Qian Liu
| Snapshot Date: 2025-10-23 14:17 -0400 (Thu, 23 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 2025-10-24 12:04 -0400 (Fri, 24 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" | 4898 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 1771/2359 | 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 | NA | ||||||||||
|
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: 2025-10-24 03:07:53 -0400 (Fri, 24 Oct 2025) |
| EndedAt: 2025-10-24 03:10:38 -0400 (Fri, 24 Oct 2025) |
| EllapsedTime: 165.3 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 6.122 0.443 6.569
* 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...
179199137050fd_GRCh38.primary_assembly.genome.fa.1.bt2 added
17919911d3df7d_GRCh38.primary_assembly.genome.fa.2.bt2 added
17919923ac8b81_GRCh38.primary_assembly.genome.fa.3.bt2 added
1791993261d3c7_GRCh38.primary_assembly.genome.fa.4.bt2 added
179199459b93ca_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1791993b06f724_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
17919930ad91ea_outfile.txt added
17919934786b92_GRCh37_to_GRCh38.chain added
179199521708d2_GRCh37_to_NCBI34.chain added
17919972bd7bd7_GRCh37_to_NCBI35.chain added
1791996845752_GRCh37_to_NCBI36.chain added
17919990a0bf1_GRCh38_to_GRCh37.chain added
17919938e4c58f_GRCh38_to_NCBI34.chain added
1791995f77e099_GRCh38_to_NCBI35.chain added
1791993d1a1229_GRCh38_to_NCBI36.chain added
1791995d4277c3_NCBI34_to_GRCh37.chain added
17919978c34078_NCBI34_to_GRCh38.chain added
1791993696d6d6_NCBI35_to_GRCh37.chain added
1791992843a78e_NCBI35_to_GRCh38.chain added
1791997eef6812_NCBI36_to_GRCh37.chain added
17919914d90677_NCBI36_to_GRCh38.chain added
1791992df525dc_GRCm38_to_NCBIM36.chain added
17919950ecf1bd_GRCm38_to_NCBIM37.chain added
1791995ae2e8be_NCBIM36_to_GRCm38.chain added
17919978d2975d_NCBIM37_to_GRCm38.chain added
17919931d44fc8_1000G_omni2.5.b37.vcf.gz added
1791993d6d0e27_1000G_omni2.5.b37.vcf.gz.tbi added
179199616496e8_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
179199627b85c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1791996d32f9bd_1000G_omni2.5.hg38.vcf.gz added
1791992bd0e2_1000G_omni2.5.hg38.vcf.gz.tbi added
17919919980959_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1791997f06d93a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
17919923d85c64_af-only-gnomad.raw.sites.vcf added
1791994bf9dd20_af-only-gnomad.raw.sites.vcf.idx added
17919944a26d04_Mutect2-exome-panel.vcf.idx added
1791995edf5388_Mutect2-WGS-panel-b37.vcf added
1791997ca76f0a_Mutect2-WGS-panel-b37.vcf.idx added
179199791ad896_small_exac_common_3.vcf added
17919930f65c5a_small_exac_common_3.vcf.idx added
1791996f64eae1_1000g_pon.hg38.vcf.gz added
1791997f9f2fe8_1000g_pon.hg38.vcf.gz.tbi added
1791993a00684c_af-only-gnomad.hg38.vcf.gz added
1791992849b071_af-only-gnomad.hg38.vcf.gz.tbi added
1791995f171082_small_exac_common_3.hg38.vcf.gz added
179199771a7a75_small_exac_common_3.hg38.vcf.gz.tbi added
17919958c2834_gencode.v41.annotation.gtf added
17919957da50fa_gencode.v42.annotation.gtf added
1791992db1514b_gencode.vM30.annotation.gtf added
1791992dcfcfc2_gencode.vM31.annotation.gtf added
17919956c9b90c_gencode.v41.transcripts.fa added
179199428a57c3_gencode.v41.transcripts.fa.fai added
1791995bc4f59f_gencode.v42.transcripts.fa added
17919927b6aac9_gencode.v42.transcripts.fa.fai added
1791991d6d4081_gencode.vM30.pc_transcripts.fa added
17919954978cfc_gencode.vM30.pc_transcripts.fa.fai added
179199598afa91_gencode.vM31.pc_transcripts.fa added
1791995ada4ea9_gencode.vM31.pc_transcripts.fa.fai added
17919935fc23e4_GRCh38.primary_assembly.genome.fa.1.ht2 added
