Qian Liu
| Snapshot Date: 2026-01-27 13:40 -0500 (Tue, 27 Jan 2026) |
| 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 Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-28 11:32 -0500 (Wed, 28 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4815 |
| 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 1766/2347 | 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 | | ||||||||
|
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: 2026-01-28 03:15:56 -0500 (Wed, 28 Jan 2026) |
| EndedAt: 2026-01-28 03:18:41 -0500 (Wed, 28 Jan 2026) |
| EllapsedTime: 164.3 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) (2026-01-15 r89304)
* 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 6.01 0.384 6.396
* 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) (2026-01-15 r89304) -- "Unsuffered Consequences"
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...
22350d7f4f79fb_GRCh38.primary_assembly.genome.fa.1.bt2 added
22350d7c83e5a8_GRCh38.primary_assembly.genome.fa.2.bt2 added
22350d37dc75d2_GRCh38.primary_assembly.genome.fa.3.bt2 added
22350d1afb6fb7_GRCh38.primary_assembly.genome.fa.4.bt2 added
22350df90b735_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
22350d1564eeb2_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
22350d4535226e_outfile.txt added
22350d56fe50f9_GRCh37_to_GRCh38.chain added
22350d315668ac_GRCh37_to_NCBI34.chain added
22350d1f2d54de_GRCh37_to_NCBI35.chain added
22350d55e9deb6_GRCh37_to_NCBI36.chain added
22350d47b748b_GRCh38_to_GRCh37.chain added
22350d2d5b166b_GRCh38_to_NCBI34.chain added
22350d3f5ec4fa_GRCh38_to_NCBI35.chain added
22350d215de5cc_GRCh38_to_NCBI36.chain added
22350d2b1e904a_NCBI34_to_GRCh37.chain added
22350d11623ff1_NCBI34_to_GRCh38.chain added
22350d69a15316_NCBI35_to_GRCh37.chain added
22350d5447dbb3_NCBI35_to_GRCh38.chain added
22350dfdfc87b_NCBI36_to_GRCh37.chain added
22350d768c36ef_NCBI36_to_GRCh38.chain added
22350d42b4844_GRCm38_to_NCBIM36.chain added
22350d31a43b09_GRCm38_to_NCBIM37.chain added
22350d83bb0dd_NCBIM36_to_GRCm38.chain added
22350d3e90068a_NCBIM37_to_GRCm38.chain added
22350d7acfb6e1_1000G_omni2.5.b37.vcf.gz added
22350d3954b915_1000G_omni2.5.b37.vcf.gz.tbi added
22350d3606f48e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
22350d47a10fe5_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
22350d110a0b1a_1000G_omni2.5.hg38.vcf.gz added
22350d3e743181_1000G_omni2.5.hg38.vcf.gz.tbi added
22350d46f089e0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
22350dd8df0c2_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
22350d7650a753_af-only-gnomad.raw.sites.vcf added
22350d61ebf997_af-only-gnomad.raw.sites.vcf.idx added
22350d1d1ea7f8_Mutect2-exome-panel.vcf.idx added
22350dbb59605_Mutect2-WGS-panel-b37.vcf added
22350d27211c05_Mutect2-WGS-panel-b37.vcf.idx added
22350d741cf8f1_small_exac_common_3.vcf added
22350d3d0bfeb1_small_exac_common_3.vcf.idx added
22350d464e70e3_1000g_pon.hg38.vcf.gz added
22350d4a06d7a7_1000g_pon.hg38.vcf.gz.tbi added
22350d4187733c_af-only-gnomad.hg38.vcf.gz added
22350d73a9874e_af-only-gnomad.hg38.vcf.gz.tbi added
22350d9659ca2_small_exac_common_3.hg38.vcf.gz added
22350d62e55908_small_exac_common_3.hg38.vcf.gz.tbi added
22350d1ec81798_gencode.v41.annotation.gtf added
22350d1ac7dc93_gencode.v42.annotation.gtf added
22350d4c86ac1e_gencode.vM30.annotation.gtf added
22350d730ff34c_gencode.vM31.annotation.gtf added
22350d2aa7a50e_gencode.v41.transcripts.fa added
22350d4312e30e_gencode.v41.transcripts.fa.fai added
22350d773b3b90_gencode.v42.transcripts.fa added
22350d5c4be017_gencode.v42.transcripts.fa.fai added
22350d4b4e93eb_gencode.vM30.pc_transcripts.fa added
22350d35cb421a_gencode.vM30.pc_transcripts.fa.fai added
