Qian Liu
| Snapshot Date: 2026-04-02 13:45 -0400 (Thu, 02 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_22 |
| git_last_commit: 2d4066b |
| git_last_commit_date: 2025-10-29 11:20:44 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-04-03 11:58 -0400 (Fri, 03 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4897 |
| 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 1773/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.10.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.3 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: 1.10.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReUseData_1.10.0.tar.gz |
| StartedAt: 2026-04-03 03:13:32 -0400 (Fri, 03 Apr 2026) |
| EndedAt: 2026-04-03 03:16:17 -0400 (Fri, 03 Apr 2026) |
| EllapsedTime: 165.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReUseData_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 24.04.4 LTS
* using session charset: UTF-8
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.10.0’
* 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 5.647 0.277 5.929
* 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-3.22-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.10.0’ ** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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...
2d57dc4408614_GRCh38.primary_assembly.genome.fa.1.bt2 added
2d57dc1bdffe7f_GRCh38.primary_assembly.genome.fa.2.bt2 added
2d57dc6a4c506f_GRCh38.primary_assembly.genome.fa.3.bt2 added
2d57dc7d1a58e5_GRCh38.primary_assembly.genome.fa.4.bt2 added
2d57dc467a1bf5_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2d57dc7fb363f1_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2d57dc4310f870_outfile.txt added
2d57dc713710b_GRCh37_to_GRCh38.chain added
2d57dc120cc5b5_GRCh37_to_NCBI34.chain added
2d57dc136f6aea_GRCh37_to_NCBI35.chain added
2d57dc31bfa64e_GRCh37_to_NCBI36.chain added
2d57dc4bbfe331_GRCh38_to_GRCh37.chain added
2d57dc4607e90a_GRCh38_to_NCBI34.chain added
2d57dc7a16786a_GRCh38_to_NCBI35.chain added
2d57dc430d034a_GRCh38_to_NCBI36.chain added
2d57dc26379cf9_NCBI34_to_GRCh37.chain added
2d57dcf11efe8_NCBI34_to_GRCh38.chain added
2d57dc732def21_NCBI35_to_GRCh37.chain added
2d57dc6b66f830_NCBI35_to_GRCh38.chain added
2d57dc142c77ca_NCBI36_to_GRCh37.chain added
2d57dc62c69b1d_NCBI36_to_GRCh38.chain added
2d57dc251fa8_GRCm38_to_NCBIM36.chain added
2d57dc38fc4c36_GRCm38_to_NCBIM37.chain added
2d57dc61a414fe_NCBIM36_to_GRCm38.chain added
2d57dc1344a091_NCBIM37_to_GRCm38.chain added
2d57dc4e54cae9_1000G_omni2.5.b37.vcf.gz added
2d57dc31967943_1000G_omni2.5.b37.vcf.gz.tbi added
2d57dc56f8e859_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2d57dc4cba4f3b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2d57dc60adfa69_1000G_omni2.5.hg38.vcf.gz added
2d57dc6156597d_1000G_omni2.5.hg38.vcf.gz.tbi added
2d57dc50fad54f_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2d57dc7c8df8e9_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2d57dc4ba2a9ed_af-only-gnomad.raw.sites.vcf added
2d57dc4e152e34_af-only-gnomad.raw.sites.vcf.idx added
2d57dc430814de_Mutect2-exome-panel.vcf.idx added
2d57dc4b560dde_Mutect2-WGS-panel-b37.vcf added
2d57dc112626a4_Mutect2-WGS-panel-b37.vcf.idx added
2d57dc4a1b85e9_small_exac_common_3.vcf added
2d57dc5d62d393_small_exac_common_3.vcf.idx added
2d57dc2495918f_1000g_pon.hg38.vcf.gz added
2d57dc7bdb2c37_1000g_pon.hg38.vcf.gz.tbi added
2d57dc2922b6c5_af-only-gnomad.hg38.vcf.gz added
2d57dc6a9d7a99_af-only-gnomad.hg38.vcf.gz.tbi added
2d57dc75f1a4a1_small_exac_common_3.hg38.vcf.gz added
2d57dc6c2fba0f_small_exac_common_3.hg38.vcf.gz.tbi added
2d57dc10d51793_gencode.v41.annotation.gtf added
2d57dc503948a_gencode.v42.annotation.gtf added
2d57dc5f5da930_gencode.vM30.annotation.gtf added
2d57dc7c3c0fc3_gencode.vM31.annotation.gtf added
2d57dc19300c54_gencode.v41.transcripts.fa added
2d57dc4224444e_gencode.v41.transcripts.fa.fai added
