Qian Liu
| Snapshot Date: 2025-11-11 13:40 -0500 (Tue, 11 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 Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-12 11:32 -0500 (Wed, 12 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" | 4823 |
| 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 | | ||||||||
|
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: 2025-11-12 03:08:36 -0500 (Wed, 12 Nov 2025) |
| EndedAt: 2025-11-12 03:11:24 -0500 (Wed, 12 Nov 2025) |
| EllapsedTime: 168.3 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) (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 6.076 0.37 6.449
* 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...
3a8759238e3052_GRCh38.primary_assembly.genome.fa.1.bt2 added
3a87593a6d9de1_GRCh38.primary_assembly.genome.fa.2.bt2 added
3a8759339f2ed5_GRCh38.primary_assembly.genome.fa.3.bt2 added
3a87593170a4aa_GRCh38.primary_assembly.genome.fa.4.bt2 added
3a8759575feaea_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3a87593e622766_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3a87596a28fcf4_outfile.txt added
3a875967590290_GRCh37_to_GRCh38.chain added
3a87594e8cd856_GRCh37_to_NCBI34.chain added
3a875967bdf103_GRCh37_to_NCBI35.chain added
3a8759a1e188f_GRCh37_to_NCBI36.chain added
3a87593477b20a_GRCh38_to_GRCh37.chain added
3a87593434668b_GRCh38_to_NCBI34.chain added
3a87596d174554_GRCh38_to_NCBI35.chain added
3a87596d8e5aa0_GRCh38_to_NCBI36.chain added
3a8759a6e0430_NCBI34_to_GRCh37.chain added
3a87593967f715_NCBI34_to_GRCh38.chain added
3a875948c90e15_NCBI35_to_GRCh37.chain added
3a87597bd11006_NCBI35_to_GRCh38.chain added
3a87594519ac4c_NCBI36_to_GRCh37.chain added
3a875968f5c158_NCBI36_to_GRCh38.chain added
3a87597a83114d_GRCm38_to_NCBIM36.chain added
3a87592ccfb42d_GRCm38_to_NCBIM37.chain added
3a8759455bc37c_NCBIM36_to_GRCm38.chain added
3a875914c764e0_NCBIM37_to_GRCm38.chain added
3a87597f969fbf_1000G_omni2.5.b37.vcf.gz added
3a875917005910_1000G_omni2.5.b37.vcf.gz.tbi added
3a875947dc613b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3a87592b6dc28_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3a875944edef03_1000G_omni2.5.hg38.vcf.gz added
3a87592ff7b571_1000G_omni2.5.hg38.vcf.gz.tbi added
3a875926450c7a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3a87597f5b8ce4_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3a87596396e447_af-only-gnomad.raw.sites.vcf added
3a875957b5b124_af-only-gnomad.raw.sites.vcf.idx added
3a875956bb77ce_Mutect2-exome-panel.vcf.idx added
3a875921f90bad_Mutect2-WGS-panel-b37.vcf added
3a875941deae18_Mutect2-WGS-panel-b37.vcf.idx added
3a87593e147a5e_small_exac_common_3.vcf added
3a87597085e403_small_exac_common_3.vcf.idx added
3a8759299c9f1b_1000g_pon.hg38.vcf.gz added
3a8759483292ee_1000g_pon.hg38.vcf.gz.tbi added
3a875924fd960e_af-only-gnomad.hg38.vcf.gz added
3a87595dd105a6_af-only-gnomad.hg38.vcf.gz.tbi added
3a87593549d842_small_exac_common_3.hg38.vcf.gz added
3a8759128bf0ae_small_exac_common_3.hg38.vcf.gz.tbi added
3a8759683f09d7_gencode.v41.annotation.gtf added
3a87596eb1cf58_gencode.v42.annotation.gtf added
3a87595b54fec3_gencode.vM30.annotation.gtf added
3a8759641019dd_gencode.vM31.annotation.gtf added
3a875933cb7ba4_gencode.v41.transcripts.fa added
3a8759444ac01b_gencode.v41.transcripts.fa.fai added
3a87595e932b2b_gencode.v42.transcripts.fa added
3a8759609b2fd1_gencode.v42.transcripts.fa.fai added
3a87599a68398_gencode.vM30.pc_transcripts.fa added
3a8759735a900b_gencode.vM30.pc_transcripts.fa.fai added
3a87596031cf90_gencode.vM31.pc_transcripts.fa added
3a875920a6dca8_gencode.vM31.pc_transcripts.fa.fai added
