Qian Liu
| Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 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 2025-10-18 12:05 -0400 (Sat, 18 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: 2025-10-18 00:54:28 -0400 (Sat, 18 Oct 2025) |
| EndedAt: 2025-10-18 00:57:00 -0400 (Sat, 18 Oct 2025) |
| EllapsedTime: 151.6 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 7.449 0.924 8.532
* 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...
22fb5ebdb23c_GRCh38.primary_assembly.genome.fa.1.bt2 added
22fb7800b1bb_GRCh38.primary_assembly.genome.fa.2.bt2 added
22fb7594a989_GRCh38.primary_assembly.genome.fa.3.bt2 added
22fb73069dad_GRCh38.primary_assembly.genome.fa.4.bt2 added
22fb375a03da_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
22fb76b2f999_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
22fb6020e8b0_outfile.txt added
22fb108cac1e_GRCh37_to_GRCh38.chain added
22fb377ee0f_GRCh37_to_NCBI34.chain added
22fb36ae1c90_GRCh37_to_NCBI35.chain added
22fb60d54dfb_GRCh37_to_NCBI36.chain added
22fb53f2cb67_GRCh38_to_GRCh37.chain added
22fb6908023f_GRCh38_to_NCBI34.chain added
22fbccbabf8_GRCh38_to_NCBI35.chain added
22fbf872d58_GRCh38_to_NCBI36.chain added
22fb73b1f45e_NCBI34_to_GRCh37.chain added
22fb282282a9_NCBI34_to_GRCh38.chain added
22fb71b039d4_NCBI35_to_GRCh37.chain added
22fb68a4c79b_NCBI35_to_GRCh38.chain added
22fb1a2cc6c9_NCBI36_to_GRCh37.chain added
22fb71aec38b_NCBI36_to_GRCh38.chain added
22fb8a814fc_GRCm38_to_NCBIM36.chain added
22fb52f9b0d4_GRCm38_to_NCBIM37.chain added
22fb6c858db_NCBIM36_to_GRCm38.chain added
22fb4b419557_NCBIM37_to_GRCm38.chain added
22fb3eb3a95a_1000G_omni2.5.b37.vcf.gz added
22fb53373df_1000G_omni2.5.b37.vcf.gz.tbi added
22fb74fc3823_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
22fb5ac9bdd5_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
22fb72ce1983_1000G_omni2.5.hg38.vcf.gz added
22fb38ed2257_1000G_omni2.5.hg38.vcf.gz.tbi added
22fb58699af3_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
22fb7d3bf4dd_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
22fb6b491966_af-only-gnomad.raw.sites.vcf added
22fbc22ae91_af-only-gnomad.raw.sites.vcf.idx added
22fb38f2b7d0_Mutect2-exome-panel.vcf.idx added
22fb4701d5e5_Mutect2-WGS-panel-b37.vcf added
22fb4981d1ce_Mutect2-WGS-panel-b37.vcf.idx added
22fb69f55115_small_exac_common_3.vcf added
22fb689e700b_small_exac_common_3.vcf.idx added
22fb79ce17d5_1000g_pon.hg38.vcf.gz added
22fb497edf6c_1000g_pon.hg38.vcf.gz.tbi added
22fb287e5126_af-only-gnomad.hg38.vcf.gz added
22fb7d01aa8e_af-only-gnomad.hg38.vcf.gz.tbi added
22fb786490bf_small_exac_common_3.hg38.vcf.gz added
22fb125b2959_small_exac_common_3.hg38.vcf.gz.tbi added
22fb1ef79b79_gencode.v41.annotation.gtf added
22fb120034d1_gencode.v42.annotation.gtf added
22fb4b8b8e92_gencode.vM30.annotation.gtf added
22fb373d39fd_gencode.vM31.annotation.gtf added
22fb14aa2d60_gencode.v41.transcripts.fa added
22fb30890439_gencode.v41.transcripts.fa.fai added
22fb73745313_gencode.v42.transcripts.fa added
22fb59fa3f9c_gencode.v42.transcripts.fa.fai added
22fb3c6648ea_gencode.vM30.pc_transcripts.fa added
22fb5f3d19a0_gencode.vM30.pc_transcripts.fa.fai added
22fb245d8839_gencode.vM31.pc_transcripts.fa added
22fb789a68d5_gencode.vM31.pc_transcripts.fa.fai added
22fb6158b5ce_GRCh38.primary_assembly.genome.fa.1.ht2 added
22fb7081950_GRCh38.primary_assembly.genome.fa.2.ht2 added