2d57dc7c612f6b_gencode.v42.transcripts.fa added
2d57dc522c588b_gencode.v42.transcripts.fa.fai added
2d57dc23c8594c_gencode.vM30.pc_transcripts.fa added
2d57dcfa5cffd_gencode.vM30.pc_transcripts.fa.fai added
2d57dc20812374_gencode.vM31.pc_transcripts.fa added
2d57dc555ed28f_gencode.vM31.pc_transcripts.fa.fai added
2d57dc669eb856_GRCh38.primary_assembly.genome.fa.1.ht2 added
2d57dc6d3b72af_GRCh38.primary_assembly.genome.fa.2.ht2 added
2d57dc360cccf9_GRCh38.primary_assembly.genome.fa.3.ht2 added
2d57dc47f511d4_GRCh38.primary_assembly.genome.fa.4.ht2 added
2d57dc3e3647fe_GRCh38.primary_assembly.genome.fa.5.ht2 added
2d57dc329ac5e2_GRCh38.primary_assembly.genome.fa.6.ht2 added
2d57dc1397bbc1_GRCh38.primary_assembly.genome.fa.7.ht2 added
2d57dcc4b7633_GRCh38.primary_assembly.genome.fa.8.ht2 added
2d57dc75a2dac0_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2d57dc5eedc99f_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2d57dc1d719cd7_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2d57dc3fbe60a9_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2d57dc3c509d33_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2d57dc42072e66_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2d57dc3b998ce1_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2d57dc657353f8_GRCh38.primary_assembly.genome.fa.fai added
2d57dc2ca4a900_GRCh38.primary_assembly.genome.fa.amb added
2d57dc318b3182_GRCh38.primary_assembly.genome.fa.ann added
2d57dc51a30e07_GRCh38.primary_assembly.genome.fa.bwt added
2d57dc3d79c093_GRCh38.primary_assembly.genome.fa.pac added
2d57dc368ec60c_GRCh38.primary_assembly.genome.fa.sa added
2d57dc3100b737_GRCh38.primary_assembly.genome.fa added
2d57dc39b5d056_hs37d5.fa.fai added
2d57dc4fbed261_hs37d5.fa.amb added
2d57dc7324fb85_hs37d5.fa.ann added
2d57dc3616ffc2_hs37d5.fa.bwt added
2d57dc21eb2aec_hs37d5.fa.pac added
2d57dc16ed54d2_hs37d5.fa.sa added
2d57dc45bccfbf_hs37d5.fa added
2d57dc426c4e60_complete_ref_lens.bin added
2d57dc6c4c2761_ctable.bin added
2d57dc2c5b8815_ctg_offsets.bin added
2d57dc2fa7c110_duplicate_clusters.tsv added
2d57dc2258f45a_info.json added
2d57dc745099e9_mphf.bin added
2d57dc6dde090e_pos.bin added
2d57dc54f3ba3c_pre_indexing.log added
2d57dc7e855aa_rank.bin added
2d57dc7a297f41_ref_indexing.log added
2d57dc4a9694fc_refAccumLengths.bin added
2d57dc66d61f4a_reflengths.bin added
2d57dc179b1c19_refseq.bin added
2d57dca54f5a6_seq.bin added
2d57dc2326bc7d_versionInfo.json added
2d57dc59a24a7f_salmon_index added
2d57dc45ee8287_chrLength.txt added
2d57dc89a1075_chrName.txt added
2d57dc646f37f_chrNameLength.txt added
2d57dc7779b409_chrStart.txt added
2d57dc5a3d1e7c_exonGeTrInfo.tab added
2d57dc43c0b412_exonInfo.tab added
2d57dc2e087a16_geneInfo.tab added
2d57dcb3dd5b3_Genome added
2d57dc7d768469_genomeParameters.txt added
2d57dc7dc74c77_Log.out added
2d57dc7e62d139_SA added
2d57dc338d842b_SAindex added
2d57dc1fb27763_sjdbInfo.txt added
2d57dc1550260b_sjdbList.fromGTF.out.tab added
2d57dc794a53ea_sjdbList.out.tab added
2d57dc621ec5c3_transcriptInfo.tab added
2d57dc19c4d6c_GRCh38.GENCODE.v42_100 added
2d57dc25a5dbff_knownGene_hg38.sql added
2d57dc11c686d3_knownGene_hg38.txt added
2d57dc23f541c7_refGene_hg38.sql added
2d57dc19f675e9_refGene_hg38.txt added
2d57dc7fa48fe2_knownGene_mm39.sql added
2d57dc78e8fc03_knownGene_mm39.txt added
2d57dc21decb93_refGene_mm39.sql added
2d57dc79ce0f23_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/Rtmp481iKe/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
19.412 1.349 21.245
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.647 | 0.277 | 5.929 | |
| dataSearch | 1.093 | 0.016 | 1.110 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.615 | 0.093 | 3.487 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.129 | 0.003 | 0.131 | |
| recipeLoad | 1.244 | 0.027 | 1.271 | |
| recipeMake | 0.001 | 0.000 | 0.000 | |
| recipeSearch | 0.533 | 0.006 | 0.539 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |