Qian Liu
| Snapshot Date: 2025-11-18 13:40 -0500 (Tue, 18 Nov 2025) |
| 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 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-19 10:12 -0500 (Wed, 19 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4827 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4600 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4564 |
| 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 1748/2325 | 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 | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
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: /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_1.11.0.tar.gz |
| StartedAt: 2025-11-19 03:59:40 -0500 (Wed, 19 Nov 2025) |
| EndedAt: 2025-11-19 04:02:23 -0500 (Wed, 19 Nov 2025) |
| EllapsedTime: 163.2 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_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘1.11.0’
* 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 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 5.729 0.363 6.093
* 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 ‘1.11.0’ ** 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 Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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...
31bbca5bd3d41e_GRCh38.primary_assembly.genome.fa.1.bt2 added
31bbca3a7a77e3_GRCh38.primary_assembly.genome.fa.2.bt2 added
31bbca2e14e51_GRCh38.primary_assembly.genome.fa.3.bt2 added
31bbca73869401_GRCh38.primary_assembly.genome.fa.4.bt2 added
31bbca13ebc697_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
31bbca7d1b7e5d_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
31bbca5303b45b_outfile.txt added
31bbca216d9f39_GRCh37_to_GRCh38.chain added
31bbca6bd2d306_GRCh37_to_NCBI34.chain added
31bbca593cc26_GRCh37_to_NCBI35.chain added
31bbca684dc2d1_GRCh37_to_NCBI36.chain added
31bbca3cf4aacc_GRCh38_to_GRCh37.chain added
31bbca15311bf5_GRCh38_to_NCBI34.chain added
31bbca53e83ba4_GRCh38_to_NCBI35.chain added
31bbca272d7053_GRCh38_to_NCBI36.chain added
31bbca68eddce5_NCBI34_to_GRCh37.chain added
31bbca244fdc2_NCBI34_to_GRCh38.chain added
31bbca41a6e900_NCBI35_to_GRCh37.chain added
31bbca5fa02f91_NCBI35_to_GRCh38.chain added
31bbca32533d43_NCBI36_to_GRCh37.chain added
31bbca3368bdb2_NCBI36_to_GRCh38.chain added
31bbca18f446dc_GRCm38_to_NCBIM36.chain added
31bbca2a410e61_GRCm38_to_NCBIM37.chain added
31bbca47f055f_NCBIM36_to_GRCm38.chain added
31bbcad219f0c_NCBIM37_to_GRCm38.chain added
31bbca1c14c931_1000G_omni2.5.b37.vcf.gz added
31bbca2e01b69b_1000G_omni2.5.b37.vcf.gz.tbi added
31bbca1ecc2462_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
31bbca4ad50a06_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
31bbca559c7e23_1000G_omni2.5.hg38.vcf.gz added
31bbca605b9549_1000G_omni2.5.hg38.vcf.gz.tbi added
31bbca26a8de25_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
31bbca1016f606_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
31bbca633ce39a_af-only-gnomad.raw.sites.vcf added
31bbca1a2f7226_af-only-gnomad.raw.sites.vcf.idx added
31bbca2402bc9d_Mutect2-exome-panel.vcf.idx added
31bbca605861f7_Mutect2-WGS-panel-b37.vcf added
31bbca6d332681_Mutect2-WGS-panel-b37.vcf.idx added
31bbca45705bd6_small_exac_common_3.vcf added
31bbca4c2b34fe_small_exac_common_3.vcf.idx added
31bbca72c6f2a8_1000g_pon.hg38.vcf.gz added
31bbca2dbe1ea7_1000g_pon.hg38.vcf.gz.tbi added
31bbca91fdfca_af-only-gnomad.hg38.vcf.gz added
31bbca7f80e9d_af-only-gnomad.hg38.vcf.gz.tbi added
31bbca1a65a4c_small_exac_common_3.hg38.vcf.gz added
31bbca304d501d_small_exac_common_3.hg38.vcf.gz.tbi added
31bbca70e5eb82_gencode.v41.annotation.gtf added
31bbca3eb580e_gencode.v42.annotation.gtf added
31bbca71f4391d_gencode.vM30.annotation.gtf added
31bbca50861b13_gencode.vM31.annotation.gtf added
31bbca363e9551_gencode.v41.transcripts.fa added
31bbca255cf6cf_gencode.v41.transcripts.fa.fai added
31bbca697a61ef_gencode.v42.transcripts.fa added
