_to_NCBI34.chain added
8b33cee709a_GRCh37_to_NCBI35.chain added
8b337a229517_GRCh37_to_NCBI36.chain added
8b33746a57a5_GRCh38_to_GRCh37.chain added
8b3371a04d58_GRCh38_to_NCBI34.chain added
8b33533606af_GRCh38_to_NCBI35.chain added
8b337ff0f5d6_GRCh38_to_NCBI36.chain added
8b33249bf639_NCBI34_to_GRCh37.chain added
8b337b422af5_NCBI34_to_GRCh38.chain added
8b3335127a0b_NCBI35_to_GRCh37.chain added
8b33500a8365_NCBI35_to_GRCh38.chain added
8b33623884f0_NCBI36_to_GRCh37.chain added
8b336c9fdaf0_NCBI36_to_GRCh38.chain added
8b3372defa46_GRCm38_to_NCBIM36.chain added
8b33d014495_GRCm38_to_NCBIM37.chain added
8b334e3d98de_NCBIM36_to_GRCm38.chain added
8b332dff3ef3_NCBIM37_to_GRCm38.chain added
8b33507ddb1c_1000G_omni2.5.b37.vcf.gz added
8b3376bc348c_1000G_omni2.5.b37.vcf.gz.tbi added
8b333e1e103a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
8b3327bb6fb2_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
8b332a2237f_1000G_omni2.5.hg38.vcf.gz added
8b3362c86832_1000G_omni2.5.hg38.vcf.gz.tbi added
8b335330dd48_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
8b332d0fcca3_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
8b336843f871_af-only-gnomad.raw.sites.vcf added
8b33466bf831_af-only-gnomad.raw.sites.vcf.idx added
8b335a737d15_Mutect2-exome-panel.vcf.idx added
8b3354191c17_Mutect2-WGS-panel-b37.vcf added
8b333c835523_Mutect2-WGS-panel-b37.vcf.idx added
8b33524a8bde_small_exac_common_3.vcf added
8b331c24c607_small_exac_common_3.vcf.idx added
8b3332450400_1000g_pon.hg38.vcf.gz added
8b335109b5c8_1000g_pon.hg38.vcf.gz.tbi added
8b33547d8708_af-only-gnomad.hg38.vcf.gz added
8b337d2c498d_af-only-gnomad.hg38.vcf.gz.tbi added
8b336691082e_small_exac_common_3.hg38.vcf.gz added
8b333bb0389d_small_exac_common_3.hg38.vcf.gz.tbi added
8b332e54ea08_gencode.v41.annotation.gtf added
8b3348d0cafb_gencode.v42.annotation.gtf added
8b333be4a16_gencode.vM30.annotation.gtf added
8b3341f1ec45_gencode.vM31.annotation.gtf added
8b3371cec7d5_gencode.v41.transcripts.fa added
8b333ea1ab52_gencode.v41.transcripts.fa.fai added
8b3367f6b49d_gencode.v42.transcripts.fa added
8b3375cbe4bd_gencode.v42.transcripts.fa.fai added
8b331d1670b6_gencode.vM30.pc_transcripts.fa added
8b332c41cba5_gencode.vM30.pc_transcripts.fa.fai added
8b3313a0d456_gencode.vM31.pc_transcripts.fa added
8b3323d4642b_gencode.vM31.pc_transcripts.fa.fai added
8b334cfc556d_GRCh38.primary_assembly.genome.fa.1.ht2 added
8b334a4c8e97_GRCh38.primary_assembly.genome.fa.2.ht2 added
8b336825819c_GRCh38.primary_assembly.genome.fa.3.ht2 added
8b3376605e2e_GRCh38.primary_assembly.genome.fa.4.ht2 added
8b3330c75ab9_GRCh38.primary_assembly.genome.fa.5.ht2 added
8b33701540b3_GRCh38.primary_assembly.genome.fa.6.ht2 added
8b3334ae142_GRCh38.primary_assembly.genome.fa.7.ht2 added
8b33290ab5be_GRCh38.primary_assembly.genome.fa.8.ht2 added
8b337e21e1fe_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
8b33627c2b63_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
8b334604a318_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
8b335a6fa091_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
8b335696bdf9_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
8b33429252d8_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
8b33147d050d_GRCh38_full_analysis_set_plus_decoy_hla.fa added
8b331bd6a2fd_GRCh38.primary_assembly.genome.fa.fai added
8b3328669e52_GRCh38.primary_assembly.genome.fa.amb added
8b3369242e36_GRCh38.primary_assembly.genome.fa.ann added
8b3346561127_GRCh38.primary_assembly.genome.fa.bwt added
8b333c803b84_GRCh38.primary_assembly.genome.fa.pac added
8b336c37624_GRCh38.primary_assembly.genome.fa.sa added
8b33a8138f4_GRCh38.primary_assembly.genome.fa added
8b3329c2208f_hs37d5.fa.fai added
8b337e7a1b4_hs37d5.fa.amb added
8b3378293479_hs37d5.fa.ann added
8b3359343190_hs37d5.fa.bwt added
8b3371a212b0_hs37d5.fa.pac added
8b3347791b18_hs37d5.fa.sa added
8b335fe1e950_hs37d5.fa added
8b33689cb45d_complete_ref_lens.bin added
8b338057b53_ctable.bin added
8b331fe38a42_ctg_offsets.bin added
8b33138a0369_duplicate_clusters.tsv added
8b3349e5ec84_info.json added
8b33160af403_mphf.bin added
8b332919fc43_pos.bin added
8b336900a7c9_pre_indexing.log added
8b332a07b2fa_rank.bin added
8b335f7750a4_ref_indexing.log added
8b33124f6ff3_refAccumLengths.bin added
8b331d3ec3e9_reflengths.bin added
8b333b004ff_refseq.bin added
8b331918033d_seq.bin added
8b33777ca6a9_versionInfo.json added
8b3318a1de88_salmon_index added
8b332b18bf5a_chrLength.txt added
8b3365bac3d0_chrName.txt added
8b33488dc0dd_chrNameLength.txt added
8b3352711261_chrStart.txt added
8b337d6dc88f_exonGeTrInfo.tab added
8b33328a649e_exonInfo.tab added
8b331bd3dafe_geneInfo.tab added
8b3371ce67f7_Genome added
8b33260bc380_genomeParameters.txt added
8b334e501c03_Log.out added
8b336d5f311f_SA added
8b334922252_SAindex added
8b33160b37d6_sjdbInfo.txt added
8b333a7ecde8_sjdbList.fromGTF.out.tab added
8b335b005858_sjdbList.out.tab added
8b3373a82814_transcriptInfo.tab added
8b3324df745e_GRCh38.GENCODE.v42_100 added
8b334a50da3b_knownGene_hg38.sql added
8b332277d9b_knownGene_hg38.txt added
8b336ea74c37_refGene_hg38.sql added
8b33297ce7a2_refGene_hg38.txt added
8b33474b51f5_knownGene_mm39.sql added
8b3321f1d064_knownGene_mm39.txt added
8b33aa866a5_refGene_mm39.sql added
8b3335eae01a_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/Rtmpk3qDeS/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
22.412 2.481 26.102
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.604 | 0.922 | 8.665 | |
| dataSearch | 1.344 | 0.062 | 1.423 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.733 | 0.156 | 7.047 | |
| getData | 0.000 | 0.001 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.158 | 0.014 | 0.175 | |
| recipeLoad | 1.615 | 0.108 | 1.738 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.649 | 0.041 | 0.695 | |
| recipeUpdate | 0 | 0 | 0 | |