Qian Liu
| Snapshot Date: 2025-10-28 13:45 -0400 (Tue, 28 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 2025-10-29 12:06 -0400 (Wed, 29 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" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| 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 1773/2361 | 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 | | ||||||||
|
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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReUseData_1.9.0.tar.gz |
| StartedAt: 2025-10-28 23:38:37 -0400 (Tue, 28 Oct 2025) |
| EndedAt: 2025-10-28 23:41:02 -0400 (Tue, 28 Oct 2025) |
| EllapsedTime: 144.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReUseData_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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 7.268 0.875 8.257
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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...
122b6e8f7d6f_GRCh38.primary_assembly.genome.fa.1.bt2 added
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122b679946555_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
122b67d88edce_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
122b628b4afc5_outfile.txt added
122b66e7fc363_GRCh37_to_GRCh38.chain added
122b65f4d142_GRCh37_to_NCBI34.chain added
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122b663cbe1f1_GRCh38_to_GRCh37.chain added
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122b620b6d0f1_GRCh38_to_NCBI35.chain added
122b6424f8efe_GRCh38_to_NCBI36.chain added
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122b6532fafd6_NCBI35_to_GRCh37.chain added
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122b65903479_NCBI36_to_GRCh37.chain added
122b63e64f6c9_NCBI36_to_GRCh38.chain added
122b65686261f_GRCm38_to_NCBIM36.chain added
122b6130e99a_GRCm38_to_NCBIM37.chain added
122b632387e12_NCBIM36_to_GRCm38.chain added
122b61adce980_NCBIM37_to_GRCm38.chain added
122b61d65e047_1000G_omni2.5.b37.vcf.gz added
122b6b676465_1000G_omni2.5.b37.vcf.gz.tbi added
122b630f028bc_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
122b6670267bd_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
122b64ee8de20_1000G_omni2.5.hg38.vcf.gz added
122b61a4f2f59_1000G_omni2.5.hg38.vcf.gz.tbi added
122b644ad898d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
122b65d21ab34_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
122b64d6f12b0_af-only-gnomad.raw.sites.vcf added
122b637340887_af-only-gnomad.raw.sites.vcf.idx added
122b6391bf361_Mutect2-exome-panel.vcf.idx added
122b65a078291_Mutect2-WGS-panel-b37.vcf added
122b6230d2bc4_Mutect2-WGS-panel-b37.vcf.idx added
122b635b462d6_small_exac_common_3.vcf added
122b655c4eb25_small_exac_common_3.vcf.idx added
122b67329f620_1000g_pon.hg38.vcf.gz added
122b647dde9f1_1000g_pon.hg38.vcf.gz.tbi added
122b63a29f213_af-only-gnomad.hg38.vcf.gz added
122b617d3db3a_af-only-gnomad.hg38.vcf.gz.tbi added
122b655ddc90e_small_exac_common_3.hg38.vcf.gz added
122b653bae22c_small_exac_common_3.hg38.vcf.gz.tbi added
122b61256e1a6_gencode.v41.annotation.gtf added
122b65f862b2_gencode.v42.annotation.gtf added
122b67617972d_gencode.vM30.annotation.gtf added
122b66c647ed_gencode.vM31.annotation.gtf added
122b6439c1c14_gencode.v41.transcripts.fa added
122b63df787b9_gencode.v41.transcripts.fa.fai added
122b645efa277_gencode.v42.transcripts.fa added
122b67793567f_gencode.v42.transcripts.fa.fai added
122b66a13e92d_gencode.vM30.pc_transcripts.fa added
122b64131bfc3_gencode.vM30.pc_transcripts.fa.fai added
122b62924bca5_gencode.vM31.pc_transcripts.fa added
122b62add09bd_gencode.vM31.pc_transcripts.fa.fai added
