Qian Liu
| Snapshot Date: 2025-09-12 13:45 -0400 (Fri, 12 Sep 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 2025-09-13 12:04 -0400 (Sat, 13 Sep 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" | 4719 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4538 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4522 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4543 |
| 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 1747/2327 | 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: 2025-09-12 23:15:48 -0400 (Fri, 12 Sep 2025) |
| EndedAt: 2025-09-12 23:18:17 -0400 (Fri, 12 Sep 2025) |
| EllapsedTime: 149.0 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 7.496 0.855 8.464
* 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...
1535e568dca66_GRCh38.primary_assembly.genome.fa.1.bt2 added
1535e76e31aee_GRCh38.primary_assembly.genome.fa.2.bt2 added
1535e37fd3c3c_GRCh38.primary_assembly.genome.fa.3.bt2 added
1535e527da3db_GRCh38.primary_assembly.genome.fa.4.bt2 added
1535e3690a92c_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1535e5352a3b0_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1535e5678a28c_outfile.txt added
1535e9f7c1ae_GRCh37_to_GRCh38.chain added
1535e68cc8b9e_GRCh37_to_NCBI34.chain added
1535e4ce267d2_GRCh37_to_NCBI35.chain added
1535e240e336d_GRCh37_to_NCBI36.chain added
1535e20524b99_GRCh38_to_GRCh37.chain added
1535e7ae13a62_GRCh38_to_NCBI34.chain added
1535e58c036f4_GRCh38_to_NCBI35.chain added
1535e3357fab1_GRCh38_to_NCBI36.chain added
1535e550b94cc_NCBI34_to_GRCh37.chain added
1535e6b5608b2_NCBI34_to_GRCh38.chain added
1535e5d55152b_NCBI35_to_GRCh37.chain added
1535e7ce0e9eb_NCBI35_to_GRCh38.chain added
1535e121d835a_NCBI36_to_GRCh37.chain added
1535e4f9a9300_NCBI36_to_GRCh38.chain added
1535e2d290dd4_GRCm38_to_NCBIM36.chain added
1535e624af075_GRCm38_to_NCBIM37.chain added
1535e25f0c3bd_NCBIM36_to_GRCm38.chain added
1535e61c2c0c0_NCBIM37_to_GRCm38.chain added
1535e38fcaf64_1000G_omni2.5.b37.vcf.gz added
1535e555eeb76_1000G_omni2.5.b37.vcf.gz.tbi added
1535e4ab4bbc3_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1535e1f932586_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1535e7584909b_1000G_omni2.5.hg38.vcf.gz added
1535e5231ec63_1000G_omni2.5.hg38.vcf.gz.tbi added
1535e4b9681bd_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1535e61fc610_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1535e10044794_af-only-gnomad.raw.sites.vcf added
1535e8f74dc3_af-only-gnomad.raw.sites.vcf.idx added
1535e241241ce_Mutect2-exome-panel.vcf.idx added
1535e2a9e4de2_Mutect2-WGS-panel-b37.vcf added
1535e7f0b4649_Mutect2-WGS-panel-b37.vcf.idx added
1535e3d33a3c8_small_exac_common_3.vcf added
1535e945bedc_small_exac_common_3.vcf.idx added
1535e41f56245_1000g_pon.hg38.vcf.gz added
1535e5506c1d7_1000g_pon.hg38.vcf.gz.tbi added
1535e2ea035dd_af-only-gnomad.hg38.vcf.gz added
1535e18305815_af-only-gnomad.hg38.vcf.gz.tbi added
1535ede6d71b_small_exac_common_3.hg38.vcf.gz added
1535e2e3434be_small_exac_common_3.hg38.vcf.gz.tbi added
1535e6572bda4_gencode.v41.annotation.gtf added
1535e50008e04_gencode.v42.annotation.gtf added
1535e546bd1a4_gencode.vM30.annotation.gtf added
1535e72909148_gencode.vM31.annotation.gtf added
1535e713248ba_gencode.v41.transcripts.fa added
1535e1c44e565_gencode.v41.transcripts.fa.fai added
1535e6f305862_gencode.v42.transcripts.fa added
1535e4efac2f5_gencode.v42.transcripts.fa.fai added
1535e31158b55_gencode.vM30.pc_transcripts.fa added
1535e7d6e929f_gencode.vM30.pc_transcripts.fa.fai added
1535e665c450e_gencode.vM31.pc_transcripts.fa added
