Qian Liu
| Snapshot Date: 2026-01-01 13:40 -0500 (Thu, 01 Jan 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 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-03 11:35 -0500 (Sat, 03 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" | 4809 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4593 |
| 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 1754/2332 | 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 | | ||||||||
|
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: 2026-01-01 21:57:12 -0500 (Thu, 01 Jan 2026) |
| EndedAt: 2026-01-01 21:58:08 -0500 (Thu, 01 Jan 2026) |
| EllapsedTime: 56.7 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 Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* 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-arm64/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 Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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...
10b3a180b2c1f_GRCh38.primary_assembly.genome.fa.1.bt2 added
10b3a57db38e_GRCh38.primary_assembly.genome.fa.2.bt2 added
10b3a7f973272_GRCh38.primary_assembly.genome.fa.3.bt2 added
10b3a1f711bcf_GRCh38.primary_assembly.genome.fa.4.bt2 added
10b3a3ad8c329_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
10b3a6cf4d6ed_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
10b3a3e4a997d_outfile.txt added
10b3a13a2fd7e_GRCh37_to_GRCh38.chain added
10b3a31b06544_GRCh37_to_NCBI34.chain added
10b3a33c86cd8_GRCh37_to_NCBI35.chain added
10b3a2b61f377_GRCh37_to_NCBI36.chain added
10b3a2bb71fe1_GRCh38_to_GRCh37.chain added
10b3a38e0333_GRCh38_to_NCBI34.chain added
10b3a60740b17_GRCh38_to_NCBI35.chain added
10b3a62844479_GRCh38_to_NCBI36.chain added
10b3a59ab9676_NCBI34_to_GRCh37.chain added
10b3a10234af8_NCBI34_to_GRCh38.chain added
10b3a7d0ee80e_NCBI35_to_GRCh37.chain added
10b3a5da52f46_NCBI35_to_GRCh38.chain added
10b3a7c2ccb2_NCBI36_to_GRCh37.chain added
10b3a60cbe19_NCBI36_to_GRCh38.chain added
10b3a2e945e69_GRCm38_to_NCBIM36.chain added
10b3aec25763_GRCm38_to_NCBIM37.chain added
10b3a78f72c26_NCBIM36_to_GRCm38.chain added
10b3a2b73b0d5_NCBIM37_to_GRCm38.chain added
10b3a385e863c_1000G_omni2.5.b37.vcf.gz added
10b3a45beea0d_1000G_omni2.5.b37.vcf.gz.tbi added
10b3a78f81f40_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
10b3a69cbe0cb_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
10b3a481365b0_1000G_omni2.5.hg38.vcf.gz added
10b3a71792ac7_1000G_omni2.5.hg38.vcf.gz.tbi added
10b3a49e7a904_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
10b3a8096b84_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
10b3a2271ab3b_af-only-gnomad.raw.sites.vcf added
10b3a54a0c027_af-only-gnomad.raw.sites.vcf.idx added
10b3a5a76bd9_Mutect2-exome-panel.vcf.idx added
10b3a32997675_Mutect2-WGS-panel-b37.vcf added
10b3a79301546_Mutect2-WGS-panel-b37.vcf.idx added
10b3a43c4e4d2_small_exac_common_3.vcf added
10b3a338ab9c0_small_exac_common_3.vcf.idx added
10b3a58a906af_1000g_pon.hg38.vcf.gz added
10b3a40f5f8a2_1000g_pon.hg38.vcf.gz.tbi added
10b3a549674ff_af-only-gnomad.hg38.vcf.gz added
10b3a61db3cbb_af-only-gnomad.hg38.vcf.gz.tbi added
10b3a704b2e_small_exac_common_3.hg38.vcf.gz added
10b3a4c57b93b_small_exac_common_3.hg38.vcf.gz.tbi added
10b3a1341f7a5_gencode.v41.annotation.gtf added
10b3a4fe97b83_gencode.v42.annotation.gtf added
10b3a69abfe71_gencode.vM30.annotation.gtf added
10b3a1acde2ea_gencode.vM31.annotation.gtf added
10b3a42ec7e65_gencode.v41.transcripts.fa added
10b3a345e3b36_gencode.v41.transcripts.fa.fai added
10b3a16817116_gencode.v42.transcripts.fa added
10b3ac2766e5_gencode.v42.transcripts.fa.fai added
10b3a6ed44a9e_gencode.vM30.pc_transcripts.fa added
10b3a336f03ea_gencode.vM30.pc_transcripts.fa.fai added
10b3a3d6a1207_gencode.vM31.pc_transcripts.fa added
10b3a7ec5a910_gencode.vM31.pc_transcripts.fa.fai added
10b3a62de9a75_GRCh38.primary_assembly.genome.fa.1.ht2 added
10b3a46eaa09_GRCh38.primary_assembly.genome.fa.2.ht2 added
10b3a7d5d3724_GRCh38.primary_assembly.genome.fa.3.ht2 added
10b3a72cf5cc8_GRCh38.primary_assembly.genome.fa.4.ht2 added
10b3abd4895b_GRCh38.primary_assembly.genome.fa.5.ht2 added
10b3a2e85bb6e_GRCh38.primary_assembly.genome.fa.6.ht2 added
10b3a4dd44a9e_GRCh38.primary_assembly.genome.fa.7.ht2 added
10b3a2c6ef2fd_GRCh38.primary_assembly.genome.fa.8.ht2 added
10b3a2812d6d5_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
10b3a6cd64e80_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
10b3a69bbed52_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
10b3a30d9d8b9_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
10b3a2e2372bd_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
10b3a1941edf5_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
10b3a376d7cc7_GRCh38_full_analysis_set_plus_decoy_hla.fa added
10b3a751b093e_GRCh38.primary_assembly.genome.fa.fai added
10b3a41fc0182_GRCh38.primary_assembly.genome.fa.amb added
10b3a7c71fa6_GRCh38.primary_assembly.genome.fa.ann added
10b3a21eecf47_GRCh38.primary_assembly.genome.fa.bwt added
10b3a456a4fb8_GRCh38.primary_assembly.genome.fa.pac added
10b3a4697dca2_GRCh38.primary_assembly.genome.fa.sa added
10b3a1c1633e3_GRCh38.primary_assembly.genome.fa added
10b3a75a88a7c_hs37d5.fa.fai added
10b3ac1c0f3d_hs37d5.fa.amb added
10b3a62c7401_hs37d5.fa.ann added
10b3a5073f0d1_hs37d5.fa.bwt added
10b3a6bc7529a_hs37d5.fa.pac added
10b3a6b0033bd_hs37d5.fa.sa added
10b3a5a44f42c_hs37d5.fa added
10b3a64faa300_complete_ref_lens.bin added
10b3a2e388cb_ctable.bin added
10b3a2829c8e8_ctg_offsets.bin added
10b3a4f450bf1_duplicate_clusters.tsv added
10b3a3e1323df_info.json added
10b3a5a98254f_mphf.bin added
10b3a3ab99400_pos.bin added
10b3a6da3aa1e_pre_indexing.log added
10b3a13f5cfce_rank.bin added
10b3a6f1de79e_ref_indexing.log added
10b3a14516f10_refAccumLengths.bin added
10b3a6e528ddb_reflengths.bin added
10b3a6ddf5d72_refseq.bin added
10b3a63701fb8_seq.bin added
10b3a56329c08_versionInfo.json added
10b3a14a1fd6e_salmon_index added
10b3a17054b57_chrLength.txt added
10b3a5c95488f_chrName.txt added
10b3a4cced3c5_chrNameLength.txt added
10b3a1eb151e8_chrStart.txt added
10b3ab786616_exonGeTrInfo.tab added
10b3ad76343c_exonInfo.tab added
10b3a4b5f560b_geneInfo.tab added
10b3a600a12d5_Genome added
10b3a355a8f35_genomeParameters.txt added
10b3a4c6ffbf0_Log.out added
10b3a4c0570c4_SA added
10b3a792e7ad9_SAindex added
10b3a5a837ab6_sjdbInfo.txt added
10b3a6ded7126_sjdbList.fromGTF.out.tab added
10b3a7f9fae2b_sjdbList.out.tab added
10b3a4c63ca82_transcriptInfo.tab added
10b3a2b8443fc_GRCh38.GENCODE.v42_100 added
10b3a788b6bb5_knownGene_hg38.sql added
10b3a94c75e7_knownGene_hg38.txt added
10b3a7ad09575_refGene_hg38.sql added
10b3a14047351_refGene_hg38.txt added
10b3a302ed51b_knownGene_mm39.sql added
10b3a52a8f853_knownGene_mm39.txt added
10b3a53473b8a_refGene_mm39.sql added
10b3a69960bbc_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:
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN46dtB/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
7.078 0.852 8.660
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.057 | 0.257 | 2.394 | |
| dataSearch | 0.365 | 0.016 | 0.403 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.916 | 0.064 | 2.137 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.001 | 0.000 | |
| recipeHub-class | 0.044 | 0.006 | 0.055 | |
| recipeLoad | 0.426 | 0.030 | 0.480 | |
| recipeMake | 0.000 | 0.001 | 0.000 | |
| recipeSearch | 0.172 | 0.012 | 0.187 | |
| recipeUpdate | 0 | 0 | 0 | |