Qian Liu
| Snapshot Date: 2025-11-05 13:45 -0500 (Wed, 05 Nov 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 2025-11-06 12:00 -0500 (Thu, 06 Nov 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" | 4902 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4638 |
| 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 | | ||||||||
| 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: 1.10.0 |
| 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: 2025-11-06 03:21:39 -0500 (Thu, 06 Nov 2025) |
| EndedAt: 2025-11-06 03:24:23 -0500 (Thu, 06 Nov 2025) |
| EllapsedTime: 164.2 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 4.5.1 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 ‘1.10.0’
* 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 5.776 0.245 6.024
* 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 4.5.1 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...
369f5b157e8920_GRCh38.primary_assembly.genome.fa.1.bt2 added
369f5b49421ba7_GRCh38.primary_assembly.genome.fa.2.bt2 added
369f5b7d62921f_GRCh38.primary_assembly.genome.fa.3.bt2 added
369f5b1a1ae3d3_GRCh38.primary_assembly.genome.fa.4.bt2 added
369f5b49ba1964_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
369f5b22876ab_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
369f5b1ab1f502_outfile.txt added
369f5b73488fef_GRCh37_to_GRCh38.chain added
369f5b152b5081_GRCh37_to_NCBI34.chain added
369f5b99a9b07_GRCh37_to_NCBI35.chain added
369f5b62bd652_GRCh37_to_NCBI36.chain added
369f5b465f6de2_GRCh38_to_GRCh37.chain added
369f5b3d40323c_GRCh38_to_NCBI34.chain added
369f5bb3004a2_GRCh38_to_NCBI35.chain added
369f5b40386476_GRCh38_to_NCBI36.chain added
369f5b70667fe1_NCBI34_to_GRCh37.chain added
369f5b15a2ad48_NCBI34_to_GRCh38.chain added
369f5b51b54a63_NCBI35_to_GRCh37.chain added
369f5b339858ab_NCBI35_to_GRCh38.chain added
369f5b485c0694_NCBI36_to_GRCh37.chain added
369f5b15018d0f_NCBI36_to_GRCh38.chain added
369f5b19f8abe7_GRCm38_to_NCBIM36.chain added
369f5b1190151_GRCm38_to_NCBIM37.chain added
369f5b3187add7_NCBIM36_to_GRCm38.chain added
369f5b67e4fec7_NCBIM37_to_GRCm38.chain added
369f5b349b180f_1000G_omni2.5.b37.vcf.gz added
369f5b6f41abf1_1000G_omni2.5.b37.vcf.gz.tbi added
369f5bdaa8cbd_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
369f5b48e6cbaf_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
369f5b262b721c_1000G_omni2.5.hg38.vcf.gz added
369f5b4cfb9a8_1000G_omni2.5.hg38.vcf.gz.tbi added
369f5b5e6554cf_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
369f5b6f6d8dc3_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
369f5b2324bc7_af-only-gnomad.raw.sites.vcf added
369f5b788038a3_af-only-gnomad.raw.sites.vcf.idx added
369f5b3927a728_Mutect2-exome-panel.vcf.idx added
369f5b45ac273_Mutect2-WGS-panel-b37.vcf added
369f5b13322da5_Mutect2-WGS-panel-b37.vcf.idx added
369f5b2c703717_small_exac_common_3.vcf added
369f5b198612f4_small_exac_common_3.vcf.idx added
369f5b1cccc8ac_1000g_pon.hg38.vcf.gz added
369f5b329c0d69_1000g_pon.hg38.vcf.gz.tbi added
369f5b5fe580d6_af-only-gnomad.hg38.vcf.gz added
369f5b5a0cfae8_af-only-gnomad.hg38.vcf.gz.tbi added
369f5b3dcc120c_small_exac_common_3.hg38.vcf.gz added
369f5b201de54d_small_exac_common_3.hg38.vcf.gz.tbi added
369f5b4a737ac9_gencode.v41.annotation.gtf added
369f5b536ebf54_gencode.v42.annotation.gtf added
369f5b71d32fb0_gencode.vM30.annotation.gtf added
369f5b7e0bd374_gencode.vM31.annotation.gtf added
369f5b1bcac5e8_gencode.v41.transcripts.fa added
369f5b6d4bcc0_gencode.v41.transcripts.fa.fai added
369f5b18047f5c_gencode.v42.transcripts.fa added
369f5b1ce3c739_gencode.v42.transcripts.fa.fai added
369f5b385c6a97_gencode.vM30.pc_transcripts.fa added
369f5b7fe97e23_gencode.vM30.pc_transcripts.fa.fai added
