Qian Liu
| Snapshot Date: 2025-12-18 13:45 -0500 (Thu, 18 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_22 |
| git_last_commit: 2d4066b |
| git_last_commit_date: 2025-10-29 11:20:44 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-22 12:03 -0500 (Mon, 22 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4883 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 1773/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.10.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 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: 1.10.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReUseData_1.10.0.tar.gz |
| StartedAt: 2025-12-19 03:07:42 -0500 (Fri, 19 Dec 2025) |
| EndedAt: 2025-12-19 03:10:27 -0500 (Fri, 19 Dec 2025) |
| EllapsedTime: 165.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReUseData_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.10.0’
* 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 5.956 0.225 6.184
getCloudData 2.652 0.214 5.390
* 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-3.22-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.10.0’ ** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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...
3d3cab4d912301_GRCh38.primary_assembly.genome.fa.1.bt2 added
3d3cab4c1a589f_GRCh38.primary_assembly.genome.fa.2.bt2 added
3d3cab5ba445b_GRCh38.primary_assembly.genome.fa.3.bt2 added
3d3cab682eb650_GRCh38.primary_assembly.genome.fa.4.bt2 added
3d3cabe9d35_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3d3cab6a50169c_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3d3cab55706987_outfile.txt added
3d3cab7ff76ddc_GRCh37_to_GRCh38.chain added
3d3cab46b5aab8_GRCh37_to_NCBI34.chain added
3d3cab7ef1b88e_GRCh37_to_NCBI35.chain added
3d3cab2067b54b_GRCh37_to_NCBI36.chain added
3d3cab62fc42be_GRCh38_to_GRCh37.chain added
3d3cab7f1a12e2_GRCh38_to_NCBI34.chain added
3d3cab71b69958_GRCh38_to_NCBI35.chain added
3d3cab5d5b8488_GRCh38_to_NCBI36.chain added
3d3cab40692a3a_NCBI34_to_GRCh37.chain added
3d3cab31e82d2e_NCBI34_to_GRCh38.chain added
3d3cab1e56a2e1_NCBI35_to_GRCh37.chain added
3d3cab53ddd04a_NCBI35_to_GRCh38.chain added
3d3cab55477ca3_NCBI36_to_GRCh37.chain added
3d3cab60afc2f_NCBI36_to_GRCh38.chain added
3d3cab79b3b46c_GRCm38_to_NCBIM36.chain added
3d3cab34a00ca_GRCm38_to_NCBIM37.chain added
3d3cab792c6386_NCBIM36_to_GRCm38.chain added
3d3cab226b9f51_NCBIM37_to_GRCm38.chain added
3d3cab6ba886e9_1000G_omni2.5.b37.vcf.gz added
3d3cab4d1bf5e0_1000G_omni2.5.b37.vcf.gz.tbi added
3d3cab3613a79d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3d3cab42eeb378_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3d3cab4ce716a8_1000G_omni2.5.hg38.vcf.gz added
3d3cab1c64ed3d_1000G_omni2.5.hg38.vcf.gz.tbi added
3d3cab107fd679_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3d3cab19016f47_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3d3cab221f3198_af-only-gnomad.raw.sites.vcf added
3d3cab78ae8cc9_af-only-gnomad.raw.sites.vcf.idx added
3d3cab19100c7c_Mutect2-exome-panel.vcf.idx added
3d3cabc6f4834_Mutect2-WGS-panel-b37.vcf added
3d3cab4e1ef650_Mutect2-WGS-panel-b37.vcf.idx added
3d3cab19077a58_small_exac_common_3.vcf added
3d3cab5324f2ed_small_exac_common_3.vcf.idx added
3d3cab4d10aede_1000g_pon.hg38.vcf.gz added
3d3cab396f2fa3_1000g_pon.hg38.vcf.gz.tbi added
3d3cab362135ab_af-only-gnomad.hg38.vcf.gz added
3d3cab4c2ac1c1_af-only-gnomad.hg38.vcf.gz.tbi added
3d3cab2b25c8fc_small_exac_common_3.hg38.vcf.gz added
3d3cab137cba34_small_exac_common_3.hg38.vcf.gz.tbi added
3d3cabc93ebfb_gencode.v41.annotation.gtf added
3d3cab5d0df62a_gencode.v42.annotation.gtf added
3d3cab31d35d15_gencode.vM30.annotation.gtf added
3d3cab6071bc45_gencode.vM31.annotation.gtf added
3d3cab325572cd_gencode.v41.transcripts.fa added
3d3cab37de5944_gencode.v41.transcripts.fa.fai added
3d3cab5a2570b1_gencode.v42.transcripts.fa added
3d3cab359f7397_gencode.v42.transcripts.fa.fai added
3d3cab310abccb_gencode.vM30.pc_transcripts.fa added
3d3cab7c911002_gencode.vM30.pc_transcripts.fa.fai added
3d3cab2147fa80_gencode.vM31.pc_transcripts.fa added
3d3cab7e26b2ab_gencode.vM31.pc_transcripts.fa.fai added
3d3cab32a4b7a0_GRCh38.primary_assembly.genome.fa.1.ht2 added
3d3cab6436adf8_GRCh38.primary_assembly.genome.fa.2.ht2 added
3d3cab4b0dc954_GRCh38.primary_assembly.genome.fa.3.ht2 added
3d3cab4f09a4dd_GRCh38.primary_assembly.genome.fa.4.ht2 added
3d3cab74b68472_GRCh38.primary_assembly.genome.fa.5.ht2 added
3d3cab640f389b_GRCh38.primary_assembly.genome.fa.6.ht2 added
3d3cab7128d675_GRCh38.primary_assembly.genome.fa.7.ht2 added
3d3cab6d65113b_GRCh38.primary_assembly.genome.fa.8.ht2 added
3d3cab7d1f4518_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3d3cab7d981eaa_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3d3cab3b84078c_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3d3cab1626bf70_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3d3cab50bd1197_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3d3cab894b66a_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3d3cab4f95ef14_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3d3cab6de4742_GRCh38.primary_assembly.genome.fa.fai added
3d3cab54bf782b_GRCh38.primary_assembly.genome.fa.amb added
3d3cab7abbb810_GRCh38.primary_assembly.genome.fa.ann added
3d3cab1a5b0176_GRCh38.primary_assembly.genome.fa.bwt added
3d3cab61536426_GRCh38.primary_assembly.genome.fa.pac added
3d3cab57c9ae3a_GRCh38.primary_assembly.genome.fa.sa added
3d3cab4c2e5e8c_GRCh38.primary_assembly.genome.fa added
3d3cab41c5206b_hs37d5.fa.fai added
3d3caba1f2107_hs37d5.fa.amb added
3d3cab40cb7d0_hs37d5.fa.ann added
3d3cab1bea911c_hs37d5.fa.bwt added
3d3cab3fbe949e_hs37d5.fa.pac added
3d3cab3517749b_hs37d5.fa.sa added
3d3cab187ba11f_hs37d5.fa added
3d3cab61068f1e_complete_ref_lens.bin added
3d3cab333e2747_ctable.bin added
3d3cab4b2058bf_ctg_offsets.bin added
3d3cab453d3d17_duplicate_clusters.tsv added
3d3cab7e4bf09b_info.json added
3d3cab1a29fd9c_mphf.bin added
3d3cab39f3c189_pos.bin added
3d3cab625b2936_pre_indexing.log added
3d3cabb52d411_rank.bin added
3d3cab2758d2c4_ref_indexing.log added
3d3cab5f7a6e4e_refAccumLengths.bin added
3d3cab8eaf2bb_reflengths.bin added
3d3cab62dcda50_refseq.bin added
3d3cab75a12dbf_seq.bin added
3d3cab59a80452_versionInfo.json added
3d3cab6b7190bb_salmon_index added
3d3cab45371cd3_chrLength.txt added
3d3cab60864b95_chrName.txt added
3d3cab403108e6_chrNameLength.txt added
3d3cab3ff2d4e3_chrStart.txt added
3d3cab7ae14d0b_exonGeTrInfo.tab added
3d3cab21846d0d_exonInfo.tab added
3d3cab17bc831d_geneInfo.tab added
3d3cab470fab97_Genome added
3d3cab63498d78_genomeParameters.txt added
3d3cab21dba424_Log.out added
3d3cab4b1c6368_SA added
3d3cab7f341e95_SAindex added
3d3cab619a38c2_sjdbInfo.txt added
3d3cab33d803_sjdbList.fromGTF.out.tab added
3d3cab17afbfb4_sjdbList.out.tab added
3d3cab42a0c7e0_transcriptInfo.tab added
3d3cab3371ff4a_GRCh38.GENCODE.v42_100 added
3d3cab62d01873_knownGene_hg38.sql added
3d3cab7de04f7_knownGene_hg38.txt added
3d3cab31bdefe5_refGene_hg38.sql added
3d3cab7cfa160f_refGene_hg38.txt added
3d3cab41d1c680_knownGene_mm39.sql added
3d3cab1419191c_knownGene_mm39.txt added
3d3cab84cea20_refGene_mm39.sql added
3d3cab692a9945_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/RtmpsF9gmF/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
17.784 0.951 19.248
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.956 | 0.225 | 6.184 | |
| dataSearch | 1.094 | 0.006 | 1.100 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.652 | 0.214 | 5.390 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.122 | 0.003 | 0.125 | |
| recipeLoad | 1.284 | 0.056 | 1.341 | |
| recipeMake | 0.001 | 0.000 | 0.001 | |
| recipeSearch | 0.544 | 0.016 | 0.560 | |
| recipeUpdate | 0 | 0 | 0 | |