Qian Liu
| Snapshot Date: 2026-04-01 13:40 -0400 (Wed, 01 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: 4a5d06b |
| git_last_commit_date: 2025-10-29 11:20:44 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-02 11:35 -0400 (Thu, 02 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.6.0 alpha (2026-03-30 r89742) | 4885 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-03-28 r89739) | 4619 |
| 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 1785/2374 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.11.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| See other builds for ReUseData in R Universe. | ||||||||||||||
|
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: 1.11.0 |
| 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_1.11.0.tar.gz |
| StartedAt: 2026-04-01 21:39:38 -0400 (Wed, 01 Apr 2026) |
| EndedAt: 2026-04-01 21:40:31 -0400 (Wed, 01 Apr 2026) |
| EllapsedTime: 52.6 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_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R version 4.6.0 alpha (2026-03-28 r89739)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-02 01:39:39 UTC
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.11.0’
* 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
* 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-3.23-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/4.6/Resources/library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.11.0’ ** 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 4.6.0 alpha (2026-03-28 r89739)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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...
171e62d38a831_GRCh38.primary_assembly.genome.fa.1.bt2 added
171e662aa4028_GRCh38.primary_assembly.genome.fa.2.bt2 added
171e6175a34b3_GRCh38.primary_assembly.genome.fa.3.bt2 added
171e62339dfbf_GRCh38.primary_assembly.genome.fa.4.bt2 added
171e62c9086aa_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
171e6447919c1_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
171e66a89f105_outfile.txt added
171e662eb5e8_GRCh37_to_GRCh38.chain added
171e664a89583_GRCh37_to_NCBI34.chain added
171e677efff15_GRCh37_to_NCBI35.chain added
171e62d53f937_GRCh37_to_NCBI36.chain added
171e6640ea120_GRCh38_to_GRCh37.chain added
171e67c746f31_GRCh38_to_NCBI34.chain added
171e6403039cc_GRCh38_to_NCBI35.chain added
171e61e22a100_GRCh38_to_NCBI36.chain added
171e673781674_NCBI34_to_GRCh37.chain added
171e6510a54e5_NCBI34_to_GRCh38.chain added
171e67d4baff3_NCBI35_to_GRCh37.chain added
171e6740cbac8_NCBI35_to_GRCh38.chain added
171e66fbadbfd_NCBI36_to_GRCh37.chain added
171e654c0f859_NCBI36_to_GRCh38.chain added
171e648f0c687_GRCm38_to_NCBIM36.chain added
171e63779ee7a_GRCm38_to_NCBIM37.chain added
171e62617a80a_NCBIM36_to_GRCm38.chain added
171e65b193c0f_NCBIM37_to_GRCm38.chain added
171e655b62b82_1000G_omni2.5.b37.vcf.gz added
171e62ae28fc4_1000G_omni2.5.b37.vcf.gz.tbi added
171e64ca2db_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
171e62757d804_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
171e6782702c9_1000G_omni2.5.hg38.vcf.gz added
171e6492817bf_1000G_omni2.5.hg38.vcf.gz.tbi added
171e6672f221e_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
171e64769147e_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
171e643c080d2_af-only-gnomad.raw.sites.vcf added
171e613497dbe_af-only-gnomad.raw.sites.vcf.idx added
171e63dde4ed6_Mutect2-exome-panel.vcf.idx added
171e64e09e355_Mutect2-WGS-panel-b37.vcf added
171e66b2c0979_Mutect2-WGS-panel-b37.vcf.idx added
171e618221de7_small_exac_common_3.vcf added
171e667d93511_small_exac_common_3.vcf.idx added
171e6652b245a_1000g_pon.hg38.vcf.gz added
171e6735fc499_1000g_pon.hg38.vcf.gz.tbi added
171e6146453fc_af-only-gnomad.hg38.vcf.gz added
171e646c5cfd9_af-only-gnomad.hg38.vcf.gz.tbi added
171e664d0d3db_small_exac_common_3.hg38.vcf.gz added
171e64a050292_small_exac_common_3.hg38.vcf.gz.tbi added
171e6eebe535_gencode.v41.annotation.gtf added
171e62115023a_gencode.v42.annotation.gtf added
171e66a453ecd_gencode.vM30.annotation.gtf added
171e6681e3b3c_gencode.vM31.annotation.gtf added
171e618c3158b_gencode.v41.transcripts.fa added
171e62fbb6560_gencode.v41.transcripts.fa.fai added
171e637fc9a1b_gencode.v42.transcripts.fa added
171e628e97f54_gencode.v42.transcripts.fa.fai added
171e679a678c7_gencode.vM30.pc_transcripts.fa added
171e620438f36_gencode.vM30.pc_transcripts.fa.fai added
171e6336f32c6_gencode.vM31.pc_transcripts.fa added
171e6496e7f8b_gencode.vM31.pc_transcripts.fa.fai added
171e67577a456_GRCh38.primary_assembly.genome.fa.1.ht2 added
171e61c6465a_GRCh38.primary_assembly.genome.fa.2.ht2 added
171e634bf9f_GRCh38.primary_assembly.genome.fa.3.ht2 added
171e67105fd4_GRCh38.primary_assembly.genome.fa.4.ht2 added
171e644035aeb_GRCh38.primary_assembly.genome.fa.5.ht2 added
171e638461d2f_GRCh38.primary_assembly.genome.fa.6.ht2 added
171e63261586_GRCh38.primary_assembly.genome.fa.7.ht2 added
171e6394f1207_GRCh38.primary_assembly.genome.fa.8.ht2 added
171e67628a6f5_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
171e666e95b6d_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
171e6627185e3_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
171e6b0d2c93_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
171e6de96c90_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
171e657d66912_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
171e63d8c49cb_GRCh38_full_analysis_set_plus_decoy_hla.fa added
171e64540cdfe_GRCh38.primary_assembly.genome.fa.fai added
171e621940237_GRCh38.primary_assembly.genome.fa.amb added
171e67c1d7a19_GRCh38.primary_assembly.genome.fa.ann added
171e6733b3ef7_GRCh38.primary_assembly.genome.fa.bwt added
171e636a3053b_GRCh38.primary_assembly.genome.fa.pac added
171e68ac8083_GRCh38.primary_assembly.genome.fa.sa added
171e675291ce7_GRCh38.primary_assembly.genome.fa added
171e65e28bdc8_hs37d5.fa.fai added
171e644c3c5c3_hs37d5.fa.amb added
171e610eca87a_hs37d5.fa.ann added
171e62128ea44_hs37d5.fa.bwt added
171e652c275e_hs37d5.fa.pac added
171e615cc8ef9_hs37d5.fa.sa added
171e628be889d_hs37d5.fa added
171e674fb1050_complete_ref_lens.bin added
171e6eec3030_ctable.bin added
171e6344fa6f7_ctg_offsets.bin added
171e6595abcf5_duplicate_clusters.tsv added
171e6542ba6a7_info.json added
171e67dca491c_mphf.bin added
171e66b860dc8_pos.bin added
171e62df2fc9e_pre_indexing.log added
171e62ba700a3_rank.bin added
171e6611ae3b8_ref_indexing.log added
171e62c5c76d6_refAccumLengths.bin added
171e66a7df25a_reflengths.bin added
171e672b22954_refseq.bin added
171e6eb784a0_seq.bin added
171e632642bec_versionInfo.json added
171e64e7faccc_salmon_index added
171e62029ad57_chrLength.txt added
171e610333b40_chrName.txt added
171e61376ef0f_chrNameLength.txt added
171e66548cbc4_chrStart.txt added
171e6e39e4cf_exonGeTrInfo.tab added
171e67adcd954_exonInfo.tab added
171e6394058d0_geneInfo.tab added
171e62f86dd0d_Genome added
171e63f1a98db_genomeParameters.txt added
171e66b29723a_Log.out added
171e66e0a74cc_SA added
171e6707a3584_SAindex added
171e6674fa6cc_sjdbInfo.txt added
171e61e4fd011_sjdbList.fromGTF.out.tab added
171e69e51ba3_sjdbList.out.tab added
171e620796f68_transcriptInfo.tab added
171e64812580_GRCh38.GENCODE.v42_100 added
171e63ac4f8cf_knownGene_hg38.sql added
171e659aafc2d_knownGene_hg38.txt added
171e668921c58_refGene_hg38.sql added
171e650830b0a_refGene_hg38.txt added
171e64b49e6d1_knownGene_mm39.sql added
171e660d0c9f4_knownGene_mm39.txt added
171e62b7ae3d4_refGene_mm39.sql added
171e611038999_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:
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpk4qI5A/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 1 | SKIP 0 | PASS 44 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 44 ]
> Sys.setenv(cachePath = file.path(tempdir(), "cache"))
>
>
>
> proc.time()
user system elapsed
6.841 0.956 8.399
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.070 | 0.308 | 2.399 | |
| dataSearch | 0.358 | 0.020 | 0.384 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.865 | 0.055 | 1.615 | |
| getData | 0.001 | 0.000 | 0.000 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.039 | 0.004 | 0.042 | |
| recipeLoad | 0.415 | 0.034 | 0.450 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.155 | 0.012 | 0.166 | |
| recipeUpdate | 0 | 0 | 0 | |