369f5b517edf48_gencode.vM31.pc_transcripts.fa added
369f5b279e1688_gencode.vM31.pc_transcripts.fa.fai added
369f5bd940ae0_GRCh38.primary_assembly.genome.fa.1.ht2 added
369f5b1a65aaf7_GRCh38.primary_assembly.genome.fa.2.ht2 added
369f5b4dc988a4_GRCh38.primary_assembly.genome.fa.3.ht2 added
369f5b1263c488_GRCh38.primary_assembly.genome.fa.4.ht2 added
369f5b78caffc7_GRCh38.primary_assembly.genome.fa.5.ht2 added
369f5b3d371668_GRCh38.primary_assembly.genome.fa.6.ht2 added
369f5b14961050_GRCh38.primary_assembly.genome.fa.7.ht2 added
369f5b714b386a_GRCh38.primary_assembly.genome.fa.8.ht2 added
369f5b765ebd90_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
369f5b18f0d2c3_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
369f5b47d660f_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
369f5b22cef4a7_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
369f5b3276e5b7_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
369f5b214a2ebb_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
369f5b556b0211_GRCh38_full_analysis_set_plus_decoy_hla.fa added
369f5b125c668d_GRCh38.primary_assembly.genome.fa.fai added
369f5b7b5729a3_GRCh38.primary_assembly.genome.fa.amb added
369f5b1337141d_GRCh38.primary_assembly.genome.fa.ann added
369f5b327a4bda_GRCh38.primary_assembly.genome.fa.bwt added
369f5b45caa46d_GRCh38.primary_assembly.genome.fa.pac added
369f5b66a5d371_GRCh38.primary_assembly.genome.fa.sa added
369f5b244d7b8b_GRCh38.primary_assembly.genome.fa added
369f5b43d677e1_hs37d5.fa.fai added
369f5b2709959_hs37d5.fa.amb added
369f5b2b22384b_hs37d5.fa.ann added
369f5b5bdaf73d_hs37d5.fa.bwt added
369f5b1f546092_hs37d5.fa.pac added
369f5b637ea2e2_hs37d5.fa.sa added
369f5b5bc47560_hs37d5.fa added
369f5b70d33fda_complete_ref_lens.bin added
369f5bb1cb96a_ctable.bin added
369f5b69588041_ctg_offsets.bin added
369f5bb38ead2_duplicate_clusters.tsv added
369f5b58e6420e_info.json added
369f5b7bbc44c9_mphf.bin added
369f5b403ea99_pos.bin added
369f5b161d5876_pre_indexing.log added
369f5b10525519_rank.bin added
369f5b754f2303_ref_indexing.log added
369f5bc7c1606_refAccumLengths.bin added
369f5b294327dc_reflengths.bin added
369f5b79cc8912_refseq.bin added
369f5b2f4b0aae_seq.bin added
369f5b5bba0d93_versionInfo.json added
369f5b1b16b7cd_salmon_index added
369f5b4b60cbf_chrLength.txt added
369f5b6e167421_chrName.txt added
369f5b166de170_chrNameLength.txt added
369f5b17ed20dc_chrStart.txt added
369f5b2090bffb_exonGeTrInfo.tab added
369f5b5c3885dd_exonInfo.tab added
369f5b7e92f44d_geneInfo.tab added
369f5b44de3b86_Genome added
369f5b200efdbf_genomeParameters.txt added
369f5b1038da6_Log.out added
369f5b700073d1_SA added
369f5b7be9f4fc_SAindex added
369f5b2057ee38_sjdbInfo.txt added
369f5b537f16b3_sjdbList.fromGTF.out.tab added
369f5b57ae6a5d_sjdbList.out.tab added
369f5b112b2e12_transcriptInfo.tab added
369f5b5e9bd01d_GRCh38.GENCODE.v42_100 added
369f5b4106ea9e_knownGene_hg38.sql added
369f5b1c6418e4_knownGene_hg38.txt added
369f5b3782122c_refGene_hg38.sql added
369f5b3cc32f67_refGene_hg38.txt added
369f5b2068037d_knownGene_mm39.sql added
369f5b4d9f6aa2_knownGene_mm39.txt added
369f5b4d158481_refGene_mm39.sql added
369f5b15b72680_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/RtmpoB2mfY/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
18.121 1.014 19.609
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.776 | 0.245 | 6.024 | |
| dataSearch | 1.082 | 0.010 | 1.092 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.916 | 0.501 | 4.294 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.142 | 0.003 | 0.145 | |
| recipeLoad | 1.320 | 0.137 | 1.458 | |
| recipeMake | 0.001 | 0.000 | 0.001 | |
| recipeSearch | 0.543 | 0.022 | 0.566 | |
| recipeUpdate | 0 | 0 | 0 | |