Qian Liu
| Snapshot Date: 2026-04-12 13:40 -0400 (Sun, 12 Apr 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 2026-04-13 11:36 -0400 (Mon, 13 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4919 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4632 |
| 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 1793/2390 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.11.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.4 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: 2026-04-12 21:44:18 -0400 (Sun, 12 Apr 2026) |
| EndedAt: 2026-04-12 21:45:10 -0400 (Sun, 12 Apr 2026) |
| EllapsedTime: 52.6 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 version 4.6.0 alpha (2026-04-08 r89818)
* 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: 2026-04-13 01:44:18 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 (2026-04-08 r89818)
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...
15a9d413f166f_GRCh38.primary_assembly.genome.fa.1.bt2 added
15a9d14d9f2e0_GRCh38.primary_assembly.genome.fa.2.bt2 added
15a9d70d85ad1_GRCh38.primary_assembly.genome.fa.3.bt2 added
15a9dc328938_GRCh38.primary_assembly.genome.fa.4.bt2 added
15a9d49cec1c9_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
15a9d251498fa_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
15a9d6b47581a_outfile.txt added
15a9d18e949fc_GRCh37_to_GRCh38.chain added
15a9d7bf84c2a_GRCh37_to_NCBI34.chain added
15a9d6a5098fb_GRCh37_to_NCBI35.chain added
15a9d516bbd44_GRCh37_to_NCBI36.chain added
15a9d7856e51e_GRCh38_to_GRCh37.chain added
15a9d10dc524b_GRCh38_to_NCBI34.chain added
15a9d709ec292_GRCh38_to_NCBI35.chain added
15a9d46f83901_GRCh38_to_NCBI36.chain added
15a9d5266950d_NCBI34_to_GRCh37.chain added
15a9d4cc3b2be_NCBI34_to_GRCh38.chain added
15a9d440bff51_NCBI35_to_GRCh37.chain added
15a9d6fa741bd_NCBI35_to_GRCh38.chain added
15a9d4dcd188f_NCBI36_to_GRCh37.chain added
15a9d54077c30_NCBI36_to_GRCh38.chain added
15a9d376a5e69_GRCm38_to_NCBIM36.chain added
15a9d285c5beb_GRCm38_to_NCBIM37.chain added
15a9d4796b600_NCBIM36_to_GRCm38.chain added
15a9d7786deb7_NCBIM37_to_GRCm38.chain added
15a9d3787fdaf_1000G_omni2.5.b37.vcf.gz added
15a9d412008a4_1000G_omni2.5.b37.vcf.gz.tbi added
15a9d1e176863_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
15a9d12c64b04_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
15a9d1866fd3d_1000G_omni2.5.hg38.vcf.gz added
15a9d117bbc4f_1000G_omni2.5.hg38.vcf.gz.tbi added
15a9d5287ef80_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
15a9d5a7ce6d4_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
15a9d3e1696b5_af-only-gnomad.raw.sites.vcf added
15a9d3d0064eb_af-only-gnomad.raw.sites.vcf.idx added
15a9d64e19f96_Mutect2-exome-panel.vcf.idx added
15a9d18b46498_Mutect2-WGS-panel-b37.vcf added
15a9d6b3843d3_Mutect2-WGS-panel-b37.vcf.idx added
15a9d3aed08a3_small_exac_common_3.vcf added
15a9d1fd2238e_small_exac_common_3.vcf.idx added
15a9d1d1c4ff4_1000g_pon.hg38.vcf.gz added
15a9d2dc52b1a_1000g_pon.hg38.vcf.gz.tbi added
15a9d6b90cf6f_af-only-gnomad.hg38.vcf.gz added
15a9d7022b794_af-only-gnomad.hg38.vcf.gz.tbi added
15a9d77428f0f_small_exac_common_3.hg38.vcf.gz added
15a9d32be5ef4_small_exac_common_3.hg38.vcf.gz.tbi added
15a9d704bff32_gencode.v41.annotation.gtf added
15a9dd5f6537_gencode.v42.annotation.gtf added
15a9d71ee04bc_gencode.vM30.annotation.gtf added
15a9d41790d13_gencode.vM31.annotation.gtf added
15a9d72497bf9_gencode.v41.transcripts.fa added
15a9d366a530d_gencode.v41.transcripts.fa.fai added
15a9d7e729663_gencode.v42.transcripts.fa added
15a9d14ef7e70_gencode.v42.transcripts.fa.fai added
15a9d7755f5cc_gencode.vM30.pc_transcripts.fa added
15a9d2c7c6149_gencode.vM30.pc_transcripts.fa.fai added
