Qian Liu
| Snapshot Date: 2025-12-15 13:40 -0500 (Mon, 15 Dec 2025) |
| 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 2025-12-16 11:34 -0500 (Tue, 16 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4875 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4583 |
| 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 1754/2332 | 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: 2025-12-16 02:38:41 -0500 (Tue, 16 Dec 2025) |
| EndedAt: 2025-12-16 02:41:29 -0500 (Tue, 16 Dec 2025) |
| EllapsedTime: 168.4 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) (2025-10-20 r88955)
* 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 6.461 0.765 7.228
* 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) (2025-10-20 r88955) -- "Unsuffered Consequences"
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...
3c36b1328a0d1_GRCh38.primary_assembly.genome.fa.1.bt2 added
3c36b2d039ebe_GRCh38.primary_assembly.genome.fa.2.bt2 added
3c36b2d5a40bc_GRCh38.primary_assembly.genome.fa.3.bt2 added
3c36b751b0c77_GRCh38.primary_assembly.genome.fa.4.bt2 added
3c36b58e5beb_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3c36b20a8c883_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3c36b2eebfee9_outfile.txt added
3c36b671132d5_GRCh37_to_GRCh38.chain added
3c36b5f6baa10_GRCh37_to_NCBI34.chain added
3c36b74f84e05_GRCh37_to_NCBI35.chain added
3c36b4af691e_GRCh37_to_NCBI36.chain added
3c36b280c7440_GRCh38_to_GRCh37.chain added
3c36b2aa39f2f_GRCh38_to_NCBI34.chain added
3c36b7f03ec53_GRCh38_to_NCBI35.chain added
3c36b24fc12fb_GRCh38_to_NCBI36.chain added
3c36b16cd28ce_NCBI34_to_GRCh37.chain added
3c36b47c71601_NCBI34_to_GRCh38.chain added
3c36b4cdc506_NCBI35_to_GRCh37.chain added
3c36b52720d3b_NCBI35_to_GRCh38.chain added
3c36b2be33f20_NCBI36_to_GRCh37.chain added
3c36b6c39b8ca_NCBI36_to_GRCh38.chain added
3c36b52eae8c3_GRCm38_to_NCBIM36.chain added
3c36b7c39bff6_GRCm38_to_NCBIM37.chain added
3c36b75d4dad4_NCBIM36_to_GRCm38.chain added
3c36b7bb2a3ad_NCBIM37_to_GRCm38.chain added
3c36b2a764fa5_1000G_omni2.5.b37.vcf.gz added
3c36b6508ae76_1000G_omni2.5.b37.vcf.gz.tbi added
3c36b3e4b4202_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3c36b46eb0bd2_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3c36b338a6d21_1000G_omni2.5.hg38.vcf.gz added
3c36b3a331f06_1000G_omni2.5.hg38.vcf.gz.tbi added
3c36b5a13aca4_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3c36b608e0bdf_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3c36b678d5fc3_af-only-gnomad.raw.sites.vcf added
3c36b4f2eb91b_af-only-gnomad.raw.sites.vcf.idx added
3c36b661c67cb_Mutect2-exome-panel.vcf.idx added
3c36b8362846_Mutect2-WGS-panel-b37.vcf added
3c36b7e1ab804_Mutect2-WGS-panel-b37.vcf.idx added
3c36b4d2d9aa0_small_exac_common_3.vcf added
3c36b67a1d257_small_exac_common_3.vcf.idx added
3c36b73130609_1000g_pon.hg38.vcf.gz added
3c36b51dd03be_1000g_pon.hg38.vcf.gz.tbi added
3c36bfae4697_af-only-gnomad.hg38.vcf.gz added
3c36b1db6a538_af-only-gnomad.hg38.vcf.gz.tbi added
3c36b50e0f012_small_exac_common_3.hg38.vcf.gz added
3c36b34aa5993_small_exac_common_3.hg38.vcf.gz.tbi added
3c36b3483ce07_gencode.v41.annotation.gtf added
3c36b18a80613_gencode.v42.annotation.gtf added
3c36b39781e99_gencode.vM30.annotation.gtf added
3c36b6f5db42_gencode.vM31.annotation.gtf added
3c36b448b4533_gencode.v41.transcripts.fa added
3c36b25b1d763_gencode.v41.transcripts.fa.fai added
3c36b59e0c405_gencode.v42.transcripts.fa added
3c36b40c50529_gencode.v42.transcripts.fa.fai added
3c36b1b86b237_gencode.vM30.pc_transcripts.fa added
3c36b559367b3_gencode.vM30.pc_transcripts.fa.fai added
3c36b6b3b54ce_gencode.vM31.pc_transcripts.fa added
3c36b8f60ad_gencode.vM31.pc_transcripts.fa.fai added
3c36b13dea9b5_GRCh38.primary_assembly.genome.fa.1.ht2 added
3c36b322660a1_GRCh38.primary_assembly.genome.fa.2.ht2 added
3c36b3419cdcf_GRCh38.primary_assembly.genome.fa.3.ht2 added
3c36b4e11c8bc_GRCh38.primary_assembly.genome.fa.4.ht2 added
3c36bc3a0d45_GRCh38.primary_assembly.genome.fa.5.ht2 added
3c36b14a7d9ae_GRCh38.primary_assembly.genome.fa.6.ht2 added
3c36b359f287f_GRCh38.primary_assembly.genome.fa.7.ht2 added
3c36b5b68c660_GRCh38.primary_assembly.genome.fa.8.ht2 added
3c36b7ac44179_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3c36b3dd550c5_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3c36b59837e65_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3c36b47f1dc19_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3c36b2577231c_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3c36b4c96846e_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3c36b19cedfd8_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3c36b352569b4_GRCh38.primary_assembly.genome.fa.fai added
3c36b6a4d29a7_GRCh38.primary_assembly.genome.fa.amb added
3c36b6aafcfea_GRCh38.primary_assembly.genome.fa.ann added
3c36b69cfc347_GRCh38.primary_assembly.genome.fa.bwt added
3c36b1ed0f7ae_GRCh38.primary_assembly.genome.fa.pac added
3c36b357d5fd_GRCh38.primary_assembly.genome.fa.sa added
3c36b2347e1e0_GRCh38.primary_assembly.genome.fa added
3c36b25c6d2f0_hs37d5.fa.fai added
3c36b47e31b30_hs37d5.fa.amb added
3c36b48f9b943_hs37d5.fa.ann added
3c36b7fa796f6_hs37d5.fa.bwt added
3c36b8a82059_hs37d5.fa.pac added
3c36b64806b7a_hs37d5.fa.sa added
3c36b553afea9_hs37d5.fa added
3c36b73e37527_complete_ref_lens.bin added
3c36b650fcc27_ctable.bin added
3c36b6919a85e_ctg_offsets.bin added
3c36b2609d5c8_duplicate_clusters.tsv added
3c36b192999f6_info.json added
3c36b372b711a_mphf.bin added
3c36b3243e30d_pos.bin added
3c36b2dd173a5_pre_indexing.log added
3c36b6cca9999_rank.bin added
3c36bdaca96e_ref_indexing.log added
3c36b2895b51e_refAccumLengths.bin added
3c36b2a9fea5f_reflengths.bin added
3c36b673027d3_refseq.bin added
3c36b70879138_seq.bin added
3c36b50170d7b_versionInfo.json added
3c36b33c6ac41_salmon_index added
3c36ba567110_chrLength.txt added
3c36b53c772f_chrName.txt added
3c36b1e13d5e8_chrNameLength.txt added
3c36b750640fa_chrStart.txt added
3c36b6f0c3a76_exonGeTrInfo.tab added
3c36b3ce4cd96_exonInfo.tab added
3c36b785e16f7_geneInfo.tab added
3c36b12541c56_Genome added
3c36b62aba087_genomeParameters.txt added
3c36b40413227_Log.out added
3c36b5b4dd599_SA added
3c36b6253377d_SAindex added
3c36b48e95280_sjdbInfo.txt added
3c36b3fce4113_sjdbList.fromGTF.out.tab added
3c36b378e3626_sjdbList.out.tab added
3c36b3cccc7a7_transcriptInfo.tab added
3c36b24de0d3b_GRCh38.GENCODE.v42_100 added
3c36b20a7de84_knownGene_hg38.sql added
3c36b62d69d70_knownGene_hg38.txt added
3c36b3e07a731_refGene_hg38.sql added
3c36b57d34f9f_refGene_hg38.txt added
3c36b151a807d_knownGene_mm39.sql added
3c36b6bd91ad6_knownGene_mm39.txt added
3c36b449de938_refGene_mm39.sql added
3c36b22c729eb_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/RtmpTi4eF1/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
17.766 1.231 19.828
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.461 | 0.765 | 7.228 | |
| dataSearch | 1.096 | 0.053 | 1.149 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.611 | 0.309 | 4.356 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.124 | 0.020 | 0.145 | |
| recipeLoad | 1.286 | 0.072 | 1.358 | |
| recipeMake | 0.001 | 0.000 | 0.001 | |
| recipeSearch | 0.542 | 0.011 | 0.552 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |