Qian Liu
| Snapshot Date: 2026-02-16 13:40 -0500 (Mon, 16 Feb 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 Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-17 11:32 -0500 (Tue, 17 Feb 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" | 4865 |
| 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 1770/2352 | 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 | | ||||||||
| 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: /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: 2026-02-17 03:24:27 -0500 (Tue, 17 Feb 2026) |
| EndedAt: 2026-02-17 03:27:13 -0500 (Tue, 17 Feb 2026) |
| EllapsedTime: 166.3 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 6.067 0.347 6.417
* 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...
eef347b3bd611_GRCh38.primary_assembly.genome.fa.1.bt2 added
eef34315d1af7_GRCh38.primary_assembly.genome.fa.2.bt2 added
eef34286afab6_GRCh38.primary_assembly.genome.fa.3.bt2 added
eef3418679e45_GRCh38.primary_assembly.genome.fa.4.bt2 added
eef347976360f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
eef347e8d0edb_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
eef3462f7d94c_outfile.txt added
eef344c80d019_GRCh37_to_GRCh38.chain added
eef3437a0be7a_GRCh37_to_NCBI34.chain added
eef347566b315_GRCh37_to_NCBI35.chain added
eef34579b2272_GRCh37_to_NCBI36.chain added
eef341f241473_GRCh38_to_GRCh37.chain added
eef34720bf18f_GRCh38_to_NCBI34.chain added
eef34145f8711_GRCh38_to_NCBI35.chain added
eef34208c7f21_GRCh38_to_NCBI36.chain added
eef341308425_NCBI34_to_GRCh37.chain added
eef3418080d30_NCBI34_to_GRCh38.chain added
eef341a404cc3_NCBI35_to_GRCh37.chain added
eef34269e03a9_NCBI35_to_GRCh38.chain added
eef34110f7ee6_NCBI36_to_GRCh37.chain added
eef34d4576b_NCBI36_to_GRCh38.chain added
eef341f4438d_GRCm38_to_NCBIM36.chain added
eef3414f86862_GRCm38_to_NCBIM37.chain added
eef341b350918_NCBIM36_to_GRCm38.chain added
eef3478120f06_NCBIM37_to_GRCm38.chain added
eef3441024d7f_1000G_omni2.5.b37.vcf.gz added
eef343ed6fb66_1000G_omni2.5.b37.vcf.gz.tbi added
eef34430591b0_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
eef341b707594_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
eef341197ce98_1000G_omni2.5.hg38.vcf.gz added
eef346284cb60_1000G_omni2.5.hg38.vcf.gz.tbi added
eef3416ac4ba6_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
eef3442f4e98f_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
eef34aefc616_af-only-gnomad.raw.sites.vcf added
eef342f13e9eb_af-only-gnomad.raw.sites.vcf.idx added
eef343c6b1f9e_Mutect2-exome-panel.vcf.idx added
eef3497cd4f2_Mutect2-WGS-panel-b37.vcf added
eef34120bc337_Mutect2-WGS-panel-b37.vcf.idx added
eef348ebefb7_small_exac_common_3.vcf added
eef34411d936c_small_exac_common_3.vcf.idx added
eef34772764c_1000g_pon.hg38.vcf.gz added
eef346087122a_1000g_pon.hg38.vcf.gz.tbi added
eef346041a7df_af-only-gnomad.hg38.vcf.gz added
eef34797e67dc_af-only-gnomad.hg38.vcf.gz.tbi added
eef3474e6993b_small_exac_common_3.hg38.vcf.gz added
eef34ce2700_small_exac_common_3.hg38.vcf.gz.tbi added
eef347aaeec01_gencode.v41.annotation.gtf added
eef34ceea66b_gencode.v42.annotation.gtf added
eef341b0e73c3_gencode.vM30.annotation.gtf added
eef34214cefaa_gencode.vM31.annotation.gtf added
eef341dfe2551_gencode.v41.transcripts.fa added
eef341be2cb2e_gencode.v41.transcripts.fa.fai added
eef3423413337_gencode.v42.transcripts.fa added
eef3432f68db4_gencode.v42.transcripts.fa.fai added
eef343717d446_gencode.vM30.pc_transcripts.fa added
eef341b53423d_gencode.vM30.pc_transcripts.fa.fai added
eef3473f8db33_gencode.vM31.pc_transcripts.fa added
eef3475eecfac_gencode.vM31.pc_transcripts.fa.fai added
eef345e58d3ed_GRCh38.primary_assembly.genome.fa.1.ht2 added
eef34f6950c8_GRCh38.primary_assembly.genome.fa.2.ht2 added
eef347869e44_GRCh38.primary_assembly.genome.fa.3.ht2 added
eef3440dd9f4d_GRCh38.primary_assembly.genome.fa.4.ht2 added
eef3426159c6e_GRCh38.primary_assembly.genome.fa.5.ht2 added
eef344a7b87d3_GRCh38.primary_assembly.genome.fa.6.ht2 added
eef344bcd6564_GRCh38.primary_assembly.genome.fa.7.ht2 added
eef3455298659_GRCh38.primary_assembly.genome.fa.8.ht2 added
eef346e6a771_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
eef34554a3a56_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
eef3467354990_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
eef34fd29728_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
eef341667cdc2_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
eef346ea7bfdc_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
eef347059a952_GRCh38_full_analysis_set_plus_decoy_hla.fa added
eef3476a975a1_GRCh38.primary_assembly.genome.fa.fai added
eef34682627b8_GRCh38.primary_assembly.genome.fa.amb added
eef346540428d_GRCh38.primary_assembly.genome.fa.ann added
eef3477779ca1_GRCh38.primary_assembly.genome.fa.bwt added
eef3462d513b9_GRCh38.primary_assembly.genome.fa.pac added
eef34722ee8f9_GRCh38.primary_assembly.genome.fa.sa added
eef3412861064_GRCh38.primary_assembly.genome.fa added
eef344220363_hs37d5.fa.fai added
eef34102d0e4a_hs37d5.fa.amb added
eef342e68db92_hs37d5.fa.ann added
eef342763369a_hs37d5.fa.bwt added
eef3443239bfe_hs37d5.fa.pac added
eef346580afd8_hs37d5.fa.sa added
eef3442b678d7_hs37d5.fa added
eef34371c7732_complete_ref_lens.bin added
eef345b6f7f84_ctable.bin added
eef34210f4cc5_ctg_offsets.bin added
eef344685c7fa_duplicate_clusters.tsv added
eef3462f61dc8_info.json added
eef3461ecec12_mphf.bin added
eef346c9b6468_pos.bin added
eef342d71a59b_pre_indexing.log added
eef342dba5176_rank.bin added
eef3441c4eac1_ref_indexing.log added
eef3434584d0c_refAccumLengths.bin added
eef343048bcc_reflengths.bin added
eef3428fa3451_refseq.bin added
eef34442ae434_seq.bin added
eef34196c598e_versionInfo.json added
eef3417a1f42d_salmon_index added
eef3434848d87_chrLength.txt added
eef341015cf2f_chrName.txt added
eef347fc81be6_chrNameLength.txt added
eef3419c4d014_chrStart.txt added
eef3478d6bd0_exonGeTrInfo.tab added
eef34629d2f9f_exonInfo.tab added
eef34bf3b90d_geneInfo.tab added
eef341a137c34_Genome added
eef3466bf3303_genomeParameters.txt added
eef341c20c758_Log.out added
eef34487c57c6_SA added
eef34e22699d_SAindex added
eef345f446356_sjdbInfo.txt added
eef342dfd079e_sjdbList.fromGTF.out.tab added
eef3450d8e275_sjdbList.out.tab added
eef341660da88_transcriptInfo.tab added
eef3496c8722_GRCh38.GENCODE.v42_100 added
eef3471e82f3a_knownGene_hg38.sql added
eef345ce6a282_knownGene_hg38.txt added
eef346c62a4ea_refGene_hg38.sql added
eef3453d51b4c_refGene_hg38.txt added
eef34498206ea_knownGene_mm39.sql added
eef3419d44a85_knownGene_mm39.txt added
eef3418f6cc3_refGene_mm39.sql added
eef34b46f1ab_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/RtmpgmsUaA/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
18.325 1.737 20.689
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.067 | 0.347 | 6.417 | |
| dataSearch | 1.103 | 0.016 | 1.121 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.610 | 0.107 | 3.608 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.123 | 0.004 | 0.127 | |
| recipeLoad | 1.286 | 0.106 | 1.392 | |
| recipeMake | 0.001 | 0.000 | 0.001 | |
| recipeSearch | 0.514 | 0.027 | 0.541 | |
| recipeUpdate | 0 | 0 | 0 | |