22fb24b5d6cb_GRCh38.primary_assembly.genome.fa.3.ht2 added
22fb1e28bc41_GRCh38.primary_assembly.genome.fa.4.ht2 added
22fb45f5edf_GRCh38.primary_assembly.genome.fa.5.ht2 added
22fb114d84b7_GRCh38.primary_assembly.genome.fa.6.ht2 added
22fb78441340_GRCh38.primary_assembly.genome.fa.7.ht2 added
22fb3d4c0c6f_GRCh38.primary_assembly.genome.fa.8.ht2 added
22fb4bc46ad9_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
22fb4c42f36b_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
22fb3f7b1cea_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
22fb2ba76735_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
22fb7b68def6_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
22fb220627c6_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
22fb421d499d_GRCh38_full_analysis_set_plus_decoy_hla.fa added
22fb10cc0454_GRCh38.primary_assembly.genome.fa.fai added
22fb42302f69_GRCh38.primary_assembly.genome.fa.amb added
22fb6978b871_GRCh38.primary_assembly.genome.fa.ann added
22fb749538cf_GRCh38.primary_assembly.genome.fa.bwt added
22fb70c4d9d4_GRCh38.primary_assembly.genome.fa.pac added
22fbbb92723_GRCh38.primary_assembly.genome.fa.sa added
22fb28b870d8_GRCh38.primary_assembly.genome.fa added
22fb64f889ca_hs37d5.fa.fai added
22fb791e608f_hs37d5.fa.amb added
22fb39558a68_hs37d5.fa.ann added
22fb1ef1cf40_hs37d5.fa.bwt added
22fb155d829f_hs37d5.fa.pac added
22fb2e2a9fae_hs37d5.fa.sa added
22fb7059702f_hs37d5.fa added
22fb7fd45748_complete_ref_lens.bin added
22fb4dae7988_ctable.bin added
22fb79acf78f_ctg_offsets.bin added
22fb4ab10bb1_duplicate_clusters.tsv added
22fb2d76b7c6_info.json added
22fb4d1b3f7b_mphf.bin added
22fb37e4cbc9_pos.bin added
22fbdff15ca_pre_indexing.log added
22fb65ef87f3_rank.bin added
22fb50c696cd_ref_indexing.log added
22fb1dd69629_refAccumLengths.bin added
22fb731c6d0c_reflengths.bin added
22fb4f3b69de_refseq.bin added
22fb45a39675_seq.bin added
22fb76eaff0a_versionInfo.json added
22fb3e0e2684_salmon_index added
22fb1302c3f0_chrLength.txt added
22fb1a8dcb50_chrName.txt added
22fb531efece_chrNameLength.txt added
22fb17eab104_chrStart.txt added
22fb310b89e0_exonGeTrInfo.tab added
22fb6c88ea47_exonInfo.tab added
22fb10cd12fc_geneInfo.tab added
22fb7996702_Genome added
22fb6839b833_genomeParameters.txt added
22fb256c51ba_Log.out added
22fb6a699d87_SA added
22fb3be540a5_SAindex added
22fb47f72f5b_sjdbInfo.txt added
22fb35462446_sjdbList.fromGTF.out.tab added
22fbff78afd_sjdbList.out.tab added
22fb44c5f03b_transcriptInfo.tab added
22fb1f1ed4c3_GRCh38.GENCODE.v42_100 added
22fb21225e2b_knownGene_hg38.sql added
22fb57546a0b_knownGene_hg38.txt added
22fb66fe24f7_refGene_hg38.sql added
22fb372d08f4_refGene_hg38.txt added
22fb6da6e778_knownGene_mm39.sql added
22fb68a6af85_knownGene_mm39.txt added
22fb174d7a70_refGene_mm39.sql added
22fb5fa15b03_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/RtmpZA0qfi/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
22.580 2.583 26.320
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.449 | 0.924 | 8.532 | |
| dataSearch | 1.282 | 0.059 | 1.354 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.921 | 0.177 | 4.151 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.157 | 0.015 | 0.175 | |
| recipeLoad | 1.626 | 0.115 | 1.764 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.677 | 0.047 | 0.732 | |
| recipeUpdate | 0 | 0 | 0 | |