31bbca607fa3b3_gencode.v42.transcripts.fa.fai added
31bbca29dbfc2f_gencode.vM30.pc_transcripts.fa added
31bbca769c00fc_gencode.vM30.pc_transcripts.fa.fai added
31bbca7c946ce4_gencode.vM31.pc_transcripts.fa added
31bbca57ddb2ca_gencode.vM31.pc_transcripts.fa.fai added
31bbca1568255e_GRCh38.primary_assembly.genome.fa.1.ht2 added
31bbca476976ea_GRCh38.primary_assembly.genome.fa.2.ht2 added
31bbca2d7a30ed_GRCh38.primary_assembly.genome.fa.3.ht2 added
31bbca75c3baa7_GRCh38.primary_assembly.genome.fa.4.ht2 added
31bbca6e12550f_GRCh38.primary_assembly.genome.fa.5.ht2 added
31bbca3d9126f3_GRCh38.primary_assembly.genome.fa.6.ht2 added
31bbca59009e42_GRCh38.primary_assembly.genome.fa.7.ht2 added
31bbca841c736_GRCh38.primary_assembly.genome.fa.8.ht2 added
31bbca6193e390_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
31bbca39590039_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
31bbca7574edb7_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
31bbca27043f67_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
31bbca5843537_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
31bbca683be05f_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
31bbca54c25e0e_GRCh38_full_analysis_set_plus_decoy_hla.fa added
31bbcaea41501_GRCh38.primary_assembly.genome.fa.fai added
31bbca7033eefc_GRCh38.primary_assembly.genome.fa.amb added
31bbca5668b85a_GRCh38.primary_assembly.genome.fa.ann added
31bbca3ef1651e_GRCh38.primary_assembly.genome.fa.bwt added
31bbca6119da7f_GRCh38.primary_assembly.genome.fa.pac added
31bbca5a541068_GRCh38.primary_assembly.genome.fa.sa added
31bbca30e59e3c_GRCh38.primary_assembly.genome.fa added
31bbca319ff592_hs37d5.fa.fai added
31bbca1092a5ba_hs37d5.fa.amb added
31bbca5642950b_hs37d5.fa.ann added
31bbca1b1a5782_hs37d5.fa.bwt added
31bbca7112496d_hs37d5.fa.pac added
31bbca1e913a_hs37d5.fa.sa added
31bbca11b6587e_hs37d5.fa added
31bbca6da6b651_complete_ref_lens.bin added
31bbca57fc4405_ctable.bin added
31bbca271e7ddc_ctg_offsets.bin added
31bbca35102d3b_duplicate_clusters.tsv added
31bbca57674f2_info.json added
31bbca1ce23883_mphf.bin added
31bbca2322824b_pos.bin added
31bbca43079be6_pre_indexing.log added
31bbca75e2d6c5_rank.bin added
31bbca2b644981_ref_indexing.log added
31bbca249b7f76_refAccumLengths.bin added
31bbca2f3bd6ff_reflengths.bin added
31bbca20d93738_refseq.bin added
31bbca4b9fbedd_seq.bin added
31bbca34c00c36_versionInfo.json added
31bbca9151798_salmon_index added
31bbca20621cec_chrLength.txt added
31bbca43642138_chrName.txt added
31bbca79490694_chrNameLength.txt added
31bbca76cad546_chrStart.txt added
31bbca2558656_exonGeTrInfo.tab added
31bbca5a62e113_exonInfo.tab added
31bbca511ee5af_geneInfo.tab added
31bbca333b2492_Genome added
31bbcac02d6a6_genomeParameters.txt added
31bbca61b18b69_Log.out added
31bbca97db99e_SA added
31bbca271d2e28_SAindex added
31bbca52c3d4d6_sjdbInfo.txt added
31bbca99c4ad8_sjdbList.fromGTF.out.tab added
31bbca38d386a6_sjdbList.out.tab added
31bbca406a8b27_transcriptInfo.tab added
31bbca61988edd_GRCh38.GENCODE.v42_100 added
31bbca5ff20482_knownGene_hg38.sql added
31bbca757ab862_knownGene_hg38.txt added
31bbca670f03d0_refGene_hg38.sql added
31bbca7cd43d05_refGene_hg38.txt added
31bbca189d3aad_knownGene_mm39.sql added
31bbca2a169fb6_knownGene_mm39.txt added
31bbca72b713cb_refGene_mm39.sql added
31bbca4401842e_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/Rtmp8pvs3M/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
17.636 1.124 19.300
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.729 | 0.363 | 6.093 | |
| dataSearch | 1.073 | 0.031 | 1.103 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.599 | 0.152 | 4.056 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.001 | 0.001 | |
| recipeHub-class | 0.129 | 0.002 | 0.132 | |
| recipeLoad | 1.325 | 0.064 | 1.389 | |
| recipeMake | 0.001 | 0.000 | 0.001 | |
| recipeSearch | 0.530 | 0.007 | 0.536 | |
| recipeUpdate | 0 | 0 | 0 | |