Qian Liu
| Snapshot Date: 2026-03-31 13:40 -0400 (Tue, 31 Mar 2026) |
| 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 Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-01 13:07 -0400 (Wed, 01 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.6.0 alpha (2026-03-30 r89742) | 4816 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-03-28 r89739) | 4539 |
| 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 1785/2374 | 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 | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| See other builds for ReUseData in R Universe. | ||||||||||||||
|
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: /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_1.11.0.tar.gz |
| StartedAt: 2026-03-31 21:09:32 -0400 (Tue, 31 Mar 2026) |
| EndedAt: 2026-03-31 21:10:24 -0400 (Tue, 31 Mar 2026) |
| EllapsedTime: 52.5 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_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R version 4.6.0 alpha (2026-03-28 r89739)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-01 01:09:32 UTC
* using option ‘--no-vignettes’
* 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 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
* 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-3.23-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/4.6/Resources/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 version 4.6.0 alpha (2026-03-28 r89739)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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...
64e37e0073ec_GRCh38.primary_assembly.genome.fa.1.bt2 added
64e34fbacb94_GRCh38.primary_assembly.genome.fa.2.bt2 added
64e3708b8a70_GRCh38.primary_assembly.genome.fa.3.bt2 added
64e3592df8c9_GRCh38.primary_assembly.genome.fa.4.bt2 added
64e3592881dc_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
64e37265c03e_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
64e37630611e_outfile.txt added
64e362383530_GRCh37_to_GRCh38.chain added
64e3582c14b0_GRCh37_to_NCBI34.chain added
64e336025c09_GRCh37_to_NCBI35.chain added
64e354e86e92_GRCh37_to_NCBI36.chain added
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64e33b7c66cc_GRCh38_to_NCBI36.chain added
64e36440f996_NCBI34_to_GRCh37.chain added
64e365c21a45_NCBI34_to_GRCh38.chain added
64e32a4adc34_NCBI35_to_GRCh37.chain added
64e318beef9d_NCBI35_to_GRCh38.chain added
64e31f65391c_NCBI36_to_GRCh37.chain added
64e32e886d5e_NCBI36_to_GRCh38.chain added
64e37ec44e2f_GRCm38_to_NCBIM36.chain added
64e39e930ae_GRCm38_to_NCBIM37.chain added
64e32c7af497_NCBIM36_to_GRCm38.chain added
64e33c4ffc51_NCBIM37_to_GRCm38.chain added
64e3273e48c6_1000G_omni2.5.b37.vcf.gz added
64e36a1bd34a_1000G_omni2.5.b37.vcf.gz.tbi added
64e348ccd5b2_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
64e37fe1be74_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
64e33d9ef343_1000G_omni2.5.hg38.vcf.gz added
64e3e74d350_1000G_omni2.5.hg38.vcf.gz.tbi added
64e317dd309a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
64e33aa1dab3_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
64e3581d3bd7_af-only-gnomad.raw.sites.vcf added
64e36743cd72_af-only-gnomad.raw.sites.vcf.idx added
64e314652c55_Mutect2-exome-panel.vcf.idx added
64e37e418ae8_Mutect2-WGS-panel-b37.vcf added
64e3106c61a_Mutect2-WGS-panel-b37.vcf.idx added
64e363b7d57c_small_exac_common_3.vcf added
64e33a20f309_small_exac_common_3.vcf.idx added
64e34933f1af_1000g_pon.hg38.vcf.gz added
64e371403db4_1000g_pon.hg38.vcf.gz.tbi added
64e330932e82_af-only-gnomad.hg38.vcf.gz added
64e3ed271b8_af-only-gnomad.hg38.vcf.gz.tbi added
64e31a27eea2_small_exac_common_3.hg38.vcf.gz added
64e333a3db18_small_exac_common_3.hg38.vcf.gz.tbi added
64e34a851f24_gencode.v41.annotation.gtf added
64e369bf9ab4_gencode.v42.annotation.gtf added
64e32245d5a9_gencode.vM30.annotation.gtf added
64e316ce5bd3_gencode.vM31.annotation.gtf added
64e345ee8557_gencode.v41.transcripts.fa added
64e32e74369f_gencode.v41.transcripts.fa.fai added
64e34fae188c_gencode.v42.transcripts.fa added
64e32ecdb832_gencode.v42.transcripts.fa.fai added
64e343f7f29f_gencode.vM30.pc_transcripts.fa added
64e34b59c795_gencode.vM30.pc_transcripts.fa.fai added
64e3733e2dd8_gencode.vM31.pc_transcripts.fa added
64e37733fb03_gencode.vM31.pc_transcripts.fa.fai added
64e375a4bf18_GRCh38.primary_assembly.genome.fa.1.ht2 added
64e312fdfcff_GRCh38.primary_assembly.genome.fa.2.ht2 added
64e360ecd316_GRCh38.primary_assembly.genome.fa.3.ht2 added
64e35c167b10_GRCh38.primary_assembly.genome.fa.4.ht2 added
64e347e986ab_GRCh38.primary_assembly.genome.fa.5.ht2 added
64e33488696f_GRCh38.primary_assembly.genome.fa.6.ht2 added
64e367c2115a_GRCh38.primary_assembly.genome.fa.7.ht2 added
64e3760160ed_GRCh38.primary_assembly.genome.fa.8.ht2 added
64e35482a421_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
64e34ce59ddf_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
64e376dfc2e9_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
64e35c758bf7_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
64e32938348d_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
64e329022a1f_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
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64e343e394f3_GRCh38.primary_assembly.genome.fa.fai added
64e312480057_GRCh38.primary_assembly.genome.fa.amb added
64e3350e5921_GRCh38.primary_assembly.genome.fa.ann added
64e340fda0bd_GRCh38.primary_assembly.genome.fa.bwt added
64e34b43f9a0_GRCh38.primary_assembly.genome.fa.pac added
64e35bb99dfa_GRCh38.primary_assembly.genome.fa.sa added
64e37732b721_GRCh38.primary_assembly.genome.fa added
64e3229514aa_hs37d5.fa.fai added
64e3697fb6a2_hs37d5.fa.amb added
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64e33d3085f8_ctable.bin added
64e33cab7c2a_ctg_offsets.bin added
64e31e64c884_duplicate_clusters.tsv added
64e36aa861b2_info.json added
64e354a623d2_mphf.bin added
64e36779db68_pos.bin added
64e37133bdea_pre_indexing.log added
64e37bf987b5_rank.bin added
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64e337222bd2_refseq.bin added
64e3246b0445_seq.bin added
64e36de560b0_versionInfo.json added
64e36e2efb2d_salmon_index added
64e34e6c7fde_chrLength.txt added
64e3353ef00b_chrName.txt added
64e337017d7c_chrNameLength.txt added
64e342d5741a_chrStart.txt added
64e34bb9793d_exonGeTrInfo.tab added
64e37dc6baa1_exonInfo.tab added
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64e3117f8510_Genome added
64e34af8e669_genomeParameters.txt added
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64e32524697e_sjdbList.fromGTF.out.tab added
64e37989e23e_sjdbList.out.tab added
64e34b6492c8_transcriptInfo.tab added
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64e34f5daab4_refGene_hg38.sql added
64e3e723821_refGene_hg38.txt added
64e36cc305ef_knownGene_mm39.sql added
64e377bac5b1_knownGene_mm39.txt added
64e370924e0_refGene_mm39.sql added
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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:
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpKxx6mp/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 1 | SKIP 0 | PASS 44 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 44 ]
> Sys.setenv(cachePath = file.path(tempdir(), "cache"))
>
>
>
> proc.time()
user system elapsed
6.696 0.860 8.033
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 1.985 | 0.287 | 2.286 | |
| dataSearch | 0.346 | 0.023 | 0.382 | |
| dataUpdate | 0.000 | 0.001 | 0.000 | |
| getCloudData | 0.873 | 0.061 | 1.688 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.036 | 0.002 | 0.040 | |
| recipeLoad | 0.401 | 0.029 | 0.439 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.165 | 0.012 | 0.177 | |
| recipeUpdate | 0 | 0 | 0 | |