Qian Liu
| Snapshot Date: 2025-12-10 13:40 -0500 (Wed, 10 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 2025-12-11 11:36 -0500 (Thu, 11 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" | 4872 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4580 |
| 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 1753/2331 | 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: 2025-12-10 22:27:44 -0500 (Wed, 10 Dec 2025) |
| EndedAt: 2025-12-10 22:28:39 -0500 (Wed, 10 Dec 2025) |
| EllapsedTime: 55.6 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...
71c33db88418_GRCh38.primary_assembly.genome.fa.1.bt2 added
71c31ce86350_GRCh38.primary_assembly.genome.fa.2.bt2 added
71c35cd02803_GRCh38.primary_assembly.genome.fa.3.bt2 added
71c365f30c8f_GRCh38.primary_assembly.genome.fa.4.bt2 added
71c337bdb493_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
71c379a3b7c_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
71c31eb74dca_outfile.txt added
71c314541887_GRCh37_to_GRCh38.chain added
71c31d16517e_GRCh37_to_NCBI34.chain added
71c32440361d_GRCh37_to_NCBI35.chain added
71c373a0bc82_GRCh37_to_NCBI36.chain added
71c33db8361c_GRCh38_to_GRCh37.chain added
71c38e887ec_GRCh38_to_NCBI34.chain added
71c35a339b85_GRCh38_to_NCBI35.chain added
71c372276706_GRCh38_to_NCBI36.chain added
71c378dcf576_NCBI34_to_GRCh37.chain added
71c3727753f7_NCBI34_to_GRCh38.chain added
71c37829b7d6_NCBI35_to_GRCh37.chain added
71c37ae4803b_NCBI35_to_GRCh38.chain added
71c32f9ee085_NCBI36_to_GRCh37.chain added
71c367a6542f_NCBI36_to_GRCh38.chain added
71c358e10ed2_GRCm38_to_NCBIM36.chain added
71c31f942a94_GRCm38_to_NCBIM37.chain added
71c338776abe_NCBIM36_to_GRCm38.chain added
71c32800fce8_NCBIM37_to_GRCm38.chain added
71c358dbf7dc_1000G_omni2.5.b37.vcf.gz added
71c3516dba17_1000G_omni2.5.b37.vcf.gz.tbi added
71c37ad465c4_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
71c3e6565dc_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
71c3230255e6_1000G_omni2.5.hg38.vcf.gz added
71c36e5580fe_1000G_omni2.5.hg38.vcf.gz.tbi added
71c32f87dc49_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
71c38f5500_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
71c342157349_af-only-gnomad.raw.sites.vcf added
71c3e43df84_af-only-gnomad.raw.sites.vcf.idx added
71c3a075a6d_Mutect2-exome-panel.vcf.idx added
71c368c1af3f_Mutect2-WGS-panel-b37.vcf added
71c33d886d4_Mutect2-WGS-panel-b37.vcf.idx added
71c37c7bca44_small_exac_common_3.vcf added
71c3231c7635_small_exac_common_3.vcf.idx added
71c32194a395_1000g_pon.hg38.vcf.gz added
71c3257f9c6c_1000g_pon.hg38.vcf.gz.tbi added
71c35cf689af_af-only-gnomad.hg38.vcf.gz added
71c33dc96fd7_af-only-gnomad.hg38.vcf.gz.tbi added
71c373cdabf1_small_exac_common_3.hg38.vcf.gz added
71c343d3969c_small_exac_common_3.hg38.vcf.gz.tbi added
71c37844fe8d_gencode.v41.annotation.gtf added
71c379a418aa_gencode.v42.annotation.gtf added
71c344f7f4a_gencode.vM30.annotation.gtf added
71c37f2dd57b_gencode.vM31.annotation.gtf added
71c31a1abf78_gencode.v41.transcripts.fa added
71c352106cab_gencode.v41.transcripts.fa.fai added
71c3344e78a4_gencode.v42.transcripts.fa added
71c3bd271d0_gencode.v42.transcripts.fa.fai added
71c3252e14c0_gencode.vM30.pc_transcripts.fa added
71c374545c51_gencode.vM30.pc_transcripts.fa.fai added
71c34e790581_gencode.vM31.pc_transcripts.fa added
71c36b588066_gencode.vM31.pc_transcripts.fa.fai added
71c37f55df98_GRCh38.primary_assembly.genome.fa.1.ht2 added
71c35ecab577_GRCh38.primary_assembly.genome.fa.2.ht2 added
71c34e4fc83f_GRCh38.primary_assembly.genome.fa.3.ht2 added
71c357e3c843_GRCh38.primary_assembly.genome.fa.4.ht2 added
71c32b70d3c9_GRCh38.primary_assembly.genome.fa.5.ht2 added
71c37c604766_GRCh38.primary_assembly.genome.fa.6.ht2 added
71c314efb955_GRCh38.primary_assembly.genome.fa.7.ht2 added
71c36708630_GRCh38.primary_assembly.genome.fa.8.ht2 added
71c34579bc9d_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
71c33b4e0b0d_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
71c3b7a0e6_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
71c317a45c68_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
71c327aebbf8_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
71c340b6ab22_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
71c3189d665f_GRCh38_full_analysis_set_plus_decoy_hla.fa added
71c35abf399_GRCh38.primary_assembly.genome.fa.fai added
71c35c05c4b7_GRCh38.primary_assembly.genome.fa.amb added
71c37eb5f993_GRCh38.primary_assembly.genome.fa.ann added
71c35d1462e2_GRCh38.primary_assembly.genome.fa.bwt added
71c36568132b_GRCh38.primary_assembly.genome.fa.pac added
71c313c2a010_GRCh38.primary_assembly.genome.fa.sa added
71c34e9a8492_GRCh38.primary_assembly.genome.fa added
71c3275b58f_hs37d5.fa.fai added
71c37de2c08b_hs37d5.fa.amb added
71c331cf263e_hs37d5.fa.ann added
71c316d7c9fe_hs37d5.fa.bwt added
71c3310e4e69_hs37d5.fa.pac added
71c3223de8a8_hs37d5.fa.sa added
71c3e757f28_hs37d5.fa added
71c343ef2282_complete_ref_lens.bin added
71c38c2a7a6_ctable.bin added
71c3238c87c8_ctg_offsets.bin added
71c35f266db3_duplicate_clusters.tsv added
71c353ec3392_info.json added
71c3382de149_mphf.bin added
71c34c219c6f_pos.bin added
71c332a56275_pre_indexing.log added
71c37e3094d_rank.bin added
71c34a77a246_ref_indexing.log added
71c3743ec7db_refAccumLengths.bin added
71c345b3367c_reflengths.bin added
71c378be2aa3_refseq.bin added
71c3ce17143_seq.bin added
71c324d2ec50_versionInfo.json added
71c313988b13_salmon_index added
71c33d29672_chrLength.txt added
71c376931853_chrName.txt added
71c333222df6_chrNameLength.txt added
71c38f78bb4_chrStart.txt added
71c333f4db05_exonGeTrInfo.tab added
71c310573fe9_exonInfo.tab added
71c35024e260_geneInfo.tab added
71c3258a35bb_Genome added
71c314cd9b3e_genomeParameters.txt added
71c3468b0e1d_Log.out added
71c3534bb619_SA added
71c3fa04e08_SAindex added
71c36562f73b_sjdbInfo.txt added
71c34455767d_sjdbList.fromGTF.out.tab added
71c346d62b97_sjdbList.out.tab added
71c316c7ead6_transcriptInfo.tab added
71c31f0a9349_GRCh38.GENCODE.v42_100 added
71c36f4bad8a_knownGene_hg38.sql added
71c3516e781b_knownGene_hg38.txt added
71c32b8f5e61_refGene_hg38.sql added
71c3517d489e_refGene_hg38.txt added
71c3782aa6dd_knownGene_mm39.sql added
71c3383134cd_knownGene_mm39.txt added
71c326819b8d_refGene_mm39.sql added
71c370b59bb_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//RtmpS42DCB/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
6.904 0.815 8.863
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.125 | 0.251 | 2.469 | |
| dataSearch | 0.355 | 0.016 | 0.381 | |
| dataUpdate | 0.001 | 0.001 | 0.000 | |
| getCloudData | 0.923 | 0.064 | 2.395 | |
| getData | 0.001 | 0.000 | 0.000 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.047 | 0.005 | 0.053 | |
| recipeLoad | 0.412 | 0.031 | 0.450 | |
| recipeMake | 0.000 | 0.001 | 0.000 | |
| recipeSearch | 0.175 | 0.010 | 0.191 | |
| recipeUpdate | 0.001 | 0.000 | 0.000 | |