Qian Liu
| Snapshot Date: 2025-10-31 13:40 -0400 (Fri, 31 Oct 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 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-01 11:32 -0400 (Sat, 01 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" | 4774 |
| 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 1745/2321 | 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: 2025-11-01 02:48:54 -0400 (Sat, 01 Nov 2025) |
| EndedAt: 2025-11-01 02:51:37 -0400 (Sat, 01 Nov 2025) |
| EllapsedTime: 163.3 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 5.829 0.351 6.182
* 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...
253ae267832d0_GRCh38.primary_assembly.genome.fa.1.bt2 added
253ae2670f8fb3_GRCh38.primary_assembly.genome.fa.2.bt2 added
253ae23a6219a2_GRCh38.primary_assembly.genome.fa.3.bt2 added
253ae2162c98a4_GRCh38.primary_assembly.genome.fa.4.bt2 added
253ae28d615d9_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
253ae27737e482_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
253ae24b97e0ad_outfile.txt added
253ae23c308186_GRCh37_to_GRCh38.chain added
253ae22340bc85_GRCh37_to_NCBI34.chain added
253ae2514952ca_GRCh37_to_NCBI35.chain added
253ae267e8e4c5_GRCh37_to_NCBI36.chain added
253ae24dcf9113_GRCh38_to_GRCh37.chain added
253ae2203dfe8d_GRCh38_to_NCBI34.chain added
253ae21187d6d6_GRCh38_to_NCBI35.chain added
253ae241a26232_GRCh38_to_NCBI36.chain added
253ae2692c96fa_NCBI34_to_GRCh37.chain added
253ae268e55a8_NCBI34_to_GRCh38.chain added
253ae27dcf7a36_NCBI35_to_GRCh37.chain added
253ae22f233ce6_NCBI35_to_GRCh38.chain added
253ae268615c7e_NCBI36_to_GRCh37.chain added
253ae234ad083e_NCBI36_to_GRCh38.chain added
253ae26b94d1f4_GRCm38_to_NCBIM36.chain added
253ae26a615093_GRCm38_to_NCBIM37.chain added
253ae246e8f783_NCBIM36_to_GRCm38.chain added
253ae25c238378_NCBIM37_to_GRCm38.chain added
253ae2c7da344_1000G_omni2.5.b37.vcf.gz added
253ae2397f1b00_1000G_omni2.5.b37.vcf.gz.tbi added
253ae24589795c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
253ae229ca3482_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
253ae221df6202_1000G_omni2.5.hg38.vcf.gz added
253ae215dd018c_1000G_omni2.5.hg38.vcf.gz.tbi added
253ae230426752_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
253ae28eef1b6_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
253ae2503f1b2f_af-only-gnomad.raw.sites.vcf added
253ae2466efff7_af-only-gnomad.raw.sites.vcf.idx added
253ae211c5078f_Mutect2-exome-panel.vcf.idx added
253ae24776ffb1_Mutect2-WGS-panel-b37.vcf added
253ae21206e0a4_Mutect2-WGS-panel-b37.vcf.idx added
253ae24df58915_small_exac_common_3.vcf added
253ae26ab7bc36_small_exac_common_3.vcf.idx added
253ae26350336e_1000g_pon.hg38.vcf.gz added
253ae235de6dda_1000g_pon.hg38.vcf.gz.tbi added
253ae238874d49_af-only-gnomad.hg38.vcf.gz added
253ae238e31fb_af-only-gnomad.hg38.vcf.gz.tbi added
253ae2476644b1_small_exac_common_3.hg38.vcf.gz added
253ae27a29af7c_small_exac_common_3.hg38.vcf.gz.tbi added
253ae26cbac8f5_gencode.v41.annotation.gtf added
253ae24df49a59_gencode.v42.annotation.gtf added
253ae277f929b2_gencode.vM30.annotation.gtf added
253ae21bde05dc_gencode.vM31.annotation.gtf added
253ae23655f6d8_gencode.v41.transcripts.fa added
253ae22ca631f0_gencode.v41.transcripts.fa.fai added
253ae2772d7d0_gencode.v42.transcripts.fa added
253ae220b7476b_gencode.v42.transcripts.fa.fai added
253ae2738f2973_gencode.vM30.pc_transcripts.fa added
253ae263965b48_gencode.vM30.pc_transcripts.fa.fai added
253ae22d34eaaf_gencode.vM31.pc_transcripts.fa added
253ae22d0e4473_gencode.vM31.pc_transcripts.fa.fai added
253ae2291fd4a5_GRCh38.primary_assembly.genome.fa.1.ht2 added
253ae256ff1f31_GRCh38.primary_assembly.genome.fa.2.ht2 added
253ae24eeda676_GRCh38.primary_assembly.genome.fa.3.ht2 added
253ae23efcd631_GRCh38.primary_assembly.genome.fa.4.ht2 added
253ae27418684_GRCh38.primary_assembly.genome.fa.5.ht2 added
253ae257dc982c_GRCh38.primary_assembly.genome.fa.6.ht2 added
253ae2f3bf160_GRCh38.primary_assembly.genome.fa.7.ht2 added
253ae24db0867b_GRCh38.primary_assembly.genome.fa.8.ht2 added
253ae269a19fbb_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
253ae256b2f111_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
253ae25fb7671f_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
253ae2379728d0_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
253ae2416aad48_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
253ae243079a8d_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
253ae26d7596aa_GRCh38_full_analysis_set_plus_decoy_hla.fa added
253ae279f1fa91_GRCh38.primary_assembly.genome.fa.fai added
253ae24695cc88_GRCh38.primary_assembly.genome.fa.amb added
253ae234dbdb5b_GRCh38.primary_assembly.genome.fa.ann added
253ae2741baa0d_GRCh38.primary_assembly.genome.fa.bwt added
253ae23350957e_GRCh38.primary_assembly.genome.fa.pac added
253ae22d075b5_GRCh38.primary_assembly.genome.fa.sa added
253ae26c14d3bf_GRCh38.primary_assembly.genome.fa added
253ae24f2e9b5a_hs37d5.fa.fai added
253ae239266c8d_hs37d5.fa.amb added
253ae218bb05b0_hs37d5.fa.ann added
253ae256a1732a_hs37d5.fa.bwt added
253ae259ddb3f8_hs37d5.fa.pac added
253ae2c4a2f23_hs37d5.fa.sa added
253ae23a37ce73_hs37d5.fa added
253ae27129ea8_complete_ref_lens.bin added
253ae239587397_ctable.bin added
253ae26357a318_ctg_offsets.bin added
253ae25e11bdd9_duplicate_clusters.tsv added
253ae28461a0d_info.json added
253ae222547949_mphf.bin added
253ae26553445d_pos.bin added
253ae26022b239_pre_indexing.log added
253ae231906aaa_rank.bin added
253ae23303cad8_ref_indexing.log added
253ae249c451f4_refAccumLengths.bin added
253ae28435bbb_reflengths.bin added
253ae212bb31f7_refseq.bin added
253ae215b7ac4_seq.bin added
253ae249ae0903_versionInfo.json added
253ae255c2cc84_salmon_index added
253ae26ed1116e_chrLength.txt added
253ae243a00395_chrName.txt added
253ae21c58990d_chrNameLength.txt added
253ae223acecca_chrStart.txt added
253ae237bbada2_exonGeTrInfo.tab added
253ae24fa92e8b_exonInfo.tab added
253ae2267d627f_geneInfo.tab added
253ae223d08162_Genome added
253ae21ed7c9e5_genomeParameters.txt added
253ae25fa3cf0c_Log.out added
253ae23c8b8712_SA added
253ae275793d0f_SAindex added
253ae239818304_sjdbInfo.txt added
253ae248d5b635_sjdbList.fromGTF.out.tab added
253ae22fb10b82_sjdbList.out.tab added
253ae2409421ac_transcriptInfo.tab added
253ae222e29cc_GRCh38.GENCODE.v42_100 added
253ae21308ae9a_knownGene_hg38.sql added
253ae21ea5df86_knownGene_hg38.txt added
253ae2a7443d9_refGene_hg38.sql added
253ae2355d27e4_refGene_hg38.txt added
253ae23f923e3_knownGene_mm39.sql added
253ae26a96f612_knownGene_mm39.txt added
253ae266ed928e_refGene_mm39.sql added
253ae236fceebc_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/RtmpQQGh5v/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
17.590 1.116 19.367
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.829 | 0.351 | 6.182 | |
| dataSearch | 1.082 | 0.043 | 1.126 | |
| dataUpdate | 0.001 | 0.000 | 0.000 | |
| getCloudData | 2.630 | 0.117 | 3.948 | |
| getData | 0.001 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.125 | 0.008 | 0.133 | |
| recipeLoad | 1.219 | 0.023 | 1.244 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.508 | 0.013 | 0.521 | |
| recipeUpdate | 0 | 0 | 0 | |