Qian Liu
| Snapshot Date: 2026-04-09 13:40 -0400 (Thu, 09 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 2026-04-10 11:35 -0400 (Fri, 10 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) | 4917 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-26 r89717) -- "Unsuffered Consequences" | 4629 |
| 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 1791/2388 | 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: 2026-04-09 19:49:57 -0400 (Thu, 09 Apr 2026) |
| EndedAt: 2026-04-09 19:50:52 -0400 (Thu, 09 Apr 2026) |
| EllapsedTime: 54.6 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) (2026-03-26 r89717)
* 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: 2026-04-09 23:49:57 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 Under development (unstable) (2026-03-26 r89717) -- "Unsuffered Consequences"
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...
29b83eb9b6e4_GRCh38.primary_assembly.genome.fa.1.bt2 added
29b8129652e8_GRCh38.primary_assembly.genome.fa.2.bt2 added
29b84b1d06e0_GRCh38.primary_assembly.genome.fa.3.bt2 added
29b85eae82a6_GRCh38.primary_assembly.genome.fa.4.bt2 added
29b8130390da_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
29b84f1ae1f6_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
29b86de9060c_outfile.txt added
29b85d8c3633_GRCh37_to_GRCh38.chain added
29b8203a7e40_GRCh37_to_NCBI34.chain added
29b86036ac47_GRCh37_to_NCBI35.chain added
29b825689aaa_GRCh37_to_NCBI36.chain added
29b876822215_GRCh38_to_GRCh37.chain added
29b8598bcd7b_GRCh38_to_NCBI34.chain added
29b8695f742a_GRCh38_to_NCBI35.chain added
29b879c3a771_GRCh38_to_NCBI36.chain added
29b81c262a2b_NCBI34_to_GRCh37.chain added
29b8d9a7b7d_NCBI34_to_GRCh38.chain added
29b819215285_NCBI35_to_GRCh37.chain added
29b85ab0a6a6_NCBI35_to_GRCh38.chain added
29b838d0ace_NCBI36_to_GRCh37.chain added
29b820c05c34_NCBI36_to_GRCh38.chain added
29b834e56ab8_GRCm38_to_NCBIM36.chain added
29b841c17129_GRCm38_to_NCBIM37.chain added
29b82ec5c79_NCBIM36_to_GRCm38.chain added
29b86bab0d6e_NCBIM37_to_GRCm38.chain added
29b82afee7fb_1000G_omni2.5.b37.vcf.gz added
29b8453025ca_1000G_omni2.5.b37.vcf.gz.tbi added
29b85c011442_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
29b84ad9283e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
29b876e124d5_1000G_omni2.5.hg38.vcf.gz added
29b8373958ec_1000G_omni2.5.hg38.vcf.gz.tbi added
29b815fd0a47_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
29b817adc698_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
29b811c9314d_af-only-gnomad.raw.sites.vcf added
29b82fc3bf5a_af-only-gnomad.raw.sites.vcf.idx added
29b85c47c635_Mutect2-exome-panel.vcf.idx added
29b86c25f0e7_Mutect2-WGS-panel-b37.vcf added
29b82eeb0529_Mutect2-WGS-panel-b37.vcf.idx added
29b8479fdecf_small_exac_common_3.vcf added
29b850dd0cc5_small_exac_common_3.vcf.idx added
29b8607182fc_1000g_pon.hg38.vcf.gz added
29b83c4e9fdb_1000g_pon.hg38.vcf.gz.tbi added
29b84de101cb_af-only-gnomad.hg38.vcf.gz added
29b86f3cde5e_af-only-gnomad.hg38.vcf.gz.tbi added
29b852b2660_small_exac_common_3.hg38.vcf.gz added
29b853e46b46_small_exac_common_3.hg38.vcf.gz.tbi added
29b8393eebb1_gencode.v41.annotation.gtf added
29b851e3ced3_gencode.v42.annotation.gtf added
29b8431fa8a5_gencode.vM30.annotation.gtf added
29b853790b10_gencode.vM31.annotation.gtf added
29b82fc57240_gencode.v41.transcripts.fa added
29b84bcfe040_gencode.v41.transcripts.fa.fai added
29b83c8bb0a2_gencode.v42.transcripts.fa added
29b876f97abb_gencode.v42.transcripts.fa.fai added
29b874e8c802_gencode.vM30.pc_transcripts.fa added
29b85ea33744_gencode.vM30.pc_transcripts.fa.fai added
29b82d8181e6_gencode.vM31.pc_transcripts.fa added
29b811773a61_gencode.vM31.pc_transcripts.fa.fai added
29b82a99bf3c_GRCh38.primary_assembly.genome.fa.1.ht2 added
29b853da11fd_GRCh38.primary_assembly.genome.fa.2.ht2 added
29b811d3240d_GRCh38.primary_assembly.genome.fa.3.ht2 added
29b83ce3da9f_GRCh38.primary_assembly.genome.fa.4.ht2 added
29b813261bf4_GRCh38.primary_assembly.genome.fa.5.ht2 added
29b82af539fe_GRCh38.primary_assembly.genome.fa.6.ht2 added
29b849b268ba_GRCh38.primary_assembly.genome.fa.7.ht2 added
29b85ff9b122_GRCh38.primary_assembly.genome.fa.8.ht2 added
29b81dc6068_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
29b82b3d4ccc_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
29b8457cfb41_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
29b810538c0b_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
29b85d0f2e8c_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
29b8fb9190f_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
29b8411c2fd9_GRCh38_full_analysis_set_plus_decoy_hla.fa added
29b8218970f4_GRCh38.primary_assembly.genome.fa.fai added
29b84656b45f_GRCh38.primary_assembly.genome.fa.amb added
29b8665bed0c_GRCh38.primary_assembly.genome.fa.ann added
29b81d27e354_GRCh38.primary_assembly.genome.fa.bwt added
29b825bdaec0_GRCh38.primary_assembly.genome.fa.pac added
29b8481bd29b_GRCh38.primary_assembly.genome.fa.sa added
29b81a9fe319_GRCh38.primary_assembly.genome.fa added
29b876f68bf6_hs37d5.fa.fai added
29b8345f007e_hs37d5.fa.amb added
29b849196b0e_hs37d5.fa.ann added
29b823c389a0_hs37d5.fa.bwt added
29b87a8079b7_hs37d5.fa.pac added
29b88b71c36_hs37d5.fa.sa added
29b82d9d21b2_hs37d5.fa added
29b8270f4483_complete_ref_lens.bin added
29b85b5b087d_ctable.bin added
29b8358a7566_ctg_offsets.bin added
29b815219700_duplicate_clusters.tsv added
29b850408bd6_info.json added
29b83d9cb7c3_mphf.bin added
29b87be482ce_pos.bin added
29b85747e1ed_pre_indexing.log added
29b83041bb5f_rank.bin added
29b82b7472b9_ref_indexing.log added
29b86a17e5f8_refAccumLengths.bin added
29b846fb3332_reflengths.bin added
29b815de3c06_refseq.bin added
29b83136b921_seq.bin added
29b87fb43ec4_versionInfo.json added
29b81284f75c_salmon_index added
29b8578bc283_chrLength.txt added
29b8188f535c_chrName.txt added
29b869a9c99c_chrNameLength.txt added
29b89f356f6_chrStart.txt added
29b846d23594_exonGeTrInfo.tab added
29b812bbabdf_exonInfo.tab added
29b85f10c714_geneInfo.tab added
29b8467e22ce_Genome added
29b831f268a_genomeParameters.txt added
29b8721b2f9f_Log.out added
29b856d3aa3f_SA added
29b8624e3aa1_SAindex added
29b87deb5272_sjdbInfo.txt added
29b86471faf3_sjdbList.fromGTF.out.tab added
29b877129b09_sjdbList.out.tab added
29b86680a8f1_transcriptInfo.tab added
29b88d39aca_GRCh38.GENCODE.v42_100 added
29b87c57484c_knownGene_hg38.sql added
29b8464bb55a_knownGene_hg38.txt added
29b8146f4bc4_refGene_hg38.sql added
29b816d73b57_refGene_hg38.txt added
29b8c78d878_knownGene_mm39.sql added
29b851cbb4ad_knownGene_mm39.txt added
29b814c2f3cf_refGene_mm39.sql added
29b8b14a5af_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//RtmpOREZ0V/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
6.875 0.925 9.040
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.054 | 0.300 | 2.392 | |
| dataSearch | 0.354 | 0.018 | 0.372 | |
| dataUpdate | 0.000 | 0.001 | 0.001 | |
| getCloudData | 0.859 | 0.056 | 1.556 | |
| getData | 0.000 | 0.001 | 0.000 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.035 | 0.003 | 0.038 | |
| recipeLoad | 0.420 | 0.029 | 0.454 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.158 | 0.012 | 0.170 | |
| recipeUpdate | 0 | 0 | 0 | |