Qian Liu
| Snapshot Date: 2025-12-01 13:40 -0500 (Mon, 01 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 2025-12-02 11:36 -0500 (Tue, 02 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" | 4866 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4572 |
| 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 1751/2328 | 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: 2025-12-01 22:08:49 -0500 (Mon, 01 Dec 2025) |
| EndedAt: 2025-12-01 22:09:47 -0500 (Mon, 01 Dec 2025) |
| EllapsedTime: 57.6 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...
37ac4cdd8169_GRCh38.primary_assembly.genome.fa.1.bt2 added
37ac625b3beb_GRCh38.primary_assembly.genome.fa.2.bt2 added
37ac53baf3bf_GRCh38.primary_assembly.genome.fa.3.bt2 added
37ac16d8ab8b_GRCh38.primary_assembly.genome.fa.4.bt2 added
37ac6ae63e64_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
37ac320a4e10_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
37ac428b161a_outfile.txt added
37ac39582717_GRCh37_to_GRCh38.chain added
37ac4a6e746a_GRCh37_to_NCBI34.chain added
37ac199d0153_GRCh37_to_NCBI35.chain added
37ac12c1fd48_GRCh37_to_NCBI36.chain added
37ac7ddb8b96_GRCh38_to_GRCh37.chain added
37ac58a96567_GRCh38_to_NCBI34.chain added
37ac59407aaa_GRCh38_to_NCBI35.chain added
37ac18355cad_GRCh38_to_NCBI36.chain added
37ac57576e45_NCBI34_to_GRCh37.chain added
37ac2d08a0cf_NCBI34_to_GRCh38.chain added
37ac11758d22_NCBI35_to_GRCh37.chain added
37ac3c84bc22_NCBI35_to_GRCh38.chain added
37ac2e5b7b38_NCBI36_to_GRCh37.chain added
37ac77f6b14e_NCBI36_to_GRCh38.chain added
37ac64f2b569_GRCm38_to_NCBIM36.chain added
37ac7a643445_GRCm38_to_NCBIM37.chain added
37ac48a3dcc9_NCBIM36_to_GRCm38.chain added
37ac7df43560_NCBIM37_to_GRCm38.chain added
37ac2bdc723a_1000G_omni2.5.b37.vcf.gz added
37ac15cf5455_1000G_omni2.5.b37.vcf.gz.tbi added
37ac5ea9a3a2_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
37ac5336113b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
37ac2a5632b_1000G_omni2.5.hg38.vcf.gz added
37ac38119d68_1000G_omni2.5.hg38.vcf.gz.tbi added
37acc75339a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
37ac628ec9d9_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
37acc65f81c_af-only-gnomad.raw.sites.vcf added
37ac7a83fc9f_af-only-gnomad.raw.sites.vcf.idx added
37ac6f3e698f_Mutect2-exome-panel.vcf.idx added
37ac6a846457_Mutect2-WGS-panel-b37.vcf added
37ac19d7c263_Mutect2-WGS-panel-b37.vcf.idx added
37ac241afed6_small_exac_common_3.vcf added
37ac6850a61e_small_exac_common_3.vcf.idx added
37ac6ca3113_1000g_pon.hg38.vcf.gz added
37ac445bd9e0_1000g_pon.hg38.vcf.gz.tbi added
37ac6a3d242f_af-only-gnomad.hg38.vcf.gz added
37ac5412c026_af-only-gnomad.hg38.vcf.gz.tbi added
37ac1b0529e9_small_exac_common_3.hg38.vcf.gz added
37ac70028dda_small_exac_common_3.hg38.vcf.gz.tbi added
37ac37af1ca9_gencode.v41.annotation.gtf added
37ac4982b7ce_gencode.v42.annotation.gtf added
37ac24f15b16_gencode.vM30.annotation.gtf added
37ac6193144c_gencode.vM31.annotation.gtf added
37ac7f19bb9f_gencode.v41.transcripts.fa added
37ac726d04e9_gencode.v41.transcripts.fa.fai added
37ac535d97af_gencode.v42.transcripts.fa added
37ac25918ceb_gencode.v42.transcripts.fa.fai added
37ac76baab91_gencode.vM30.pc_transcripts.fa added
37ac5955f97c_gencode.vM30.pc_transcripts.fa.fai added
37ac1b6e69b6_gencode.vM31.pc_transcripts.fa added
37ac6dde39cb_gencode.vM31.pc_transcripts.fa.fai added
37ac18a476c7_GRCh38.primary_assembly.genome.fa.1.ht2 added
