Qian Liu
| Snapshot Date: 2026-01-22 13:40 -0500 (Thu, 22 Jan 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 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-23 11:35 -0500 (Fri, 23 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4808 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4542 |
| 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 1764/2345 | 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: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ReUseData_1.11.0.tar.gz |
| StartedAt: 2026-01-23 03:13:56 -0500 (Fri, 23 Jan 2026) |
| EndedAt: 2026-01-23 03:16:40 -0500 (Fri, 23 Jan 2026) |
| EllapsedTime: 164.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ReUseData_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dataHub-class 5.948 0.386 6.336
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-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) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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...
2233162986e03_GRCh38.primary_assembly.genome.fa.1.bt2 added
223316141d5ecb_GRCh38.primary_assembly.genome.fa.2.bt2 added
22331643b9e796_GRCh38.primary_assembly.genome.fa.3.bt2 added
22331632060aac_GRCh38.primary_assembly.genome.fa.4.bt2 added
2233162ecdafa2_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
223316415db98a_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2233164380052a_outfile.txt added
22331669b75d31_GRCh37_to_GRCh38.chain added
2233161c7defbd_GRCh37_to_NCBI34.chain added
22331659288f78_GRCh37_to_NCBI35.chain added
2233167a7453d5_GRCh37_to_NCBI36.chain added
2233166b2809bc_GRCh38_to_GRCh37.chain added
2233161140e1d_GRCh38_to_NCBI34.chain added
2233165e24b642_GRCh38_to_NCBI35.chain added
2233164863c0d0_GRCh38_to_NCBI36.chain added
2233161113455a_NCBI34_to_GRCh37.chain added
22331661d10518_NCBI34_to_GRCh38.chain added
2233166838ed49_NCBI35_to_GRCh37.chain added
2233163c62ef58_NCBI35_to_GRCh38.chain added
2233162589c6e9_NCBI36_to_GRCh37.chain added
223316462db9b8_NCBI36_to_GRCh38.chain added
22331677c08a6_GRCm38_to_NCBIM36.chain added
2233164781169f_GRCm38_to_NCBIM37.chain added
223316e22c88e_NCBIM36_to_GRCm38.chain added
22331621c20779_NCBIM37_to_GRCm38.chain added
2233164eb1304a_1000G_omni2.5.b37.vcf.gz added
22331614fc97d4_1000G_omni2.5.b37.vcf.gz.tbi added
22331675240521_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2233165f28e274_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
22331643971b1e_1000G_omni2.5.hg38.vcf.gz added
2233161dcaa8f7_1000G_omni2.5.hg38.vcf.gz.tbi added
22331661c15077_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
22331657b479ea_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2233166184908d_af-only-gnomad.raw.sites.vcf added
22331613c75b23_af-only-gnomad.raw.sites.vcf.idx added
223316682298c_Mutect2-exome-panel.vcf.idx added
22331622e24a18_Mutect2-WGS-panel-b37.vcf added
2233165747604d_Mutect2-WGS-panel-b37.vcf.idx added
223316703986be_small_exac_common_3.vcf added
2233163f6039d5_small_exac_common_3.vcf.idx added
223316306fefc5_1000g_pon.hg38.vcf.gz added
2233166aadda93_1000g_pon.hg38.vcf.gz.tbi added
2233162a884391_af-only-gnomad.hg38.vcf.gz added
2233163183fde3_af-only-gnomad.hg38.vcf.gz.tbi added
22331648d290d5_small_exac_common_3.hg38.vcf.gz added
22331672ec0462_small_exac_common_3.hg38.vcf.gz.tbi added
2233164297433d_gencode.v41.annotation.gtf added
2233162aa395ed_gencode.v42.annotation.gtf added
2233165b24f1ab_gencode.vM30.annotation.gtf added
2233167efa3296_gencode.vM31.annotation.gtf added
223316502d5cd6_gencode.v41.transcripts.fa added
2233162152ab63_gencode.v41.transcripts.fa.fai added
2233166763b3c_gencode.v42.transcripts.fa added
22331617ae7375_gencode.v42.transcripts.fa.fai added
2233162f7573f2_gencode.vM30.pc_transcripts.fa added
223316283842b5_gencode.vM30.pc_transcripts.fa.fai added
223316665fa3bf_gencode.vM31.pc_transcripts.fa added
22331644720bc6_gencode.vM31.pc_transcripts.fa.fai added
2233161d5c47d6_GRCh38.primary_assembly.genome.fa.1.ht2 added
22331645888633_GRCh38.primary_assembly.genome.fa.2.ht2 added
22331680926e4_GRCh38.primary_assembly.genome.fa.3.ht2 added
2233163b26f0ce_GRCh38.primary_assembly.genome.fa.4.ht2 added
2233162749d6aa_GRCh38.primary_assembly.genome.fa.5.ht2 added
2233165fbda0ce_GRCh38.primary_assembly.genome.fa.6.ht2 added
2233161cab815b_GRCh38.primary_assembly.genome.fa.7.ht2 added
2233163b1131cd_GRCh38.primary_assembly.genome.fa.8.ht2 added
223316663fca5b_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2233163f8dcb73_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2233161258921a_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
22331656795119_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2233167eee0548_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
22331642c881e0_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
22331641272bac_GRCh38_full_analysis_set_plus_decoy_hla.fa added
223316297648da_GRCh38.primary_assembly.genome.fa.fai added
223316744c7fc3_GRCh38.primary_assembly.genome.fa.amb added
2233169f9bc82_GRCh38.primary_assembly.genome.fa.ann added
2233161c624d3c_GRCh38.primary_assembly.genome.fa.bwt added
22331636e3c300_GRCh38.primary_assembly.genome.fa.pac added
223316349d526f_GRCh38.primary_assembly.genome.fa.sa added
22331677873ee7_GRCh38.primary_assembly.genome.fa added
22331635ddf596_hs37d5.fa.fai added
2233164caaf46_hs37d5.fa.amb added
22331618d9ea4b_hs37d5.fa.ann added
2233163c5430d2_hs37d5.fa.bwt added
2233161c7922bb_hs37d5.fa.pac added
223316484f5e3d_hs37d5.fa.sa added
223316648c7387_hs37d5.fa added
2233162d8c67b_complete_ref_lens.bin added
223316cc16a03_ctable.bin added
2233161e8bb5e_ctg_offsets.bin added
22331648614cae_duplicate_clusters.tsv added
22331614ca90e7_info.json added
2233163d0fac2c_mphf.bin added
2233166fab2359_pos.bin added
223316748831b6_pre_indexing.log added
22331659bb2d87_rank.bin added
2233162abc5526_ref_indexing.log added
2233165ac7fc11_refAccumLengths.bin added
2233161948f8fb_reflengths.bin added
2233163d14e741_refseq.bin added
22331631414d2a_seq.bin added
2233161836fe43_versionInfo.json added
2233167fdd6921_salmon_index added
223316726878d6_chrLength.txt added
22331641ad471d_chrName.txt added
2233167429e8e4_chrNameLength.txt added
2233167c623558_chrStart.txt added
2233165e0f9459_exonGeTrInfo.tab added
2233162b0dabe4_exonInfo.tab added
22331630ff87c8_geneInfo.tab added
2233165596d341_Genome added
22331660eba17b_genomeParameters.txt added
22331635ca370e_Log.out added
2233166e70bd8c_SA added
2233161d3fd24d_SAindex added
223316524359c9_sjdbInfo.txt added
22331636c01bc9_sjdbList.fromGTF.out.tab added
2233161cc45d5_sjdbList.out.tab added
223316551c2044_transcriptInfo.tab added
223316438185cc_GRCh38.GENCODE.v42_100 added
2233163b50133_knownGene_hg38.sql added
2233161d7d6cf3_knownGene_hg38.txt added
223316584c16b3_refGene_hg38.sql added
22331640c4ad5f_refGene_hg38.txt added
223316d28904c_knownGene_mm39.sql added
2233164cd44869_knownGene_mm39.txt added
2233161a7fdae6_refGene_mm39.sql added
22331637e4e572_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:
/tmp/RtmpOXhvnx/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
17.976 1.255 19.829
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.948 | 0.386 | 6.336 | |
| dataSearch | 1.109 | 0.058 | 1.167 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.435 | 0.089 | 3.642 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.129 | 0.007 | 0.137 | |
| recipeLoad | 1.279 | 0.039 | 1.318 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.540 | 0.009 | 0.549 | |
| recipeUpdate | 0 | 0 | 0 | |