1791995fb2b2ed_GRCh38.primary_assembly.genome.fa.2.ht2 added
179199480d4866_GRCh38.primary_assembly.genome.fa.3.ht2 added
1791993627f4c7_GRCh38.primary_assembly.genome.fa.4.ht2 added
179199794abc46_GRCh38.primary_assembly.genome.fa.5.ht2 added
179199471421a0_GRCh38.primary_assembly.genome.fa.6.ht2 added
1791995a00512b_GRCh38.primary_assembly.genome.fa.7.ht2 added
17919945449967_GRCh38.primary_assembly.genome.fa.8.ht2 added
179199bb68ea4_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
17919938dfa4b3_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
17919941ec0871_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1791994d1673b_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
17919969d6010e_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1791993150f353_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1791994709723_GRCh38_full_analysis_set_plus_decoy_hla.fa added
17919923d6695a_GRCh38.primary_assembly.genome.fa.fai added
179199599aa3c4_GRCh38.primary_assembly.genome.fa.amb added
1791996387a7a5_GRCh38.primary_assembly.genome.fa.ann added
1791991af0e3cf_GRCh38.primary_assembly.genome.fa.bwt added
1791995f26cbf8_GRCh38.primary_assembly.genome.fa.pac added
1791993b61f89f_GRCh38.primary_assembly.genome.fa.sa added
17919948a2351b_GRCh38.primary_assembly.genome.fa added
179199cf69bbb_hs37d5.fa.fai added
179199122bb1ab_hs37d5.fa.amb added
179199b2c8cde_hs37d5.fa.ann added
17919968bb915a_hs37d5.fa.bwt added
17919939e25c74_hs37d5.fa.pac added
1791992899cd5f_hs37d5.fa.sa added
1791993d531e56_hs37d5.fa added
179199136d5705_complete_ref_lens.bin added
1791993741c08_ctable.bin added
179199734f423a_ctg_offsets.bin added
179199732009f2_duplicate_clusters.tsv added
1791994b81646e_info.json added
17919929773701_mphf.bin added
1791996c6ac639_pos.bin added
1791991295860e_pre_indexing.log added
179199377882c_rank.bin added
17919931af5fa0_ref_indexing.log added
1791991e4c14b3_refAccumLengths.bin added
1791993c572ce0_reflengths.bin added
179199739b6811_refseq.bin added
179199231d7bee_seq.bin added
179199262d2dee_versionInfo.json added
17919924ec5b64_salmon_index added
179199278e1311_chrLength.txt added
1791994a039748_chrName.txt added
1791997e86ff28_chrNameLength.txt added
179199b15bab7_chrStart.txt added
17919964f47b17_exonGeTrInfo.tab added
1791995dadcb21_exonInfo.tab added
1791994677b356_geneInfo.tab added
1791992d96b032_Genome added
1791996aa466dc_genomeParameters.txt added
17919958a36502_Log.out added
17919938c33d10_SA added
179199535ff836_SAindex added
1791991285c176_sjdbInfo.txt added
179199615d0a70_sjdbList.fromGTF.out.tab added
17919910b3168c_sjdbList.out.tab added
17919925f3187c_transcriptInfo.tab added
17919964d12678_GRCh38.GENCODE.v42_100 added
17919940258c6_knownGene_hg38.sql added
1791991913226e_knownGene_hg38.txt added
17919930528ae7_refGene_hg38.sql added
1791992d798fc8_refGene_hg38.txt added
17919957de8a7_knownGene_mm39.sql added
17919942e810f5_knownGene_mm39.txt added
17919930f117f4_refGene_mm39.sql added
179199372d4847_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/RtmpgStfn9/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
18.301 1.255 20.043
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.122 | 0.443 | 6.569 | |
| dataSearch | 1.178 | 0.014 | 1.193 | |
| dataUpdate | 0.001 | 0.000 | 0.000 | |
| getCloudData | 3.132 | 0.306 | 4.507 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.001 | 0.001 | |
| recipeHub-class | 0.155 | 0.030 | 0.186 | |
| recipeLoad | 1.408 | 0.086 | 1.495 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.584 | 0.004 | 0.587 | |
| recipeUpdate | 0 | 0 | 0 | |