Qian Liu
| Snapshot Date: 2026-05-15 13:45 -0400 (Fri, 15 May 2026) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: caf380d |
| git_last_commit_date: 2026-04-28 08:59:39 -0400 (Tue, 28 Apr 2026) |
| Back to Build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-16 11:33 -0400 (Sat, 16 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4894 |
| 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 1784/2375 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.13.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | 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: 1.13.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings ReUseData_1.13.0.tar.gz |
| StartedAt: 2026-05-16 03:40:47 -0400 (Sat, 16 May 2026) |
| EndedAt: 2026-05-16 03:43:34 -0400 (Sat, 16 May 2026) |
| EllapsedTime: 167.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings ReUseData_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/ReUseData.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-16 07:40:47 UTC
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.13.0’
* 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 5.693 0.23 5.926
* 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-3.24-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.13.0’ ** 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 RC (2026-04-17 r89917) -- "Because it was There"
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...
d62a57a469fab_GRCh38.primary_assembly.genome.fa.1.bt2 added
d62a54a0149dc_GRCh38.primary_assembly.genome.fa.2.bt2 added
d62a55dbf59a9_GRCh38.primary_assembly.genome.fa.3.bt2 added
d62a53f9de9ad_GRCh38.primary_assembly.genome.fa.4.bt2 added
d62a52ca2349e_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
d62a531399513_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
d62a574ef83b_outfile.txt added
d62a5154ff7c4_GRCh37_to_GRCh38.chain added
d62a54da34911_GRCh37_to_NCBI34.chain added
d62a51e142d66_GRCh37_to_NCBI35.chain added
d62a5661dcc26_GRCh37_to_NCBI36.chain added
d62a51398b466_GRCh38_to_GRCh37.chain added
d62a524dd631d_GRCh38_to_NCBI34.chain added
d62a557f588ca_GRCh38_to_NCBI35.chain added
d62a55654c600_GRCh38_to_NCBI36.chain added
d62a51996279c_NCBI34_to_GRCh37.chain added
d62a5504180ce_NCBI34_to_GRCh38.chain added
d62a52e5dfbcb_NCBI35_to_GRCh37.chain added
d62a5759d56d_NCBI35_to_GRCh38.chain added
d62a53af5b7c0_NCBI36_to_GRCh37.chain added
d62a518a80b93_NCBI36_to_GRCh38.chain added
d62a5110aa982_GRCm38_to_NCBIM36.chain added
d62a554d5820b_GRCm38_to_NCBIM37.chain added
d62a52fff730_NCBIM36_to_GRCm38.chain added
d62a53d6a09e_NCBIM37_to_GRCm38.chain added
d62a55f08183d_1000G_omni2.5.b37.vcf.gz added
d62a51d4b0446_1000G_omni2.5.b37.vcf.gz.tbi added
d62a5a1d29e9_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
d62a56b48abd6_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
d62a565846d47_1000G_omni2.5.hg38.vcf.gz added
d62a52e5d8012_1000G_omni2.5.hg38.vcf.gz.tbi added
d62a5658f4b81_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
d62a52f85b724_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
d62a5c1cd9bc_af-only-gnomad.raw.sites.vcf added
d62a5252d352e_af-only-gnomad.raw.sites.vcf.idx added
d62a55c27ebc2_Mutect2-exome-panel.vcf.idx added
d62a53d566ecf_Mutect2-WGS-panel-b37.vcf added
d62a52c7c2d6a_Mutect2-WGS-panel-b37.vcf.idx added
d62a57177e386_small_exac_common_3.vcf added
d62a5af9b7e0_small_exac_common_3.vcf.idx added
d62a54a905ad0_1000g_pon.hg38.vcf.gz added
d62a55795afac_1000g_pon.hg38.vcf.gz.tbi added
d62a51e926c46_af-only-gnomad.hg38.vcf.gz added
d62a56f6dbded_af-only-gnomad.hg38.vcf.gz.tbi added
d62a52f8b3876_small_exac_common_3.hg38.vcf.gz added
d62a574e73246_small_exac_common_3.hg38.vcf.gz.tbi added
d62a5903e589_gencode.v41.annotation.gtf added
d62a57fccb944_gencode.v42.annotation.gtf added
d62a523452e11_gencode.vM30.annotation.gtf added
d62a5105dbaf7_gencode.vM31.annotation.gtf added
d62a53ac27105_gencode.v41.transcripts.fa added
d62a53bed39a5_gencode.v41.transcripts.fa.fai added
d62a521686479_gencode.v42.transcripts.fa added
d62a5f97f310_gencode.v42.transcripts.fa.fai added
d62a53eed30d5_gencode.vM30.pc_transcripts.fa added
d62a5253f0517_gencode.vM30.pc_transcripts.fa.fai added
d62a56ea00b4d_gencode.vM31.pc_transcripts.fa added
d62a55c38351b_gencode.vM31.pc_transcripts.fa.fai added
d62a52f5c2f01_GRCh38.primary_assembly.genome.fa.1.ht2 added
d62a559e8b723_GRCh38.primary_assembly.genome.fa.2.ht2 added
d62a541bca262_GRCh38.primary_assembly.genome.fa.3.ht2 added
d62a55db9af13_GRCh38.primary_assembly.genome.fa.4.ht2 added
d62a53f7802a5_GRCh38.primary_assembly.genome.fa.5.ht2 added
d62a571425986_GRCh38.primary_assembly.genome.fa.6.ht2 added
d62a569d688cf_GRCh38.primary_assembly.genome.fa.7.ht2 added
d62a564a537d3_GRCh38.primary_assembly.genome.fa.8.ht2 added
d62a54d6a4548_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
d62a5272cf79e_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
d62a51121653d_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
d62a53ee228cf_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
d62a53226af7e_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
d62a55bb1c00e_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
d62a51677d87b_GRCh38_full_analysis_set_plus_decoy_hla.fa added
d62a550b91bc5_GRCh38.primary_assembly.genome.fa.fai added
d62a54b1f7dfb_GRCh38.primary_assembly.genome.fa.amb added
d62a5460310f2_GRCh38.primary_assembly.genome.fa.ann added
d62a545a04e0b_GRCh38.primary_assembly.genome.fa.bwt added
d62a554236385_GRCh38.primary_assembly.genome.fa.pac added
d62a545cfca36_GRCh38.primary_assembly.genome.fa.sa added
d62a568e57c1d_GRCh38.primary_assembly.genome.fa added
d62a564811e7c_hs37d5.fa.fai added
d62a5923b3b_hs37d5.fa.amb added
d62a524d2b5c2_hs37d5.fa.ann added
d62a55e982f5_hs37d5.fa.bwt added
d62a5102a2e4c_hs37d5.fa.pac added
d62a563bfe697_hs37d5.fa.sa added
d62a52b28880c_hs37d5.fa added
d62a57eca3999_complete_ref_lens.bin added
d62a53ff81bb2_ctable.bin added
d62a55a84b70d_ctg_offsets.bin added
d62a558b2f0bd_duplicate_clusters.tsv added
d62a51b4be14_info.json added
d62a5383e6621_mphf.bin added
d62a5182af362_pos.bin added
d62a572f7179b_pre_indexing.log added
d62a52214eef0_rank.bin added
d62a57cd02b35_ref_indexing.log added
d62a540615ce3_refAccumLengths.bin added
d62a54941e68f_reflengths.bin added
d62a5df19073_refseq.bin added
d62a57f4385b2_seq.bin added
d62a57b68960d_versionInfo.json added
d62a569a35081_salmon_index added
d62a515bb5e2e_chrLength.txt added
d62a54c21b1d2_chrName.txt added
d62a534c2ce7c_chrNameLength.txt added
d62a55bbe6f20_chrStart.txt added
d62a511c1ffde_exonGeTrInfo.tab added
d62a58e63201_exonInfo.tab added
d62a5218e3956_geneInfo.tab added
d62a57aa77bfb_Genome added
d62a56d67507d_genomeParameters.txt added
d62a522207492_Log.out added
d62a51f7a31bd_SA added
d62a57350d372_SAindex added
d62a5324aa2de_sjdbInfo.txt added
d62a533a1854_sjdbList.fromGTF.out.tab added
d62a51e795b7f_sjdbList.out.tab added
d62a53114dc77_transcriptInfo.tab added
d62a543323406_GRCh38.GENCODE.v42_100 added
d62a578fe128c_knownGene_hg38.sql added
d62a59c7cd34_knownGene_hg38.txt added
d62a544e6f21a_refGene_hg38.sql added
d62a5313c78ad_refGene_hg38.txt added
d62a521f2c096_knownGene_mm39.sql added
d62a537de09b5_knownGene_mm39.txt added
d62a55351679e_refGene_mm39.sql added
d62a51ec2ebcc_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/Rtmpho6OKD/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
18.164 1.145 20.063
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.693 | 0.230 | 5.926 | |
| dataSearch | 1.066 | 0.011 | 1.077 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.741 | 0.152 | 3.624 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.121 | 0.001 | 0.123 | |
| recipeLoad | 1.275 | 0.048 | 1.325 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.562 | 0.054 | 0.615 | |
| recipeUpdate | 0.001 | 0.000 | 0.000 | |