Qian Liu
| Snapshot Date: 2025-09-28 13:45 -0400 (Sun, 28 Sep 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 2025-09-29 12:04 -0400 (Mon, 29 Sep 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" | 4833 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4621 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4566 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
| 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 1752/2334 | 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 12.7.1 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: 2025-09-29 03:31:06 -0400 (Mon, 29 Sep 2025) |
| EndedAt: 2025-09-29 03:33:51 -0400 (Mon, 29 Sep 2025) |
| EllapsedTime: 165.2 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 5.789 0.224 6.016
* 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...
290ee773122065_GRCh38.primary_assembly.genome.fa.1.bt2 added
290ee7519a509_GRCh38.primary_assembly.genome.fa.2.bt2 added
290ee711aa2b0a_GRCh38.primary_assembly.genome.fa.3.bt2 added
290ee771b7de06_GRCh38.primary_assembly.genome.fa.4.bt2 added
290ee73453f1d8_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
290ee77c9bd32a_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
290ee75cef85ef_outfile.txt added
290ee7104bdb5_GRCh37_to_GRCh38.chain added
290ee711e95453_GRCh37_to_NCBI34.chain added
290ee7ab7dcf6_GRCh37_to_NCBI35.chain added
290ee741846aa1_GRCh37_to_NCBI36.chain added
290ee754236bef_GRCh38_to_GRCh37.chain added
290ee7448860fe_GRCh38_to_NCBI34.chain added
290ee73be39719_GRCh38_to_NCBI35.chain added
290ee713fa0f_GRCh38_to_NCBI36.chain added
290ee757370805_NCBI34_to_GRCh37.chain added
290ee7bb48681_NCBI34_to_GRCh38.chain added
290ee77e78c527_NCBI35_to_GRCh37.chain added
290ee7345ce6af_NCBI35_to_GRCh38.chain added
290ee72170e687_NCBI36_to_GRCh37.chain added
290ee719649074_NCBI36_to_GRCh38.chain added
290ee773202b51_GRCm38_to_NCBIM36.chain added
290ee7207bb967_GRCm38_to_NCBIM37.chain added
290ee73af02169_NCBIM36_to_GRCm38.chain added
290ee7325370c_NCBIM37_to_GRCm38.chain added
290ee74b989d09_1000G_omni2.5.b37.vcf.gz added
290ee769167e48_1000G_omni2.5.b37.vcf.gz.tbi added
290ee749cd1bc6_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
290ee716fe719c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
290ee76166a7c8_1000G_omni2.5.hg38.vcf.gz added
290ee746a93508_1000G_omni2.5.hg38.vcf.gz.tbi added
290ee7a109201_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
290ee766804cd1_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
290ee758536013_af-only-gnomad.raw.sites.vcf added
290ee77bc87008_af-only-gnomad.raw.sites.vcf.idx added
290ee71ad43ea9_Mutect2-exome-panel.vcf.idx added
290ee754ef333d_Mutect2-WGS-panel-b37.vcf added
290ee758b7f5f7_Mutect2-WGS-panel-b37.vcf.idx added
290ee71bd8fc5e_small_exac_common_3.vcf added
290ee766d88791_small_exac_common_3.vcf.idx added
290ee7636fd2ed_1000g_pon.hg38.vcf.gz added
290ee75d5d66ff_1000g_pon.hg38.vcf.gz.tbi added
290ee73afbf380_af-only-gnomad.hg38.vcf.gz added
290ee727f833ec_af-only-gnomad.hg38.vcf.gz.tbi added
290ee71940fe19_small_exac_common_3.hg38.vcf.gz added
290ee73b0fed90_small_exac_common_3.hg38.vcf.gz.tbi added
290ee77f2f3bf1_gencode.v41.annotation.gtf added
290ee724f5849a_gencode.v42.annotation.gtf added
290ee73988b2b7_gencode.vM30.annotation.gtf added
290ee7338c22a0_gencode.vM31.annotation.gtf added
290ee746666b21_gencode.v41.transcripts.fa added
290ee752ed432b_gencode.v41.transcripts.fa.fai added
290ee726ac4df2_gencode.v42.transcripts.fa added
290ee766e22488_gencode.v42.transcripts.fa.fai added
290ee7ddd6494_gencode.vM30.pc_transcripts.fa added
290ee729d184fe_gencode.vM30.pc_transcripts.fa.fai added
290ee7327ac191_gencode.vM31.pc_transcripts.fa added
290ee776f3e2dd_gencode.vM31.pc_transcripts.fa.fai added
290ee7739ea0c5_GRCh38.primary_assembly.genome.fa.1.ht2 added
290ee74979332d_GRCh38.primary_assembly.genome.fa.2.ht2 added
290ee7585a8aa5_GRCh38.primary_assembly.genome.fa.3.ht2 added
290ee73a47d5cd_GRCh38.primary_assembly.genome.fa.4.ht2 added
290ee75389c52f_GRCh38.primary_assembly.genome.fa.5.ht2 added
290ee73edad776_GRCh38.primary_assembly.genome.fa.6.ht2 added
290ee7129b35e0_GRCh38.primary_assembly.genome.fa.7.ht2 added
290ee74f523537_GRCh38.primary_assembly.genome.fa.8.ht2 added
290ee759af161f_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
290ee7678a691e_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
290ee7280a2b2e_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
290ee77588127d_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
290ee74e62f0af_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
290ee7b79fe1c_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
290ee752e5797c_GRCh38_full_analysis_set_plus_decoy_hla.fa added
290ee795ee42f_GRCh38.primary_assembly.genome.fa.fai added
290ee733723208_GRCh38.primary_assembly.genome.fa.amb added
290ee76c267795_GRCh38.primary_assembly.genome.fa.ann added
290ee7446ed1bf_GRCh38.primary_assembly.genome.fa.bwt added
290ee732a16df9_GRCh38.primary_assembly.genome.fa.pac added
290ee7111bfc2f_GRCh38.primary_assembly.genome.fa.sa added
290ee77df78476_GRCh38.primary_assembly.genome.fa added
290ee7662d909a_hs37d5.fa.fai added
290ee757826750_hs37d5.fa.amb added
290ee750e4c7a1_hs37d5.fa.ann added
290ee7cd9de8c_hs37d5.fa.bwt added
290ee73e648bd9_hs37d5.fa.pac added
290ee75ec22c36_hs37d5.fa.sa added
290ee736ab638a_hs37d5.fa added
290ee770df4d6a_complete_ref_lens.bin added
290ee755b60f13_ctable.bin added
290ee72a4a044f_ctg_offsets.bin added
290ee73a588098_duplicate_clusters.tsv added
290ee72e1099b8_info.json added
290ee76491da1d_mphf.bin added
290ee7de245c7_pos.bin added
290ee76ceb712e_pre_indexing.log added
290ee7772d0ffd_rank.bin added
290ee75d347afe_ref_indexing.log added
290ee7469a874d_refAccumLengths.bin added
290ee75eb7791b_reflengths.bin added
290ee753ea62c_refseq.bin added
290ee73c2299ca_seq.bin added
290ee72d1a69ca_versionInfo.json added
290ee710b8a448_salmon_index added
290ee7f081346_chrLength.txt added
290ee736794dfa_chrName.txt added
290ee7442ad650_chrNameLength.txt added
290ee77b2e8adc_chrStart.txt added
290ee77ae81fb9_exonGeTrInfo.tab added
290ee776cc444a_exonInfo.tab added
290ee7c4a870b_geneInfo.tab added
290ee778dfa430_Genome added
290ee75cf9d4e4_genomeParameters.txt added
290ee763ccee5c_Log.out added
290ee749c46bd1_SA added
290ee769d3b370_SAindex added
290ee722317a35_sjdbInfo.txt added
290ee728869807_sjdbList.fromGTF.out.tab added
290ee7207f16fa_sjdbList.out.tab added
290ee71310c79f_transcriptInfo.tab added
290ee77e3ca71a_GRCh38.GENCODE.v42_100 added
290ee74ac91b4a_knownGene_hg38.sql added
290ee74d694837_knownGene_hg38.txt added
290ee72c4d40d2_refGene_hg38.sql added
290ee72f5af567_refGene_hg38.txt added
290ee75b4b8dfe_knownGene_mm39.sql added
290ee71938b200_knownGene_mm39.txt added
290ee726880564_refGene_mm39.sql added
290ee7388008fc_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/RtmpMKJTzn/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
18.397 1.889 20.751
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.789 | 0.224 | 6.016 | |
| dataSearch | 1.075 | 0.004 | 1.080 | |
| dataUpdate | 0.001 | 0.000 | 0.000 | |
| getCloudData | 2.677 | 0.159 | 3.848 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.125 | 0.006 | 0.132 | |
| recipeLoad | 1.223 | 0.047 | 1.272 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.508 | 0.015 | 0.523 | |
| recipeUpdate | 0 | 0 | 0 | |