Qian Liu
| Snapshot Date: 2025-12-18 13:40 -0500 (Thu, 18 Dec 2025) |
| 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 2025-12-19 11:35 -0500 (Fri, 19 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4875 |
| 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: 2025-12-18 21:46:50 -0500 (Thu, 18 Dec 2025) |
| EndedAt: 2025-12-18 21:47:48 -0500 (Thu, 18 Dec 2025) |
| EllapsedTime: 57.7 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...
1675a18515fbb_GRCh38.primary_assembly.genome.fa.1.bt2 added
1675a663fa76_GRCh38.primary_assembly.genome.fa.2.bt2 added
1675add05c41_GRCh38.primary_assembly.genome.fa.3.bt2 added
1675a6a58b67c_GRCh38.primary_assembly.genome.fa.4.bt2 added
1675a6634bd6f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1675a1080f6d5_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1675a2cd226a_outfile.txt added
1675a698e5e95_GRCh37_to_GRCh38.chain added
1675a1e3be57_GRCh37_to_NCBI34.chain added
1675aee542b9_GRCh37_to_NCBI35.chain added
1675a6d7f8752_GRCh37_to_NCBI36.chain added
1675a4f8d50a7_GRCh38_to_GRCh37.chain added
1675a46aa2cbe_GRCh38_to_NCBI34.chain added
1675a4e5f9230_GRCh38_to_NCBI35.chain added
1675a6476b582_GRCh38_to_NCBI36.chain added
1675a2d869d55_NCBI34_to_GRCh37.chain added
1675a60c34ecc_NCBI34_to_GRCh38.chain added
1675a366a64b5_NCBI35_to_GRCh37.chain added
1675a2f9c2fc_NCBI35_to_GRCh38.chain added
1675a5b702fea_NCBI36_to_GRCh37.chain added
1675a2259da8c_NCBI36_to_GRCh38.chain added
1675a391b2ef2_GRCm38_to_NCBIM36.chain added
1675a27a72f28_GRCm38_to_NCBIM37.chain added
1675a5108ff6e_NCBIM36_to_GRCm38.chain added
1675a25b9b852_NCBIM37_to_GRCm38.chain added
1675a43f422d7_1000G_omni2.5.b37.vcf.gz added
1675a511b741b_1000G_omni2.5.b37.vcf.gz.tbi added
1675a6163c236_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1675a5c63992d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1675aedd88be_1000G_omni2.5.hg38.vcf.gz added
1675a723c7991_1000G_omni2.5.hg38.vcf.gz.tbi added
1675a6051592e_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1675a7cb60c68_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1675a13e8bfcf_af-only-gnomad.raw.sites.vcf added
1675a1588b93f_af-only-gnomad.raw.sites.vcf.idx added
1675a4339e224_Mutect2-exome-panel.vcf.idx added
1675ad2dcbf7_Mutect2-WGS-panel-b37.vcf added
1675a39a9cbe3_Mutect2-WGS-panel-b37.vcf.idx added
1675a3a88c1a8_small_exac_common_3.vcf added
1675a68621a9d_small_exac_common_3.vcf.idx added
1675ac16ef5_1000g_pon.hg38.vcf.gz added
1675a1b5b9736_1000g_pon.hg38.vcf.gz.tbi added
1675a1a246842_af-only-gnomad.hg38.vcf.gz added
1675a4c38d276_af-only-gnomad.hg38.vcf.gz.tbi added
1675a26816812_small_exac_common_3.hg38.vcf.gz added
1675a79d7897d_small_exac_common_3.hg38.vcf.gz.tbi added
1675a3583ac09_gencode.v41.annotation.gtf added
1675a57939e51_gencode.v42.annotation.gtf added
1675a1c7f04c2_gencode.vM30.annotation.gtf added
1675a57116b2b_gencode.vM31.annotation.gtf added
1675a389300b5_gencode.v41.transcripts.fa added
1675a3b138817_gencode.v41.transcripts.fa.fai added
1675a7f4bbc4d_gencode.v42.transcripts.fa added
1675a4537a485_gencode.v42.transcripts.fa.fai added
1675a48123b43_gencode.vM30.pc_transcripts.fa added
1675a24f0d0ac_gencode.vM30.pc_transcripts.fa.fai added
1675a3e13df26_gencode.vM31.pc_transcripts.fa added
1675aa9f57a1_gencode.vM31.pc_transcripts.fa.fai added
1675a63321079_GRCh38.primary_assembly.genome.fa.1.ht2 added
1675a6bd7aacf_GRCh38.primary_assembly.genome.fa.2.ht2 added