37ac55720f74_GRCh38.primary_assembly.genome.fa.2.ht2 added
37ac3354b47f_GRCh38.primary_assembly.genome.fa.3.ht2 added
37ac7e16182c_GRCh38.primary_assembly.genome.fa.4.ht2 added
37ac5c8d315f_GRCh38.primary_assembly.genome.fa.5.ht2 added
37ac39a48371_GRCh38.primary_assembly.genome.fa.6.ht2 added
37ac5fb18d47_GRCh38.primary_assembly.genome.fa.7.ht2 added
37ac1b26166_GRCh38.primary_assembly.genome.fa.8.ht2 added
37ac66187068_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
37ac4e7bf035_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
37ac2ad74fd4_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
37ac1db9fd45_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
37ac1da2cc42_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
37ac2b101041_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
37ac2b9b317d_GRCh38_full_analysis_set_plus_decoy_hla.fa added
37ac59ce1be8_GRCh38.primary_assembly.genome.fa.fai added
37ac6a8a4a67_GRCh38.primary_assembly.genome.fa.amb added
37ac1d1ae6d6_GRCh38.primary_assembly.genome.fa.ann added
37ac5128fa87_GRCh38.primary_assembly.genome.fa.bwt added
37ac5957deb1_GRCh38.primary_assembly.genome.fa.pac added
37ac17dd644a_GRCh38.primary_assembly.genome.fa.sa added
37ac47e34283_GRCh38.primary_assembly.genome.fa added
37ac1923cb54_hs37d5.fa.fai added
37ac7cfa04b0_hs37d5.fa.amb added
37ac249feea_hs37d5.fa.ann added
37ac47feb5d2_hs37d5.fa.bwt added
37ac235312eb_hs37d5.fa.pac added
37ac22ff146b_hs37d5.fa.sa added
37ac18958ec0_hs37d5.fa added
37ac2ceebdc_complete_ref_lens.bin added
37ac5edeb9f4_ctable.bin added
37ac708272d4_ctg_offsets.bin added
37ac440f601_duplicate_clusters.tsv added
37ac44d6bdd5_info.json added
37ac6e490e41_mphf.bin added
37ac7e4705f7_pos.bin added
37ac68d8dbe5_pre_indexing.log added
37ac754ccd29_rank.bin added
37ac5317ae9_ref_indexing.log added
37ac737c59a8_refAccumLengths.bin added
37ac68e25fd3_reflengths.bin added
37ac66014b70_refseq.bin added
37ac5effda61_seq.bin added
37ac6f5a4700_versionInfo.json added
37acfeb8a1d_salmon_index added
37ac30b87e15_chrLength.txt added
37ac205dadb0_chrName.txt added
37ac66360e69_chrNameLength.txt added
37ac66ec43eb_chrStart.txt added
37ac215f2e17_exonGeTrInfo.tab added
37ac6fcaf91e_exonInfo.tab added
37ac76a959e8_geneInfo.tab added
37ac684dcb34_Genome added
37ac4b57f86b_genomeParameters.txt added
37ac7c765f71_Log.out added
37ac3f74338d_SA added
37ac65e48e86_SAindex added
37ac4933ad_sjdbInfo.txt added
37ac45dfa300_sjdbList.fromGTF.out.tab added
37ac5d4678d6_sjdbList.out.tab added
37ac3da75971_transcriptInfo.tab added
37ac35e12956_GRCh38.GENCODE.v42_100 added
37ac5160e8bc_knownGene_hg38.sql added
37ac314fb861_knownGene_hg38.txt added
37ac68d20191_refGene_hg38.sql added
37ac33650c5a_refGene_hg38.txt added
37ac2f0e0312_knownGene_mm39.sql added
37ac40ebaae0_knownGene_mm39.txt added
37ac301f796c_refGene_mm39.sql added
37ac625cba22_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//Rtmpize6vo/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
6.996 0.798 8.878
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 1.915 | 0.233 | 2.235 | |
| dataSearch | 0.359 | 0.014 | 0.391 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.953 | 0.057 | 2.387 | |
| getData | 0.001 | 0.000 | 0.000 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.043 | 0.006 | 0.050 | |
| recipeLoad | 0.671 | 0.076 | 0.799 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.179 | 0.013 | 0.202 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |