Qian Liu
| Snapshot Date: 2025-10-06 13:45 -0400 (Mon, 06 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 2025-10-07 12:04 -0400 (Tue, 07 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" | 4853 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4640 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4585 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4584 |
| 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 1757/2341 | 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: /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_1.9.0.tar.gz |
| StartedAt: 2025-10-07 03:30:44 -0400 (Tue, 07 Oct 2025) |
| EndedAt: 2025-10-07 03:33:27 -0400 (Tue, 07 Oct 2025) |
| EllapsedTime: 163.2 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_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘1.9.0’
* 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 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 5.933 0.254 6.19
* 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 ‘1.9.0’ ** 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 (2025-08-23 r88802) -- "Great Square Root"
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...
253fc6668dca1c_GRCh38.primary_assembly.genome.fa.1.bt2 added
253fc6532311c7_GRCh38.primary_assembly.genome.fa.2.bt2 added
253fc632e46b93_GRCh38.primary_assembly.genome.fa.3.bt2 added
253fc649ebf1eb_GRCh38.primary_assembly.genome.fa.4.bt2 added
253fc636bbe2db_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
253fc61c3e664c_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
253fc65b4dfdaf_outfile.txt added
253fc6551d1fe5_GRCh37_to_GRCh38.chain added
253fc66f8e15e_GRCh37_to_NCBI34.chain added
253fc61c0f128_GRCh37_to_NCBI35.chain added
253fc650773105_GRCh37_to_NCBI36.chain added
253fc65178d263_GRCh38_to_GRCh37.chain added
253fc638684c90_GRCh38_to_NCBI34.chain added
253fc65935b2f4_GRCh38_to_NCBI35.chain added
253fc62f6b26a_GRCh38_to_NCBI36.chain added
253fc671b7417d_NCBI34_to_GRCh37.chain added
253fc6164e2399_NCBI34_to_GRCh38.chain added
253fc63bac5d53_NCBI35_to_GRCh37.chain added
253fc614b1f165_NCBI35_to_GRCh38.chain added
253fc67272f0e9_NCBI36_to_GRCh37.chain added
253fc62b1f0cd9_NCBI36_to_GRCh38.chain added
253fc65a7e0fee_GRCm38_to_NCBIM36.chain added
253fc6365af0d0_GRCm38_to_NCBIM37.chain added
253fc63519ddaf_NCBIM36_to_GRCm38.chain added
253fc63bc5e1fa_NCBIM37_to_GRCm38.chain added
253fc638a4e075_1000G_omni2.5.b37.vcf.gz added
253fc65a699869_1000G_omni2.5.b37.vcf.gz.tbi added
253fc657c44b1c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
253fc6417382b6_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
253fc65c50ffbd_1000G_omni2.5.hg38.vcf.gz added
253fc64a24b3af_1000G_omni2.5.hg38.vcf.gz.tbi added
253fc628014cd3_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
253fc62f741184_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
253fc67d091f42_af-only-gnomad.raw.sites.vcf added
253fc671ed3ebe_af-only-gnomad.raw.sites.vcf.idx added
253fc6662ff460_Mutect2-exome-panel.vcf.idx added
253fc61947858e_Mutect2-WGS-panel-b37.vcf added
253fc64d3b3c6d_Mutect2-WGS-panel-b37.vcf.idx added
253fc63b4d1445_small_exac_common_3.vcf added
253fc6204066ec_small_exac_common_3.vcf.idx added
253fc64efc2d96_1000g_pon.hg38.vcf.gz added
253fc6bc4454a_1000g_pon.hg38.vcf.gz.tbi added
253fc671b9394f_af-only-gnomad.hg38.vcf.gz added
253fc67647a26_af-only-gnomad.hg38.vcf.gz.tbi added
253fc664f9f83e_small_exac_common_3.hg38.vcf.gz added
253fc674afebb9_small_exac_common_3.hg38.vcf.gz.tbi added
253fc6791bbba3_gencode.v41.annotation.gtf added
253fc67b481bd8_gencode.v42.annotation.gtf added
253fc6305c490d_gencode.vM30.annotation.gtf added
253fc6dcdad08_gencode.vM31.annotation.gtf added
253fc66dbb0cc1_gencode.v41.transcripts.fa added
253fc65b7b55e6_gencode.v41.transcripts.fa.fai added
253fc6684bbcf6_gencode.v42.transcripts.fa added