122b615aa6d47_GRCh38.primary_assembly.genome.fa.1.ht2 added
122b667ec5b6d_GRCh38.primary_assembly.genome.fa.2.ht2 added
122b64e668668_GRCh38.primary_assembly.genome.fa.3.ht2 added
122b62d023e0e_GRCh38.primary_assembly.genome.fa.4.ht2 added
122b66e382037_GRCh38.primary_assembly.genome.fa.5.ht2 added
122b626cb3369_GRCh38.primary_assembly.genome.fa.6.ht2 added
122b6669c4664_GRCh38.primary_assembly.genome.fa.7.ht2 added
122b61dd183dd_GRCh38.primary_assembly.genome.fa.8.ht2 added
122b626283176_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
122b618c74d8c_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
122b644b42f09_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
122b6117c1b1c_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
122b66ad7d43b_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
122b67faea449_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
122b622a3f61c_GRCh38_full_analysis_set_plus_decoy_hla.fa added
122b63a72ba08_GRCh38.primary_assembly.genome.fa.fai added
122b642138132_GRCh38.primary_assembly.genome.fa.amb added
122b6e871b82_GRCh38.primary_assembly.genome.fa.ann added
122b6481efb41_GRCh38.primary_assembly.genome.fa.bwt added
122b66a018d64_GRCh38.primary_assembly.genome.fa.pac added
122b6be9d69b_GRCh38.primary_assembly.genome.fa.sa added
122b625086039_GRCh38.primary_assembly.genome.fa added
122b648e5512d_hs37d5.fa.fai added
122b6473486be_hs37d5.fa.amb added
122b6497a4877_hs37d5.fa.ann added
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122b66dad715c_hs37d5.fa.pac added
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122b61d4bce42_hs37d5.fa added
122b65bd25e14_complete_ref_lens.bin added
122b6501ea224_ctable.bin added
122b6b271294_ctg_offsets.bin added
122b63234b844_duplicate_clusters.tsv added
122b6232d921c_info.json added
122b64d37e4f_mphf.bin added
122b659097702_pos.bin added
122b67c6451f8_pre_indexing.log added
122b61e41b095_rank.bin added
122b66ab015b7_ref_indexing.log added
122b64e61d819_refAccumLengths.bin added
122b679b27982_reflengths.bin added
122b634478439_refseq.bin added
122b64339d4ff_seq.bin added
122b69ced3d4_versionInfo.json added
122b669b50853_salmon_index added
122b66c35b75c_chrLength.txt added
122b63a993084_chrName.txt added
122b61f40482a_chrNameLength.txt added
122b63541cd6d_chrStart.txt added
122b67315ca6b_exonGeTrInfo.tab added
122b61b9c71d4_exonInfo.tab added
122b63bf52375_geneInfo.tab added
122b65aeaf513_Genome added
122b6777fe106_genomeParameters.txt added
122b66c8e8e34_Log.out added
122b631a2f9a_SA added
122b62c2b290d_SAindex added
122b645942b22_sjdbInfo.txt added
122b629be8de_sjdbList.fromGTF.out.tab added
122b649d54828_sjdbList.out.tab added
122b651745ff6_transcriptInfo.tab added
122b62f483941_GRCh38.GENCODE.v42_100 added
122b62ea6f2a7_knownGene_hg38.sql added
122b65284c9de_knownGene_hg38.txt added
122b6be13825_refGene_hg38.sql added
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122b6763c45db_knownGene_mm39.sql added
122b66f0e6981_knownGene_mm39.txt added
122b61b30cd1d_refGene_mm39.sql added
122b620ea38dd_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/Rtmpd1u1BE/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
21.967 2.402 25.402
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.268 | 0.875 | 8.257 | |
| dataSearch | 1.213 | 0.051 | 1.271 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.642 | 0.158 | 3.939 | |
| getData | 0.001 | 0.001 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.002 | |
| recipeHub-class | 0.142 | 0.013 | 0.157 | |
| recipeLoad | 1.516 | 0.100 | 1.633 | |
| recipeMake | 0.001 | 0.001 | 0.001 | |
| recipeSearch | 0.627 | 0.041 | 0.670 | |
| recipeUpdate | 0 | 0 | 0 | |