22350d571b96f8_gencode.vM31.pc_transcripts.fa added
22350d4a34d00_gencode.vM31.pc_transcripts.fa.fai added
22350d6bd236a8_GRCh38.primary_assembly.genome.fa.1.ht2 added
22350d1ebca6dd_GRCh38.primary_assembly.genome.fa.2.ht2 added
22350d15ad581a_GRCh38.primary_assembly.genome.fa.3.ht2 added
22350d2a466829_GRCh38.primary_assembly.genome.fa.4.ht2 added
22350d65ad30bd_GRCh38.primary_assembly.genome.fa.5.ht2 added
22350d233b48dc_GRCh38.primary_assembly.genome.fa.6.ht2 added
22350d20970f7c_GRCh38.primary_assembly.genome.fa.7.ht2 added
22350d47992a54_GRCh38.primary_assembly.genome.fa.8.ht2 added
22350d4059f0d4_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
22350d2c4ca582_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
22350d6eba4659_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
22350d3476e9c6_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
22350d6958a433_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
22350d3508b73d_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
22350d7e7dc16d_GRCh38_full_analysis_set_plus_decoy_hla.fa added
22350d2ae01770_GRCh38.primary_assembly.genome.fa.fai added
22350d28b23e8b_GRCh38.primary_assembly.genome.fa.amb added
22350d7e35e0f_GRCh38.primary_assembly.genome.fa.ann added
22350ddc57078_GRCh38.primary_assembly.genome.fa.bwt added
22350d477a5624_GRCh38.primary_assembly.genome.fa.pac added
22350d22ab3aa2_GRCh38.primary_assembly.genome.fa.sa added
22350d5a4c1c97_GRCh38.primary_assembly.genome.fa added
22350d3a8a4970_hs37d5.fa.fai added
22350d4d52dfb0_hs37d5.fa.amb added
22350d1d5effa5_hs37d5.fa.ann added
22350d31c58500_hs37d5.fa.bwt added
22350d299ebfc7_hs37d5.fa.pac added
22350d68ad9390_hs37d5.fa.sa added
22350d6790c71a_hs37d5.fa added
22350dba56bf_complete_ref_lens.bin added
22350d6d50e090_ctable.bin added
22350d5362fdc2_ctg_offsets.bin added
22350d1f76fd9c_duplicate_clusters.tsv added
22350d2fe38aa_info.json added
22350d7da965eb_mphf.bin added
22350d5242e59_pos.bin added
22350d26398186_pre_indexing.log added
22350d1e407567_rank.bin added
22350d4cbd58ad_ref_indexing.log added
22350d6693725b_refAccumLengths.bin added
22350d4a8d1ae9_reflengths.bin added
22350d3b779f07_refseq.bin added
22350d1b0a5c21_seq.bin added
22350d33e5bf1d_versionInfo.json added
22350d70805644_salmon_index added
22350d19881d8e_chrLength.txt added
22350d5ec5d68d_chrName.txt added
22350d193294cf_chrNameLength.txt added
22350d216b7b9e_chrStart.txt added
22350d6c8b4705_exonGeTrInfo.tab added
22350d60aceaf3_exonInfo.tab added
22350d4416b640_geneInfo.tab added
22350d46d7639c_Genome added
22350d1b373463_genomeParameters.txt added
22350d116995f1_Log.out added
22350d64366341_SA added
22350d4cfcb963_SAindex added
22350d3b0855b8_sjdbInfo.txt added
22350d4ce3f6d1_sjdbList.fromGTF.out.tab added
22350d348d807d_sjdbList.out.tab added
22350d3bc2ac78_transcriptInfo.tab added
22350d3a34d761_GRCh38.GENCODE.v42_100 added
22350d7f07e3f_knownGene_hg38.sql added
22350d5b39aa14_knownGene_hg38.txt added
22350d3d33100b_refGene_hg38.sql added
22350d599e42a_refGene_hg38.txt added
22350d605dd86e_knownGene_mm39.sql added
22350d636c9192_knownGene_mm39.txt added
22350d23da5992_refGene_mm39.sql added
22350d2d1b311b_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/RtmpylcOHF/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
17.573 1.101 19.438
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.010 | 0.384 | 6.396 | |
| dataSearch | 1.120 | 0.019 | 1.141 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.616 | 0.167 | 3.865 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.120 | 0.002 | 0.123 | |
| recipeLoad | 1.274 | 0.069 | 1.343 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.532 | 0.006 | 0.539 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |