Qian Liu
| Snapshot Date: 2025-10-19 13:45 -0400 (Sun, 19 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: c5927b9 |
| git_last_commit_date: 2025-04-15 13:01:44 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-20 12:04 -0400 (Mon, 20 Oct 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" | 4887 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4632 |
| 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 1765/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.9.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.9.0 |
| 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_1.9.0.tar.gz |
| StartedAt: 2025-10-20 03:53:22 -0400 (Mon, 20 Oct 2025) |
| EndedAt: 2025-10-20 03:56:02 -0400 (Mon, 20 Oct 2025) |
| EllapsedTime: 160.1 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_1.9.0.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 ‘1.9.0’
* 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 5.709 0.235 5.946
* 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 ‘1.9.0’ ** 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...
48c963e8b0e7f_GRCh38.primary_assembly.genome.fa.1.bt2 added
48c964ce35e39_GRCh38.primary_assembly.genome.fa.2.bt2 added
48c9646295bb7_GRCh38.primary_assembly.genome.fa.3.bt2 added
48c9618a67f58_GRCh38.primary_assembly.genome.fa.4.bt2 added
48c9667d229f6_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
48c9667e74452_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
48c963a30f7e5_outfile.txt added
48c965da4743b_GRCh37_to_GRCh38.chain added
48c966d294ac9_GRCh37_to_NCBI34.chain added
48c9666568e93_GRCh37_to_NCBI35.chain added
48c9668b8c985_GRCh37_to_NCBI36.chain added
48c963da244b9_GRCh38_to_GRCh37.chain added
48c962fd4685c_GRCh38_to_NCBI34.chain added
48c9668f743de_GRCh38_to_NCBI35.chain added
48c9615512cdc_GRCh38_to_NCBI36.chain added
48c963759daae_NCBI34_to_GRCh37.chain added
48c96338901aa_NCBI34_to_GRCh38.chain added
48c9630b9d12d_NCBI35_to_GRCh37.chain added
48c964c793644_NCBI35_to_GRCh38.chain added
48c965bc78be8_NCBI36_to_GRCh37.chain added
48c962444fc54_NCBI36_to_GRCh38.chain added
48c962bb9c01e_GRCm38_to_NCBIM36.chain added
48c96443a670c_GRCm38_to_NCBIM37.chain added
48c963d6aa0d1_NCBIM36_to_GRCm38.chain added
48c9648888760_NCBIM37_to_GRCm38.chain added
48c96160b24ed_1000G_omni2.5.b37.vcf.gz added
48c967f786105_1000G_omni2.5.b37.vcf.gz.tbi added
48c9620b47611_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
48c96271f4a1e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
48c966fbd857e_1000G_omni2.5.hg38.vcf.gz added
48c9661241aa9_1000G_omni2.5.hg38.vcf.gz.tbi added
48c9665aa589d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
48c963ca0e3b7_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
48c96274d7661_af-only-gnomad.raw.sites.vcf added
48c967e50d7f5_af-only-gnomad.raw.sites.vcf.idx added
48c9624730dae_Mutect2-exome-panel.vcf.idx added
48c96f34bab3_Mutect2-WGS-panel-b37.vcf added
48c963881cfda_Mutect2-WGS-panel-b37.vcf.idx added
48c9621781e9_small_exac_common_3.vcf added
48c967c5e057d_small_exac_common_3.vcf.idx added
48c961ed85e6d_1000g_pon.hg38.vcf.gz added
48c966ad04b6e_1000g_pon.hg38.vcf.gz.tbi added
48c963a004a36_af-only-gnomad.hg38.vcf.gz added
48c964eacc6ca_af-only-gnomad.hg38.vcf.gz.tbi added
48c9653c78f4d_small_exac_common_3.hg38.vcf.gz added
48c964f517712_small_exac_common_3.hg38.vcf.gz.tbi added
48c96606a178_gencode.v41.annotation.gtf added
48c9675090f7_gencode.v42.annotation.gtf added
48c96b483f_gencode.vM30.annotation.gtf added
48c96527fd7bc_gencode.vM31.annotation.gtf added
48c9663181cdf_gencode.v41.transcripts.fa added
48c9624504493_gencode.v41.transcripts.fa.fai added
48c967e3997da_gencode.v42.transcripts.fa added
48c96275283eb_gencode.v42.transcripts.fa.fai added
48c9661bae565_gencode.vM30.pc_transcripts.fa added
48c9646c21f3a_gencode.vM30.pc_transcripts.fa.fai added
48c963d5da8d9_gencode.vM31.pc_transcripts.fa added
48c966133466a_gencode.vM31.pc_transcripts.fa.fai added
48c966776954b_GRCh38.primary_assembly.genome.fa.1.ht2 added
48c96647cf2f7_GRCh38.primary_assembly.genome.fa.2.ht2 added
48c9650f0cbe8_GRCh38.primary_assembly.genome.fa.3.ht2 added
48c96489aaff5_GRCh38.primary_assembly.genome.fa.4.ht2 added
48c964a274b94_GRCh38.primary_assembly.genome.fa.5.ht2 added
48c96d91afa0_GRCh38.primary_assembly.genome.fa.6.ht2 added
48c966fe82656_GRCh38.primary_assembly.genome.fa.7.ht2 added
48c9648782389_GRCh38.primary_assembly.genome.fa.8.ht2 added
48c963204bd4e_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
48c967f1ce109_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
48c96f9f364_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
48c96341c3f37_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
48c967b7ae686_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
48c961fd251d1_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
48c961eec8aa5_GRCh38_full_analysis_set_plus_decoy_hla.fa added
48c96357b30bc_GRCh38.primary_assembly.genome.fa.fai added
48c966e7f189b_GRCh38.primary_assembly.genome.fa.amb added
48c9672b419f2_GRCh38.primary_assembly.genome.fa.ann added
48c964cca7cf_GRCh38.primary_assembly.genome.fa.bwt added
48c967485ba14_GRCh38.primary_assembly.genome.fa.pac added
48c967a04aaea_GRCh38.primary_assembly.genome.fa.sa added
48c964d7f00e_GRCh38.primary_assembly.genome.fa added
48c96470591d0_hs37d5.fa.fai added
48c965d1cc7c9_hs37d5.fa.amb added
48c96292834a2_hs37d5.fa.ann added
48c96453f29ab_hs37d5.fa.bwt added
48c9646f4bb5_hs37d5.fa.pac added
48c96ae31a07_hs37d5.fa.sa added
48c96c0148e5_hs37d5.fa added
48c9641ccf48e_complete_ref_lens.bin added
48c966c166071_ctable.bin added
48c967377de31_ctg_offsets.bin added
48c962649e785_duplicate_clusters.tsv added
48c963d072c5a_info.json added
48c963c128e26_mphf.bin added
48c9670713319_pos.bin added
48c964a98dbfa_pre_indexing.log added
48c962bfab47c_rank.bin added
48c9638e956a2_ref_indexing.log added
48c967c9d9948_refAccumLengths.bin added
48c962b179585_reflengths.bin added
48c9639e34a06_refseq.bin added
48c9630b9d87f_seq.bin added
48c9626927c0c_versionInfo.json added
48c9659b59bd8_salmon_index added
48c964fa66324_chrLength.txt added
48c965c0dacc8_chrName.txt added
48c964834b473_chrNameLength.txt added
48c96425a7d17_chrStart.txt added
48c9660da5497_exonGeTrInfo.tab added
48c963cba6e87_exonInfo.tab added
48c963c5f2801_geneInfo.tab added
48c9665b244a6_Genome added
48c963c00058_genomeParameters.txt added
48c96197befca_Log.out added
48c96eda7948_SA added
48c9648ff2a03_SAindex added
48c961deb3b7f_sjdbInfo.txt added
48c9619bd934f_sjdbList.fromGTF.out.tab added
48c96550072e8_sjdbList.out.tab added
48c965fb8300d_transcriptInfo.tab added
48c965d3f3c0_GRCh38.GENCODE.v42_100 added
48c9648785119_knownGene_hg38.sql added
48c966021792_knownGene_hg38.txt added
48c9642db201a_refGene_hg38.sql added
48c9648adf3f_refGene_hg38.txt added
48c9676734aab_knownGene_mm39.sql added
48c96d73fc14_knownGene_mm39.txt added
48c96308593bb_refGene_mm39.sql added
48c962f5ca14e_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/RtmpAkdfMv/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
17.737 0.908 19.145
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.709 | 0.235 | 5.946 | |
| dataSearch | 1.136 | 0.010 | 1.147 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.621 | 0.104 | 3.761 | |
| getData | 0.001 | 0.000 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.124 | 0.004 | 0.129 | |
| recipeLoad | 1.250 | 0.018 | 1.268 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.519 | 0.005 | 0.524 | |
| recipeUpdate | 0.001 | 0.000 | 0.000 | |