Qian Liu
| Snapshot Date: 2026-04-22 13:40 -0400 (Wed, 22 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 2026-04-23 11:40 -0400 (Thu, 23 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4783 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4701 |
| 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 1803/2404 | 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: 2026-04-22 21:46:10 -0400 (Wed, 22 Apr 2026) |
| EndedAt: 2026-04-22 21:47:04 -0400 (Wed, 22 Apr 2026) |
| EllapsedTime: 53.5 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: 2026-04-23 01:46:11 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...
474031fb2ecc_GRCh38.primary_assembly.genome.fa.1.bt2 added
474061bd6cb6_GRCh38.primary_assembly.genome.fa.2.bt2 added
47405b2c52db_GRCh38.primary_assembly.genome.fa.3.bt2 added
47403af3d6a0_GRCh38.primary_assembly.genome.fa.4.bt2 added
47405e8fc09c_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
47402fae7244_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
474065cfe6d0_outfile.txt added
4740343a95e8_GRCh37_to_GRCh38.chain added
47407247cd21_GRCh37_to_NCBI34.chain added
474047ec6c24_GRCh37_to_NCBI35.chain added
474072afd45f_GRCh37_to_NCBI36.chain added
4740759fe3cb_GRCh38_to_GRCh37.chain added
4740542460c1_GRCh38_to_NCBI34.chain added
4740204c4a0f_GRCh38_to_NCBI35.chain added
474070922f59_GRCh38_to_NCBI36.chain added
4740d62b5cc_NCBI34_to_GRCh37.chain added
47404b8d6af1_NCBI34_to_GRCh38.chain added
474031681af7_NCBI35_to_GRCh37.chain added
474029c26778_NCBI35_to_GRCh38.chain added
47401a170cb3_NCBI36_to_GRCh37.chain added
47405f42c926_NCBI36_to_GRCh38.chain added
474019a40ea6_GRCm38_to_NCBIM36.chain added
474061bdc170_GRCm38_to_NCBIM37.chain added
474070e6d231_NCBIM36_to_GRCm38.chain added
474041f1c8df_NCBIM37_to_GRCm38.chain added
474068baca4b_1000G_omni2.5.b37.vcf.gz added
47403f3737a4_1000G_omni2.5.b37.vcf.gz.tbi added
474042261068_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
474050ff3dc5_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
474025307a0e_1000G_omni2.5.hg38.vcf.gz added
4740119d4035_1000G_omni2.5.hg38.vcf.gz.tbi added
47406ae2609b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
4740343496ef_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
474068a13faf_af-only-gnomad.raw.sites.vcf added
4740325c2fd3_af-only-gnomad.raw.sites.vcf.idx added
47404247df79_Mutect2-exome-panel.vcf.idx added
47407ca0a2ed_Mutect2-WGS-panel-b37.vcf added
47401628b587_Mutect2-WGS-panel-b37.vcf.idx added
47404aa5bd6e_small_exac_common_3.vcf added
47404737a70b_small_exac_common_3.vcf.idx added
474016b7e7b4_1000g_pon.hg38.vcf.gz added
47403cce613_1000g_pon.hg38.vcf.gz.tbi added
4740114eb58_af-only-gnomad.hg38.vcf.gz added
4740466def6_af-only-gnomad.hg38.vcf.gz.tbi added
47407db7eabb_small_exac_common_3.hg38.vcf.gz added
47403593db78_small_exac_common_3.hg38.vcf.gz.tbi added
47407e2dbec2_gencode.v41.annotation.gtf added
47406d46f345_gencode.v42.annotation.gtf added
47404d0d6f0f_gencode.vM30.annotation.gtf added
47402cf6694e_gencode.vM31.annotation.gtf added
4740657b96f1_gencode.v41.transcripts.fa added
474014f2dc44_gencode.v41.transcripts.fa.fai added
4740545aff1a_gencode.v42.transcripts.fa added
474022222f3a_gencode.v42.transcripts.fa.fai added
4740724a9a57_gencode.vM30.pc_transcripts.fa added
47407fdb005f_gencode.vM30.pc_transcripts.fa.fai added
47402f59e8d_gencode.vM31.pc_transcripts.fa added
47404b7c3c7f_gencode.vM31.pc_transcripts.fa.fai added
47404967dc90_GRCh38.primary_assembly.genome.fa.1.ht2 added
474041c19796_GRCh38.primary_assembly.genome.fa.2.ht2 added
4740cc71a94_GRCh38.primary_assembly.genome.fa.3.ht2 added
474063a1f119_GRCh38.primary_assembly.genome.fa.4.ht2 added
47401cdbd369_GRCh38.primary_assembly.genome.fa.5.ht2 added
47402414a14c_GRCh38.primary_assembly.genome.fa.6.ht2 added
474046699715_GRCh38.primary_assembly.genome.fa.7.ht2 added
47403e3e07d0_GRCh38.primary_assembly.genome.fa.8.ht2 added
47405a73089c_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
4740363a6828_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
4740348c35e8_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
474061272d4b_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
4740530ec8c1_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
47406f9e2180_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
474076a993bf_GRCh38_full_analysis_set_plus_decoy_hla.fa added
474077231d75_GRCh38.primary_assembly.genome.fa.fai added
47402263296e_GRCh38.primary_assembly.genome.fa.amb added
47401c350665_GRCh38.primary_assembly.genome.fa.ann added
47405d36df5a_GRCh38.primary_assembly.genome.fa.bwt added
47403d81bd85_GRCh38.primary_assembly.genome.fa.pac added
474010c1864f_GRCh38.primary_assembly.genome.fa.sa added
47401158b521_GRCh38.primary_assembly.genome.fa added
474056db926c_hs37d5.fa.fai added
4740696a1d00_hs37d5.fa.amb added
474035962111_hs37d5.fa.ann added
47401354fe93_hs37d5.fa.bwt added
474031156ecf_hs37d5.fa.pac added
4740761df135_hs37d5.fa.sa added
474027c70b28_hs37d5.fa added
47407cad837e_complete_ref_lens.bin added
474063940524_ctable.bin added
4740addb18f_ctg_offsets.bin added
474060b428db_duplicate_clusters.tsv added
474053e67376_info.json added
47403ea67302_mphf.bin added
474021c8a870_pos.bin added
47407caa6263_pre_indexing.log added
474016219186_rank.bin added
474075d8ffc3_ref_indexing.log added
4740797f97a6_refAccumLengths.bin added
474027bd519b_reflengths.bin added
47407e38ab7e_refseq.bin added
47403a831def_seq.bin added
4740762253eb_versionInfo.json added
474047b3a5e4_salmon_index added
474063504082_chrLength.txt added
474029bb49be_chrName.txt added
474046e66e59_chrNameLength.txt added
47404256b96c_chrStart.txt added
47404ba7837a_exonGeTrInfo.tab added
474062a8e563_exonInfo.tab added
47403e6bf92f_geneInfo.tab added
474022b49cad_Genome added
47407f9a33a7_genomeParameters.txt added
474064b55a63_Log.out added
47403e414d3c_SA added
47403135be12_SAindex added
47403f51a8fb_sjdbInfo.txt added
4740a2d1737_sjdbList.fromGTF.out.tab added
4740164f2119_sjdbList.out.tab added
47402505fbc0_transcriptInfo.tab added
47402bd30d3d_GRCh38.GENCODE.v42_100 added
47402d0a3645_knownGene_hg38.sql added
47407971031c_knownGene_hg38.txt added
47406a83618d_refGene_hg38.sql added
47405779a69c_refGene_hg38.txt added
474073a978a1_knownGene_mm39.sql added
47407b2ecd59_knownGene_mm39.txt added
47403dabcd3d_refGene_mm39.sql added
47405a2f7f6c_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//RtmpfVxbgv/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
6.859 0.860 8.614
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.102 | 0.299 | 2.419 | |
| dataSearch | 0.363 | 0.018 | 0.381 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.883 | 0.058 | 1.770 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.044 | 0.004 | 0.048 | |
| recipeLoad | 0.439 | 0.031 | 0.473 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.170 | 0.013 | 0.183 | |
| recipeUpdate | 0 | 0 | 0 | |