1675a1c0f3359_GRCh38.primary_assembly.genome.fa.3.ht2 added
1675a29f42673_GRCh38.primary_assembly.genome.fa.4.ht2 added
1675a5c085d89_GRCh38.primary_assembly.genome.fa.5.ht2 added
1675a2934fc93_GRCh38.primary_assembly.genome.fa.6.ht2 added
1675a55b22c07_GRCh38.primary_assembly.genome.fa.7.ht2 added
1675a2468ab85_GRCh38.primary_assembly.genome.fa.8.ht2 added
1675a53d4bb6f_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1675a335d9f68_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1675a478c7f30_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1675a58f24d02_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1675ab9debed_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1675a2cec1a90_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1675a40c3fafa_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1675a292544e_GRCh38.primary_assembly.genome.fa.fai added
1675a54dcce33_GRCh38.primary_assembly.genome.fa.amb added
1675a6c65a1cb_GRCh38.primary_assembly.genome.fa.ann added
1675a4614e06_GRCh38.primary_assembly.genome.fa.bwt added
1675a10496e29_GRCh38.primary_assembly.genome.fa.pac added
1675a44df4e19_GRCh38.primary_assembly.genome.fa.sa added
1675a20806ea2_GRCh38.primary_assembly.genome.fa added
1675a4fdf5e59_hs37d5.fa.fai added
1675a51ab4e06_hs37d5.fa.amb added
1675a458f95cd_hs37d5.fa.ann added
1675a55b3e968_hs37d5.fa.bwt added
1675a16a0d6cd_hs37d5.fa.pac added
1675a19763856_hs37d5.fa.sa added
1675a206ca329_hs37d5.fa added
1675a3c4be960_complete_ref_lens.bin added
1675a1bc6bc8d_ctable.bin added
1675a1484db3a_ctg_offsets.bin added
1675a1e54c75c_duplicate_clusters.tsv added
1675a4fec7892_info.json added
1675a2ddfe23c_mphf.bin added
1675a457de8ab_pos.bin added
1675a4d365631_pre_indexing.log added
1675a2a54d291_rank.bin added
1675a26cc434d_ref_indexing.log added
1675a2c568821_refAccumLengths.bin added
1675a65034544_reflengths.bin added
1675a39b8a72b_refseq.bin added
1675a9e715a8_seq.bin added
1675a223ecdac_versionInfo.json added
1675a4930e8c4_salmon_index added
1675a2a01c166_chrLength.txt added
1675a59402515_chrName.txt added
1675a242b37a_chrNameLength.txt added
1675a69150fbe_chrStart.txt added
1675a65bcb8d7_exonGeTrInfo.tab added
1675a490b5f6f_exonInfo.tab added
1675a9a695e0_geneInfo.tab added
1675a17b9aa13_Genome added
1675a1e4cd190_genomeParameters.txt added
1675a4552547a_Log.out added
1675a20283924_SA added
1675a30bf7afa_SAindex added
1675a6b22cc16_sjdbInfo.txt added
1675a3984ef4d_sjdbList.fromGTF.out.tab added
1675a467ac5bb_sjdbList.out.tab added
1675a264b9c23_transcriptInfo.tab added
1675a2df7d179_GRCh38.GENCODE.v42_100 added
1675a68d97682_knownGene_hg38.sql added
1675a1cf38695_knownGene_hg38.txt added
1675a3808af0c_refGene_hg38.sql added
1675a421c5991_refGene_hg38.txt added
1675a533c607f_knownGene_mm39.sql added
1675a20e35c8a_knownGene_mm39.txt added
1675a2ed078e4_refGene_mm39.sql added
1675a78b0d8be_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//RtmpQfVupC/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
6.980 0.842 8.874
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.093 | 0.283 | 2.488 | |
| dataSearch | 0.372 | 0.019 | 0.397 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.893 | 0.063 | 2.112 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.045 | 0.006 | 0.052 | |
| recipeLoad | 0.436 | 0.032 | 0.505 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.181 | 0.012 | 0.204 | |
| recipeUpdate | 0 | 0 | 0 | |