1535e33b9cea2_gencode.vM31.pc_transcripts.fa.fai added
1535e6bad0835_GRCh38.primary_assembly.genome.fa.1.ht2 added
1535e2cf606cd_GRCh38.primary_assembly.genome.fa.2.ht2 added
1535e4c3893ca_GRCh38.primary_assembly.genome.fa.3.ht2 added
1535e166ed9de_GRCh38.primary_assembly.genome.fa.4.ht2 added
1535e47a18953_GRCh38.primary_assembly.genome.fa.5.ht2 added
1535e3e3ecce2_GRCh38.primary_assembly.genome.fa.6.ht2 added
1535ecfd295b_GRCh38.primary_assembly.genome.fa.7.ht2 added
1535e40a61c06_GRCh38.primary_assembly.genome.fa.8.ht2 added
1535e5979ef12_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1535e543eb4a2_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1535e60c522e3_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1535e2e7596b7_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1535e29f9e035_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1535e53eecd1a_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1535e62db9102_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1535e3d0d4d02_GRCh38.primary_assembly.genome.fa.fai added
1535e343add9e_GRCh38.primary_assembly.genome.fa.amb added
1535e4abcadc_GRCh38.primary_assembly.genome.fa.ann added
1535e2a9333e9_GRCh38.primary_assembly.genome.fa.bwt added
1535e26351bd5_GRCh38.primary_assembly.genome.fa.pac added
1535e68b6508b_GRCh38.primary_assembly.genome.fa.sa added
1535e19620b62_GRCh38.primary_assembly.genome.fa added
1535e73d95bf2_hs37d5.fa.fai added
1535e4323a849_hs37d5.fa.amb added
1535e59fd730e_hs37d5.fa.ann added
1535ee8cca4a_hs37d5.fa.bwt added
1535e3d34c7bc_hs37d5.fa.pac added
1535e54252708_hs37d5.fa.sa added
1535e5325a960_hs37d5.fa added
1535e4d930845_complete_ref_lens.bin added
1535e700411cc_ctable.bin added
1535e1b2ca188_ctg_offsets.bin added
1535ef20f5a8_duplicate_clusters.tsv added
1535e3cdff05a_info.json added
1535e121cc3ef_mphf.bin added
1535e1e838933_pos.bin added
1535e4da482eb_pre_indexing.log added
1535e6b8f3a1f_rank.bin added
1535e8310064_ref_indexing.log added
1535e4910a96f_refAccumLengths.bin added
1535e64e3dbe2_reflengths.bin added
1535e2b79062d_refseq.bin added
1535e16848aa7_seq.bin added
1535e57aae57d_versionInfo.json added
1535e14c09e82_salmon_index added
1535e71e67372_chrLength.txt added
1535e50a57bc9_chrName.txt added
1535e2061f27c_chrNameLength.txt added
1535e7e76bb7f_chrStart.txt added
1535e250fcfb6_exonGeTrInfo.tab added
1535e310dc8bc_exonInfo.tab added
1535e7ff5c7cc_geneInfo.tab added
1535e611063b5_Genome added
1535e7b0231db_genomeParameters.txt added
1535e4d175ff4_Log.out added
1535e399cb3b6_SA added
1535e5eda8f46_SAindex added
1535e5ef46d50_sjdbInfo.txt added
1535e134cfe4_sjdbList.fromGTF.out.tab added
1535e323c825a_sjdbList.out.tab added
1535e2291fc7a_transcriptInfo.tab added
1535e1e56bf51_GRCh38.GENCODE.v42_100 added
1535e512a6e66_knownGene_hg38.sql added
1535e38b6142b_knownGene_hg38.txt added
1535e39e63023_refGene_hg38.sql added
1535e37626787_refGene_hg38.txt added
1535e1d7aec79_knownGene_mm39.sql added
1535e713b0b0d_knownGene_mm39.txt added
1535e5b52bc8e_refGene_mm39.sql added
1535e14d93d79_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/RtmpyjcxTC/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
22.075 2.403 25.570
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.496 | 0.855 | 8.464 | |
| dataSearch | 1.341 | 0.058 | 1.408 | |
| dataUpdate | 0.001 | 0.000 | 0.001 | |
| getCloudData | 2.856 | 0.165 | 4.255 | |
| getData | 0.001 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.146 | 0.014 | 0.162 | |
| recipeLoad | 1.614 | 0.103 | 1.731 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.698 | 0.044 | 0.746 | |
| recipeUpdate | 0 | 0 | 0 | |