Qian Liu
| Snapshot Date: 2026-05-01 13:45 -0400 (Fri, 01 May 2026) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: caf380d |
| git_last_commit_date: 2026-04-28 08:59:39 -0400 (Tue, 28 Apr 2026) |
| Back to Build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-02 11:33 -0400 (Sat, 02 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4844 |
| 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 1775/2366 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.13.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for ReUseData in R Universe. | ||||||||||||||
|
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: 1.13.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings ReUseData_1.13.0.tar.gz |
| StartedAt: 2026-05-02 03:43:01 -0400 (Sat, 02 May 2026) |
| EndedAt: 2026-05-02 03:45:48 -0400 (Sat, 02 May 2026) |
| EllapsedTime: 167.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings ReUseData_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/ReUseData.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-02 07:43:01 UTC
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.13.0’
* 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 5.793 0.206 6.003
* 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-3.24-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.13.0’ ** 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 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
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...
31e86b572e523e_GRCh38.primary_assembly.genome.fa.1.bt2 added
31e86b59fea93f_GRCh38.primary_assembly.genome.fa.2.bt2 added
31e86b5cf2dec1_GRCh38.primary_assembly.genome.fa.3.bt2 added
31e86b55f7ba76_GRCh38.primary_assembly.genome.fa.4.bt2 added
31e86b538de7a4_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
31e86b7dc2e941_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
31e86b47629710_outfile.txt added
31e86b718f200f_GRCh37_to_GRCh38.chain added
31e86b4f00722c_GRCh37_to_NCBI34.chain added
31e86b2acf2926_GRCh37_to_NCBI35.chain added
31e86b610a99da_GRCh37_to_NCBI36.chain added
31e86b31120d7f_GRCh38_to_GRCh37.chain added
31e86b274b283_GRCh38_to_NCBI34.chain added
31e86b62fe2750_GRCh38_to_NCBI35.chain added
31e86b1503b9bc_GRCh38_to_NCBI36.chain added
31e86bebc1e4_NCBI34_to_GRCh37.chain added
31e86b5a8d81c1_NCBI34_to_GRCh38.chain added
31e86b7082358c_NCBI35_to_GRCh37.chain added
31e86b6f4d7626_NCBI35_to_GRCh38.chain added
31e86b4678f237_NCBI36_to_GRCh37.chain added
31e86b23683d21_NCBI36_to_GRCh38.chain added
31e86b56dba94b_GRCm38_to_NCBIM36.chain added
31e86b40e55ac3_GRCm38_to_NCBIM37.chain added
31e86b701d1c9e_NCBIM36_to_GRCm38.chain added
31e86b4adb7149_NCBIM37_to_GRCm38.chain added
31e86b740b5a5f_1000G_omni2.5.b37.vcf.gz added
31e86b634847f2_1000G_omni2.5.b37.vcf.gz.tbi added
31e86b7d79e722_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
31e86b76de6bb8_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
31e86b364fe972_1000G_omni2.5.hg38.vcf.gz added
31e86b7e8d140_1000G_omni2.5.hg38.vcf.gz.tbi added
31e86b4e0cbdf6_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
31e86b104e92b1_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
31e86b64dbb001_af-only-gnomad.raw.sites.vcf added
31e86b2404786c_af-only-gnomad.raw.sites.vcf.idx added
31e86b63dc7a56_Mutect2-exome-panel.vcf.idx added
31e86b629e9942_Mutect2-WGS-panel-b37.vcf added
31e86b6b670f7c_Mutect2-WGS-panel-b37.vcf.idx added
31e86b556b9a65_small_exac_common_3.vcf added
31e86b319f0b6e_small_exac_common_3.vcf.idx added
31e86b163638a2_1000g_pon.hg38.vcf.gz added
31e86b3676343f_1000g_pon.hg38.vcf.gz.tbi added
31e86b62b118ee_af-only-gnomad.hg38.vcf.gz added
31e86b18aaeb26_af-only-gnomad.hg38.vcf.gz.tbi added
31e86b19745b8f_small_exac_common_3.hg38.vcf.gz added
31e86b77b4d2aa_small_exac_common_3.hg38.vcf.gz.tbi added
31e86b1996ad0a_gencode.v41.annotation.gtf added
31e86b7401dd51_gencode.v42.annotation.gtf added
31e86b68370836_gencode.vM30.annotation.gtf added
31e86b8e42331_gencode.vM31.annotation.gtf added
31e86b3a7acf88_gencode.v41.transcripts.fa added
31e86bb9f4557_gencode.v41.transcripts.fa.fai added
31e86b5fbfcc7c_gencode.v42.transcripts.fa added
31e86b7b602a4c_gencode.v42.transcripts.fa.fai added
31e86b7bbc61f6_gencode.vM30.pc_transcripts.fa added
31e86b2a9b3dc5_gencode.vM30.pc_transcripts.fa.fai added
31e86b6f6b84ab_gencode.vM31.pc_transcripts.fa added
31e86b5f04a9e8_gencode.vM31.pc_transcripts.fa.fai added
31e86b281524e7_GRCh38.primary_assembly.genome.fa.1.ht2 added
31e86b6649f063_GRCh38.primary_assembly.genome.fa.2.ht2 added
31e86b1554935b_GRCh38.primary_assembly.genome.fa.3.ht2 added
31e86b2ffdf628_GRCh38.primary_assembly.genome.fa.4.ht2 added
31e86b3456ae59_GRCh38.primary_assembly.genome.fa.5.ht2 added
31e86b25a3260c_GRCh38.primary_assembly.genome.fa.6.ht2 added
31e86b14d9a629_GRCh38.primary_assembly.genome.fa.7.ht2 added
31e86b585b26c6_GRCh38.primary_assembly.genome.fa.8.ht2 added
31e86b97fa062_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
31e86b77783f6c_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
31e86b43c23642_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
31e86b5eeb3ac8_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
31e86b29174ada_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
31e86b59f86ee5_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
31e86b15616f07_GRCh38_full_analysis_set_plus_decoy_hla.fa added
31e86bbc863c8_GRCh38.primary_assembly.genome.fa.fai added
31e86b72a35a0b_GRCh38.primary_assembly.genome.fa.amb added
31e86b2ed5ca97_GRCh38.primary_assembly.genome.fa.ann added
31e86b37d3672_GRCh38.primary_assembly.genome.fa.bwt added
31e86bc3a0715_GRCh38.primary_assembly.genome.fa.pac added
31e86b22d7a7e8_GRCh38.primary_assembly.genome.fa.sa added
31e86b6bb43ea8_GRCh38.primary_assembly.genome.fa added
31e86b151e2a46_hs37d5.fa.fai added
31e86b5d527770_hs37d5.fa.amb added
31e86b77538400_hs37d5.fa.ann added
31e86b74ddf6c3_hs37d5.fa.bwt added
31e86b58b2a1bc_hs37d5.fa.pac added
31e86b730fe5f6_hs37d5.fa.sa added
31e86b1f793488_hs37d5.fa added
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31e86b52148fde_ctable.bin added
31e86b478e5970_ctg_offsets.bin added
31e86b2e6816cb_duplicate_clusters.tsv added
31e86b67692339_info.json added
31e86b778c4f98_mphf.bin added
31e86b62bec525_pos.bin added
31e86bd0c4946_pre_indexing.log added
31e86bc65f5c1_rank.bin added
31e86b3b19ebeb_ref_indexing.log added
31e86b168be9a8_refAccumLengths.bin added
31e86b3de352d_reflengths.bin added
31e86b7edc222d_refseq.bin added
31e86b75772470_seq.bin added
31e86b2cf58008_versionInfo.json added
31e86b58d49112_salmon_index added
31e86bad89378_chrLength.txt added
31e86b38bde3d0_chrName.txt added
31e86b4b77eb1d_chrNameLength.txt added
31e86b39ae5e0f_chrStart.txt added
31e86b3c3b1a43_exonGeTrInfo.tab added
31e86b57b1f233_exonInfo.tab added
31e86b5c8605f7_geneInfo.tab added
31e86b27ef58eb_Genome added
31e86b6cd01c79_genomeParameters.txt added
31e86b39d87d67_Log.out added
31e86b1f42dceb_SA added
31e86b61ae133c_SAindex added
31e86b128b1f24_sjdbInfo.txt added
31e86b1252c2e1_sjdbList.fromGTF.out.tab added
31e86b12747c5_sjdbList.out.tab added
31e86b5aa9458c_transcriptInfo.tab added
31e86b646752c0_GRCh38.GENCODE.v42_100 added
31e86b48b5a135_knownGene_hg38.sql added
31e86b9115c57_knownGene_hg38.txt added
31e86b4bd075f9_refGene_hg38.sql added
31e86b4041f0cd_refGene_hg38.txt added
31e86b6bd0217c_knownGene_mm39.sql added
31e86b58dcbf3f_knownGene_mm39.txt added
31e86b4ca7e68e_refGene_mm39.sql added
31e86b26ea0d67_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/Rtmp4JtmBV/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 1 | SKIP 0 | PASS 44 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 44 ]
> Sys.setenv(cachePath = file.path(tempdir(), "cache"))
>
>
>
> proc.time()
user system elapsed
18.695 1.027 20.367
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.793 | 0.206 | 6.003 | |
| dataSearch | 1.111 | 0.011 | 1.121 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.994 | 0.410 | 4.062 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.135 | 0.007 | 0.143 | |
| recipeLoad | 1.370 | 0.130 | 1.501 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.572 | 0.002 | 0.574 | |
| recipeUpdate | 0 | 0 | 0 | |