253fc62415fd91_gencode.v42.transcripts.fa.fai added
253fc610953395_gencode.vM30.pc_transcripts.fa added
253fc624119ef0_gencode.vM30.pc_transcripts.fa.fai added
253fc65cbade07_gencode.vM31.pc_transcripts.fa added
253fc66afecbfe_gencode.vM31.pc_transcripts.fa.fai added
253fc67bd5ea0d_GRCh38.primary_assembly.genome.fa.1.ht2 added
253fc61e2e60bd_GRCh38.primary_assembly.genome.fa.2.ht2 added
253fc6474fcbbb_GRCh38.primary_assembly.genome.fa.3.ht2 added
253fc645fa9dbc_GRCh38.primary_assembly.genome.fa.4.ht2 added
253fc6462fad90_GRCh38.primary_assembly.genome.fa.5.ht2 added
253fc676c3dd3f_GRCh38.primary_assembly.genome.fa.6.ht2 added
253fc64303bcff_GRCh38.primary_assembly.genome.fa.7.ht2 added
253fc6381cec4e_GRCh38.primary_assembly.genome.fa.8.ht2 added
253fc65cf3d19f_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
253fc65c4b428d_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
253fc655828bc_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
253fc61840e5e4_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
253fc67c8ba97a_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
253fc654545652_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
253fc624052b2f_GRCh38_full_analysis_set_plus_decoy_hla.fa added
253fc66e44e2c9_GRCh38.primary_assembly.genome.fa.fai added
253fc65bb8d078_GRCh38.primary_assembly.genome.fa.amb added
253fc68ff236d_GRCh38.primary_assembly.genome.fa.ann added
253fc662f4ce83_GRCh38.primary_assembly.genome.fa.bwt added
253fc654d48c1b_GRCh38.primary_assembly.genome.fa.pac added
253fc64473f45_GRCh38.primary_assembly.genome.fa.sa added
253fc613511790_GRCh38.primary_assembly.genome.fa added
253fc662a23924_hs37d5.fa.fai added
253fc672024c06_hs37d5.fa.amb added
253fc66ecc6d76_hs37d5.fa.ann added
253fc64aedf61a_hs37d5.fa.bwt added
253fc616184998_hs37d5.fa.pac added
253fc67f61a10b_hs37d5.fa.sa added
253fc66eff950b_hs37d5.fa added
253fc672d3279f_complete_ref_lens.bin added
253fc66a606d09_ctable.bin added
253fc66ad57f18_ctg_offsets.bin added
253fc61101885c_duplicate_clusters.tsv added
253fc631b038c4_info.json added
253fc630d01cd4_mphf.bin added
253fc6573135ed_pos.bin added
253fc628741603_pre_indexing.log added
253fc673d3d9d3_rank.bin added
253fc6f4e223b_ref_indexing.log added
253fc6567e7a3_refAccumLengths.bin added
253fc6501f1c61_reflengths.bin added
253fc614a64af7_refseq.bin added
253fc61da8cd87_seq.bin added
253fc64caac5db_versionInfo.json added
253fc668faa149_salmon_index added
253fc641adf8b6_chrLength.txt added
253fc63aefa8a4_chrName.txt added
253fc644b371c1_chrNameLength.txt added
253fc64aad1c24_chrStart.txt added
253fc61de47727_exonGeTrInfo.tab added
253fc61987fddd_exonInfo.tab added
253fc64ef45b69_geneInfo.tab added
253fc631358eb7_Genome added
253fc67c2a3701_genomeParameters.txt added
253fc640f6a770_Log.out added
253fc62001fc2d_SA added
253fc647182d1b_SAindex added
253fc6570ef108_sjdbInfo.txt added
253fc61f639d38_sjdbList.fromGTF.out.tab added
253fc63617c226_sjdbList.out.tab added
253fc649e218a7_transcriptInfo.tab added
253fc69c40a41_GRCh38.GENCODE.v42_100 added
253fc620ed413e_knownGene_hg38.sql added
253fc65ae3a103_knownGene_hg38.txt added
253fc63b744305_refGene_hg38.sql added
253fc651bd5e13_refGene_hg38.txt added
253fc63214d6f0_knownGene_mm39.sql added
253fc663e85909_knownGene_mm39.txt added
253fc6459137e6_refGene_mm39.sql added
253fc64162f92c_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/RtmpalqvlW/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
17.748 1.058 19.258
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.933 | 0.254 | 6.190 | |
| dataSearch | 1.090 | 0.008 | 1.098 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.621 | 0.104 | 3.781 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.125 | 0.001 | 0.127 | |
| recipeLoad | 1.256 | 0.013 | 1.272 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.541 | 0.008 | 0.550 | |
| recipeUpdate | 0 | 0 | 0 | |