3a87593b36f147_GRCh38.primary_assembly.genome.fa.1.ht2 added
3a875962e8abb8_GRCh38.primary_assembly.genome.fa.2.ht2 added
3a87596594cbab_GRCh38.primary_assembly.genome.fa.3.ht2 added
3a87596b2ea6b8_GRCh38.primary_assembly.genome.fa.4.ht2 added
3a875992db832_GRCh38.primary_assembly.genome.fa.5.ht2 added
3a875964f05890_GRCh38.primary_assembly.genome.fa.6.ht2 added
3a87594ec58aff_GRCh38.primary_assembly.genome.fa.7.ht2 added
3a875960e36956_GRCh38.primary_assembly.genome.fa.8.ht2 added
3a87593babd05e_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3a875970be96ad_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3a875922c2176e_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3a875979c04abd_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3a875961447ab0_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3a87594c5eb689_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3a875941f2ddab_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3a875964210be_GRCh38.primary_assembly.genome.fa.fai added
3a87592a2fbc30_GRCh38.primary_assembly.genome.fa.amb added
3a8759773cb5ed_GRCh38.primary_assembly.genome.fa.ann added
3a875918ce016c_GRCh38.primary_assembly.genome.fa.bwt added
3a8759126ec607_GRCh38.primary_assembly.genome.fa.pac added
3a875965ee8545_GRCh38.primary_assembly.genome.fa.sa added
3a87597423002f_GRCh38.primary_assembly.genome.fa added
3a8759767edfe4_hs37d5.fa.fai added
3a875919ba00e9_hs37d5.fa.amb added
3a8759386dc04b_hs37d5.fa.ann added
3a875955120b0f_hs37d5.fa.bwt added
3a87597a5530bb_hs37d5.fa.pac added
3a8759421443e3_hs37d5.fa.sa added
3a8759486c9b1b_hs37d5.fa added
3a87595a87004b_complete_ref_lens.bin added
3a875962bb208b_ctable.bin added
3a87593a38c62_ctg_offsets.bin added
3a87593d6fac04_duplicate_clusters.tsv added
3a8759484fec37_info.json added
3a87596ed2331a_mphf.bin added
3a8759469d6436_pos.bin added
3a87592d4044c7_pre_indexing.log added
3a87593d97be1a_rank.bin added
3a87592780cd8d_ref_indexing.log added
3a875968ec1525_refAccumLengths.bin added
3a87592e5654c7_reflengths.bin added
3a87594a42e4fb_refseq.bin added
3a875962ac5fe2_seq.bin added
3a8759f9acf77_versionInfo.json added
3a875916a19b85_salmon_index added
3a8759249f3d8d_chrLength.txt added
3a875915dce036_chrName.txt added
3a875940d157b5_chrNameLength.txt added
3a87591bdbf37b_chrStart.txt added
3a87592eaae1a2_exonGeTrInfo.tab added
3a875953401dbc_exonInfo.tab added
3a87591ca78c0_geneInfo.tab added
3a875922cde1d2_Genome added
3a875949befda0_genomeParameters.txt added
3a87591b8479aa_Log.out added
3a87595b3ba21d_SA added
3a87591ed108b0_SAindex added
3a875915d9aa65_sjdbInfo.txt added
3a87591d4fe600_sjdbList.fromGTF.out.tab added
3a8759673da3cb_sjdbList.out.tab added
3a87597060aab0_transcriptInfo.tab added
3a8759b068b_GRCh38.GENCODE.v42_100 added
3a87596ae1302d_knownGene_hg38.sql added
3a87592dd056b4_knownGene_hg38.txt added
3a8759485af2c2_refGene_hg38.sql added
3a875959b36347_refGene_hg38.txt added
3a8759746dbaeb_knownGene_mm39.sql added
3a8759759b3789_knownGene_mm39.txt added
3a8759174b2161_refGene_mm39.sql added
3a87591bee8878_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/RtmpSoOOHZ/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
18.628 1.609 21.167
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.076 | 0.370 | 6.449 | |
| dataSearch | 1.102 | 0.046 | 1.147 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.596 | 0.126 | 3.706 | |
| getData | 0.001 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.120 | 0.004 | 0.124 | |
| recipeLoad | 1.203 | 0.024 | 1.229 | |
| recipeMake | 0.000 | 0.001 | 0.000 | |
| recipeSearch | 0.541 | 0.011 | 0.551 | |
| recipeUpdate | 0 | 0 | 0 | |