Qian Liu
| Snapshot Date: 2026-04-28 14:14 -0400 (Tue, 28 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_23 |
| git_last_commit: bb3489b |
| git_last_commit_date: 2026-04-28 08:59:39 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-29 10:15 -0400 (Wed, 29 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4988 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There" | 4694 |
| 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 1812/2415 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.12.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.4 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: 1.12.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ReUseData_1.12.0.tar.gz |
| StartedAt: 2026-04-29 04:15:10 -0400 (Wed, 29 Apr 2026) |
| EndedAt: 2026-04-29 04:17:58 -0400 (Wed, 29 Apr 2026) |
| EllapsedTime: 168.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ReUseData_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-29 08:15:10 UTC
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.12.0’
* 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 loading without being on the library search path ... 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 6.165 0.409 6.579
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.12.0’ ** 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 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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...
26b4ce7cc58867_GRCh38.primary_assembly.genome.fa.1.bt2 added
26b4ce19a2d734_GRCh38.primary_assembly.genome.fa.2.bt2 added
26b4ce1af63509_GRCh38.primary_assembly.genome.fa.3.bt2 added
26b4ce630243bc_GRCh38.primary_assembly.genome.fa.4.bt2 added
26b4ce402e6c27_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
26b4ce39e5641_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
26b4ce5ee23887_outfile.txt added
26b4ce2ec4f443_GRCh37_to_GRCh38.chain added
26b4ce5584840b_GRCh37_to_NCBI34.chain added
26b4ce5860385c_GRCh37_to_NCBI35.chain added
26b4ce1d8b2c21_GRCh37_to_NCBI36.chain added
26b4ce1b72feb6_GRCh38_to_GRCh37.chain added
26b4ce3bb6b925_GRCh38_to_NCBI34.chain added
26b4ce68dfadbb_GRCh38_to_NCBI35.chain added
26b4ce15d7fa7f_GRCh38_to_NCBI36.chain added
26b4ce402abf06_NCBI34_to_GRCh37.chain added
26b4ce3ffbe97d_NCBI34_to_GRCh38.chain added
26b4ce17702a7c_NCBI35_to_GRCh37.chain added
26b4ce3b37bc7f_NCBI35_to_GRCh38.chain added
26b4ce686417f4_NCBI36_to_GRCh37.chain added
26b4ce1453333b_NCBI36_to_GRCh38.chain added
26b4ce111bc62_GRCm38_to_NCBIM36.chain added
26b4ce44446531_GRCm38_to_NCBIM37.chain added
26b4ce4cd709fd_NCBIM36_to_GRCm38.chain added
26b4ce734fd9ea_NCBIM37_to_GRCm38.chain added
26b4ce6342a7a0_1000G_omni2.5.b37.vcf.gz added
26b4ce3e333a75_1000G_omni2.5.b37.vcf.gz.tbi added
26b4ce344fe2f5_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
26b4ce392423c9_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
26b4ce67bd8347_1000G_omni2.5.hg38.vcf.gz added
26b4ce47c78f76_1000G_omni2.5.hg38.vcf.gz.tbi added
26b4ce35e9ac30_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
26b4ce1605a7b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
26b4ce62bdc480_af-only-gnomad.raw.sites.vcf added
26b4ce18ebefed_af-only-gnomad.raw.sites.vcf.idx added
26b4ce418ec6a2_Mutect2-exome-panel.vcf.idx added
26b4ce665c1ac1_Mutect2-WGS-panel-b37.vcf added
26b4ce77ce2874_Mutect2-WGS-panel-b37.vcf.idx added
26b4ce7053bae5_small_exac_common_3.vcf added
26b4ce3be09ecc_small_exac_common_3.vcf.idx added
26b4ce502e60d0_1000g_pon.hg38.vcf.gz added
26b4ceddee706_1000g_pon.hg38.vcf.gz.tbi added
26b4ce57539d82_af-only-gnomad.hg38.vcf.gz added
26b4cebe519f6_af-only-gnomad.hg38.vcf.gz.tbi added
26b4ce76be94c1_small_exac_common_3.hg38.vcf.gz added
26b4ce6d2b9802_small_exac_common_3.hg38.vcf.gz.tbi added
26b4ce4c0fd8fc_gencode.v41.annotation.gtf added
26b4ce36ba7e3f_gencode.v42.annotation.gtf added
26b4ce49bc27e_gencode.vM30.annotation.gtf added
26b4ce747957c_gencode.vM31.annotation.gtf added
26b4ce1f1e9633_gencode.v41.transcripts.fa added
26b4ce18eef5b9_gencode.v41.transcripts.fa.fai added
26b4ce85951de_gencode.v42.transcripts.fa added
26b4ce6362fb65_gencode.v42.transcripts.fa.fai added
26b4ce65c5ffb7_gencode.vM30.pc_transcripts.fa added
26b4ce7ba92bc8_gencode.vM30.pc_transcripts.fa.fai added
26b4ce46a5a305_gencode.vM31.pc_transcripts.fa added
26b4ce23f93a2c_gencode.vM31.pc_transcripts.fa.fai added
26b4ce2ff90ebd_GRCh38.primary_assembly.genome.fa.1.ht2 added
26b4ce7fc9c6ce_GRCh38.primary_assembly.genome.fa.2.ht2 added
26b4cebb6bd73_GRCh38.primary_assembly.genome.fa.3.ht2 added
26b4ce77c09e34_GRCh38.primary_assembly.genome.fa.4.ht2 added
26b4ce35b372ff_GRCh38.primary_assembly.genome.fa.5.ht2 added
26b4ced1717ef_GRCh38.primary_assembly.genome.fa.6.ht2 added
26b4ce5a7e62b4_GRCh38.primary_assembly.genome.fa.7.ht2 added
26b4ce4e9f62ec_GRCh38.primary_assembly.genome.fa.8.ht2 added
26b4ce4ea5de91_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
26b4ce40da7d75_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
26b4ce466d8b60_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
26b4ce3ef99977_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
26b4ce7cbb1c42_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
26b4ce169bec30_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
26b4ce4cd8807d_GRCh38_full_analysis_set_plus_decoy_hla.fa added
26b4ce540eb9c4_GRCh38.primary_assembly.genome.fa.fai added
26b4ce22810626_GRCh38.primary_assembly.genome.fa.amb added
26b4ce4397153f_GRCh38.primary_assembly.genome.fa.ann added
26b4ce413a51c6_GRCh38.primary_assembly.genome.fa.bwt added
26b4ce6e90df23_GRCh38.primary_assembly.genome.fa.pac added
26b4ce7a51937e_GRCh38.primary_assembly.genome.fa.sa added
26b4ce45d61444_GRCh38.primary_assembly.genome.fa added
26b4ce75d8749f_hs37d5.fa.fai added
26b4ce197029b1_hs37d5.fa.amb added
26b4ce5ec509fe_hs37d5.fa.ann added
26b4ce7e31c67d_hs37d5.fa.bwt added
26b4ce7cd32516_hs37d5.fa.pac added
26b4ce448b09b5_hs37d5.fa.sa added
26b4ce79daf246_hs37d5.fa added
26b4ce4378c81c_complete_ref_lens.bin added
26b4ce688443e1_ctable.bin added
26b4ce29d40103_ctg_offsets.bin added
26b4ce43428eea_duplicate_clusters.tsv added
26b4ce743b0155_info.json added
26b4ce21949f37_mphf.bin added
26b4ce78f601e9_pos.bin added
26b4ce1521944_pre_indexing.log added
26b4ce7c1301eb_rank.bin added
26b4ce479564d5_ref_indexing.log added
26b4ce4ff7f7d5_refAccumLengths.bin added
26b4ce3ced7f61_reflengths.bin added
26b4cee02f035_refseq.bin added
26b4ceef1914c_seq.bin added
26b4ce39a89ba3_versionInfo.json added
26b4ce249edc66_salmon_index added
26b4ce5bca11ca_chrLength.txt added
26b4cedb75567_chrName.txt added
26b4ce471fe28c_chrNameLength.txt added
26b4ce1f612709_chrStart.txt added
26b4ce4ef1a72e_exonGeTrInfo.tab added
26b4ce35b0c1af_exonInfo.tab added
26b4ce19b2ba87_geneInfo.tab added
26b4ce14c7bb72_Genome added
26b4ce2b89364e_genomeParameters.txt added
26b4ce3322e438_Log.out added
26b4ce738cc570_SA added
26b4ce29bafccc_SAindex added
26b4ce2ff6094f_sjdbInfo.txt added
26b4ce3817cf25_sjdbList.fromGTF.out.tab added
26b4ce2395ef12_sjdbList.out.tab added
26b4ce736ed16b_transcriptInfo.tab added
26b4ce209c1307_GRCh38.GENCODE.v42_100 added
26b4ce4d69f015_knownGene_hg38.sql added
26b4ce36b16055_knownGene_hg38.txt added
26b4ce14d7145c_refGene_hg38.sql added
26b4ce6efe8f4d_refGene_hg38.txt added
26b4ce2fa7623f_knownGene_mm39.sql added
26b4ce16292da0_knownGene_mm39.txt added
26b4ce6b119138_refGene_mm39.sql added
26b4ce773cc714_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/RtmpvGdwvp/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
18.967 1.835 21.663
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.165 | 0.409 | 6.579 | |
| dataSearch | 1.161 | 0.034 | 1.200 | |
| dataUpdate | 0.000 | 0.001 | 0.001 | |
| getCloudData | 2.818 | 0.139 | 3.595 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.119 | 0.004 | 0.122 | |
| recipeLoad | 1.264 | 0.057 | 1.321 | |
| recipeMake | 0.001 | 0.000 | 0.001 | |
| recipeSearch | 0.535 | 0.012 | 0.547 | |
| recipeUpdate | 0 | 0 | 0 | |