15a9d19d71670_gencode.vM31.pc_transcripts.fa added
15a9d78022050_gencode.vM31.pc_transcripts.fa.fai added
15a9d5397a1bd_GRCh38.primary_assembly.genome.fa.1.ht2 added
15a9d7fbaa2b_GRCh38.primary_assembly.genome.fa.2.ht2 added
15a9d1b60f125_GRCh38.primary_assembly.genome.fa.3.ht2 added
15a9d7977c22d_GRCh38.primary_assembly.genome.fa.4.ht2 added
15a9d256d56a8_GRCh38.primary_assembly.genome.fa.5.ht2 added
15a9d2d5442ca_GRCh38.primary_assembly.genome.fa.6.ht2 added
15a9d76ecf305_GRCh38.primary_assembly.genome.fa.7.ht2 added
15a9d3e470a42_GRCh38.primary_assembly.genome.fa.8.ht2 added
15a9d29f292ff_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
15a9d7490b8dc_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
15a9d4958af4d_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
15a9d5d5d0dd9_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
15a9d8385172_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
15a9d296b1795_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
15a9d35d94c71_GRCh38_full_analysis_set_plus_decoy_hla.fa added
15a9d4d29aa55_GRCh38.primary_assembly.genome.fa.fai added
15a9d6a6dda06_GRCh38.primary_assembly.genome.fa.amb added
15a9d5204f680_GRCh38.primary_assembly.genome.fa.ann added
15a9d43d37791_GRCh38.primary_assembly.genome.fa.bwt added
15a9d704ef360_GRCh38.primary_assembly.genome.fa.pac added
15a9d4f4c5d3a_GRCh38.primary_assembly.genome.fa.sa added
15a9d1e7cb382_GRCh38.primary_assembly.genome.fa added
15a9dced2b71_hs37d5.fa.fai added
15a9d26bf0e58_hs37d5.fa.amb added
15a9d4946c747_hs37d5.fa.ann added
15a9d45c52be6_hs37d5.fa.bwt added
15a9d13c52cd3_hs37d5.fa.pac added
15a9d7601dac8_hs37d5.fa.sa added
15a9d73c2bcfe_hs37d5.fa added
15a9d76060311_complete_ref_lens.bin added
15a9d4b38da0_ctable.bin added
15a9d281705c9_ctg_offsets.bin added
15a9d7f7ce3ae_duplicate_clusters.tsv added
15a9d6047f5e5_info.json added
15a9d1460bec5_mphf.bin added
15a9d5b8c81f6_pos.bin added
15a9d65a86c6e_pre_indexing.log added
15a9d1466dde6_rank.bin added
15a9d6d723180_ref_indexing.log added
15a9d641002a2_refAccumLengths.bin added
15a9d571d0d00_reflengths.bin added
15a9d3440a7ae_refseq.bin added
15a9dc0ab4f_seq.bin added
15a9d692ecfeb_versionInfo.json added
15a9d548340_salmon_index added
15a9d2c74deeb_chrLength.txt added
15a9d2cd72d1a_chrName.txt added
15a9d62d21cf5_chrNameLength.txt added
15a9d506b4b82_chrStart.txt added
15a9d342a6d0d_exonGeTrInfo.tab added
15a9d4d5d8b3c_exonInfo.tab added
15a9d386037d2_geneInfo.tab added
15a9d34f0d8e8_Genome added
15a9d3030827f_genomeParameters.txt added
15a9d40c77890_Log.out added
15a9d67bc5729_SA added
15a9d7dfe79f3_SAindex added
15a9d4df88124_sjdbInfo.txt added
15a9d75e68a79_sjdbList.fromGTF.out.tab added
15a9d728d4a67_sjdbList.out.tab added
15a9d1a0feaf2_transcriptInfo.tab added
15a9db09c33c_GRCh38.GENCODE.v42_100 added
15a9d2df09dcd_knownGene_hg38.sql added
15a9d1008154b_knownGene_hg38.txt added
15a9d2adf726_refGene_hg38.sql added
15a9d6b3ce129_refGene_hg38.txt added
15a9d69e281bf_knownGene_mm39.sql added
15a9d15b458e8_knownGene_mm39.txt added
15a9d7338f279_refGene_mm39.sql added
15a9d1fb72108_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//Rtmpbp4TpL/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
6.880 0.922 8.646
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.171 | 0.302 | 2.487 | |
| dataSearch | 0.347 | 0.019 | 0.365 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.883 | 0.058 | 1.692 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.001 | 0.000 | |
| recipeHub-class | 0.041 | 0.003 | 0.045 | |
| recipeLoad | 0.399 | 0.029 | 0.431 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.160 | 0.012 | 0.172 | |
| recipeUpdate | 0 | 0 | 0 | |