Qian Liu
| Snapshot Date: 2025-10-23 14:17 -0400 (Thu, 23 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 2025-10-24 12:05 -0400 (Fri, 24 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" | 4898 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 |
| 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 1771/2359 | 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 | 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: 2025-10-23 23:36:39 -0400 (Thu, 23 Oct 2025) |
| EndedAt: 2025-10-23 23:39:08 -0400 (Thu, 23 Oct 2025) |
| EllapsedTime: 149.1 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 7.383 0.882 8.386
getCloudData 2.744 0.156 9.415
* 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...
1741f1fdf9f38_GRCh38.primary_assembly.genome.fa.1.bt2 added
1741f124e25e1_GRCh38.primary_assembly.genome.fa.2.bt2 added
1741f4898e02a_GRCh38.primary_assembly.genome.fa.3.bt2 added
1741f2ca50aa2_GRCh38.primary_assembly.genome.fa.4.bt2 added
1741f75d2894_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1741f75131052_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1741f3694b38a_outfile.txt added
1741f5c974504_GRCh37_to_GRCh38.chain added
1741f4f343919_GRCh37_to_NCBI34.chain added
1741f6d90c0ee_GRCh37_to_NCBI35.chain added
1741f3a6a8174_GRCh37_to_NCBI36.chain added
1741f265904a2_GRCh38_to_GRCh37.chain added
1741f1e3f3b59_GRCh38_to_NCBI34.chain added
1741f49515f92_GRCh38_to_NCBI35.chain added
1741f7d598fd8_GRCh38_to_NCBI36.chain added
1741f2f2ee33_NCBI34_to_GRCh37.chain added
1741f1af457c8_NCBI34_to_GRCh38.chain added
1741f1faf194b_NCBI35_to_GRCh37.chain added
1741f20a59b2d_NCBI35_to_GRCh38.chain added
1741f586eb819_NCBI36_to_GRCh37.chain added
1741f4cf89eaa_NCBI36_to_GRCh38.chain added
1741f5678d260_GRCm38_to_NCBIM36.chain added
1741f163bc8fa_GRCm38_to_NCBIM37.chain added
1741f2f07a07d_NCBIM36_to_GRCm38.chain added
1741f1db986aa_NCBIM37_to_GRCm38.chain added
1741f7f381224_1000G_omni2.5.b37.vcf.gz added
1741f3a2f3abc_1000G_omni2.5.b37.vcf.gz.tbi added
1741f72b92a7b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1741f5a942c14_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1741f35da0381_1000G_omni2.5.hg38.vcf.gz added
1741f7c1c25c5_1000G_omni2.5.hg38.vcf.gz.tbi added
1741f1bf3e82b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1741f2a0f6d63_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1741f5ad69427_af-only-gnomad.raw.sites.vcf added
1741f3d98bb08_af-only-gnomad.raw.sites.vcf.idx added
1741f761f29cf_Mutect2-exome-panel.vcf.idx added
1741f77f2119e_Mutect2-WGS-panel-b37.vcf added
1741f3562d997_Mutect2-WGS-panel-b37.vcf.idx added
1741f6cbb63e2_small_exac_common_3.vcf added
1741f29ac233_small_exac_common_3.vcf.idx added
1741f7e43a39a_1000g_pon.hg38.vcf.gz added
1741faaa1439_1000g_pon.hg38.vcf.gz.tbi added
1741f2415afa7_af-only-gnomad.hg38.vcf.gz added
1741fbbf0f73_af-only-gnomad.hg38.vcf.gz.tbi added
1741f2c8f4d0b_small_exac_common_3.hg38.vcf.gz added
1741f740b2407_small_exac_common_3.hg38.vcf.gz.tbi added
1741f76a8316_gencode.v41.annotation.gtf added
1741f61c41d27_gencode.v42.annotation.gtf added
1741f12561d96_gencode.vM30.annotation.gtf added
1741f53b06c41_gencode.vM31.annotation.gtf added
1741f63934a53_gencode.v41.transcripts.fa added
1741f5af4c237_gencode.v41.transcripts.fa.fai added
1741f7afad787_gencode.v42.transcripts.fa added
1741f6a5c1f24_gencode.v42.transcripts.fa.fai added
1741f4600ab09_gencode.vM30.pc_transcripts.fa added
1741f55dcffc6_gencode.vM30.pc_transcripts.fa.fai added
1741f201c4c34_gencode.vM31.pc_transcripts.fa added
1741f21cefa64_gencode.vM31.pc_transcripts.fa.fai added
1741f1b98cc93_GRCh38.primary_assembly.genome.fa.1.ht2 added
1741f4c9ed50c_GRCh38.primary_assembly.genome.fa.2.ht2 added
1741f4fb52e20_GRCh38.primary_assembly.genome.fa.3.ht2 added
1741f7fe75fc1_GRCh38.primary_assembly.genome.fa.4.ht2 added
1741f2f3fb981_GRCh38.primary_assembly.genome.fa.5.ht2 added
1741fabdc63_GRCh38.primary_assembly.genome.fa.6.ht2 added
1741f1311e7ed_GRCh38.primary_assembly.genome.fa.7.ht2 added
1741f7c918262_GRCh38.primary_assembly.genome.fa.8.ht2 added
1741f35072fd2_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1741f6ad49f30_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1741f2d1f3f1b_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1741f5e681cc1_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1741f537f353_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1741f1c47d0d2_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1741f2ede997f_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1741f182f78e3_GRCh38.primary_assembly.genome.fa.fai added
1741f54a98b7c_GRCh38.primary_assembly.genome.fa.amb added
1741f4704a550_GRCh38.primary_assembly.genome.fa.ann added
1741f2014b9d_GRCh38.primary_assembly.genome.fa.bwt added
1741f230b3172_GRCh38.primary_assembly.genome.fa.pac added
1741f33db4557_GRCh38.primary_assembly.genome.fa.sa added
1741fa56d5a_GRCh38.primary_assembly.genome.fa added
1741f6cae300a_hs37d5.fa.fai added
1741f1fd41844_hs37d5.fa.amb added
1741f1d8528af_hs37d5.fa.ann added
1741f1132084d_hs37d5.fa.bwt added
1741f6bbf000c_hs37d5.fa.pac added
1741f489c4b17_hs37d5.fa.sa added
1741fd05f83f_hs37d5.fa added
1741f2ecf6c7_complete_ref_lens.bin added
1741f133d8451_ctable.bin added
1741f2bb9ebb5_ctg_offsets.bin added
1741f3b21ce80_duplicate_clusters.tsv added
1741f287c53d4_info.json added
1741f7a63980f_mphf.bin added
1741f20943f8f_pos.bin added
1741f64d8d5fe_pre_indexing.log added
1741f57c94a6b_rank.bin added
1741f6034e3d3_ref_indexing.log added
1741f305962fd_refAccumLengths.bin added
1741f3c71e8d7_reflengths.bin added
1741f5a6d9a41_refseq.bin added
1741f51aa4fc8_seq.bin added
1741f45bfd5b_versionInfo.json added
1741f33566399_salmon_index added
1741f6ca4ec23_chrLength.txt added
1741f3f8b258e_chrName.txt added
1741f484eae39_chrNameLength.txt added
1741f25904545_chrStart.txt added
1741f22b3c847_exonGeTrInfo.tab added
1741f4921bf1d_exonInfo.tab added
1741f468a2e6d_geneInfo.tab added
1741f19ee1a49_Genome added
1741f5effbbeb_genomeParameters.txt added
1741f678a7206_Log.out added
1741f32441d05_SA added
1741f15cd4d0b_SAindex added
1741f597d185b_sjdbInfo.txt added
1741f23ca2c43_sjdbList.fromGTF.out.tab added
1741f2e1ff510_sjdbList.out.tab added
1741f34120518_transcriptInfo.tab added
1741fb0c855d_GRCh38.GENCODE.v42_100 added
1741f6307a255_knownGene_hg38.sql added
1741fa32ad3e_knownGene_hg38.txt added
1741f50bc6ad_refGene_hg38.sql added
1741f48208a71_refGene_hg38.txt added
1741f506125b5_knownGene_mm39.sql added
1741f19f2b74d_knownGene_mm39.txt added
1741fde02d8a_refGene_mm39.sql added
1741f78cdc623_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/RtmpmUNIQV/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
21.585 2.390 24.870
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.383 | 0.882 | 8.386 | |
| dataSearch | 1.303 | 0.059 | 1.371 | |
| dataUpdate | 0.000 | 0.001 | 0.000 | |
| getCloudData | 2.744 | 0.156 | 9.415 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.001 | 0.001 | |
| recipeHub-class | 0.138 | 0.011 | 0.150 | |
| recipeLoad | 1.438 | 0.097 | 1.549 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.606 | 0.040 | 0.651 | |
| recipeUpdate | 0 | 0 | 0 | |