Qian Liu
| Snapshot Date: 2026-03-09 13:45 -0400 (Mon, 09 Mar 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 2026-03-10 11:58 -0400 (Tue, 10 Mar 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" | 4892 |
| 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: 2026-03-10 03:06:13 -0400 (Tue, 10 Mar 2026) |
| EndedAt: 2026-03-10 03:09:00 -0400 (Tue, 10 Mar 2026) |
| EllapsedTime: 167.2 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 24.04.3 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 5.837 0.288 6.13
* 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...
3312107eea5e0e_GRCh38.primary_assembly.genome.fa.1.bt2 added
33121016a7ef72_GRCh38.primary_assembly.genome.fa.2.bt2 added
3312106f58e6fd_GRCh38.primary_assembly.genome.fa.3.bt2 added
3312105d837c10_GRCh38.primary_assembly.genome.fa.4.bt2 added
3312103a78b4a5_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3312104237c0c9_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3312102b682db8_outfile.txt added
3312103b4f4cb6_GRCh37_to_GRCh38.chain added
3312103a59750b_GRCh37_to_NCBI34.chain added
331210569aa19f_GRCh37_to_NCBI35.chain added
3312103529cd24_GRCh37_to_NCBI36.chain added
3312107c08c9c1_GRCh38_to_GRCh37.chain added
3312106b05e3fc_GRCh38_to_NCBI34.chain added
331210318a7615_GRCh38_to_NCBI35.chain added
3312106229077d_GRCh38_to_NCBI36.chain added
331210450fe6b2_NCBI34_to_GRCh37.chain added
331210482d5cfb_NCBI34_to_GRCh38.chain added
3312107febbd7b_NCBI35_to_GRCh37.chain added
3312101bf5aac5_NCBI35_to_GRCh38.chain added
33121015e997_NCBI36_to_GRCh37.chain added
331210d0dacd1_NCBI36_to_GRCh38.chain added
3312106be8c7c0_GRCm38_to_NCBIM36.chain added
3312107d5e346a_GRCm38_to_NCBIM37.chain added
3312101b19f422_NCBIM36_to_GRCm38.chain added
3312101369f15d_NCBIM37_to_GRCm38.chain added
331210678caf64_1000G_omni2.5.b37.vcf.gz added
331210616a380a_1000G_omni2.5.b37.vcf.gz.tbi added
33121033576ac_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3312107de0493e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3312106564e9fe_1000G_omni2.5.hg38.vcf.gz added
33121020a0afc4_1000G_omni2.5.hg38.vcf.gz.tbi added
3312107ccaa74c_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3312107c0cd970_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
331210ff996c1_af-only-gnomad.raw.sites.vcf added
3312105a4e235d_af-only-gnomad.raw.sites.vcf.idx added
33121036858e15_Mutect2-exome-panel.vcf.idx added
3312105231578b_Mutect2-WGS-panel-b37.vcf added
3312105b65115_Mutect2-WGS-panel-b37.vcf.idx added
33121071d4dacc_small_exac_common_3.vcf added
331210c8acc96_small_exac_common_3.vcf.idx added
3312105c50f2b5_1000g_pon.hg38.vcf.gz added
33121026fea7f0_1000g_pon.hg38.vcf.gz.tbi added
3312108939657_af-only-gnomad.hg38.vcf.gz added
3312104756d6b1_af-only-gnomad.hg38.vcf.gz.tbi added
33121058891e06_small_exac_common_3.hg38.vcf.gz added
3312106abc9dd5_small_exac_common_3.hg38.vcf.gz.tbi added
331210c66bd63_gencode.v41.annotation.gtf added
33121020b67b01_gencode.v42.annotation.gtf added
3312106aa85b50_gencode.vM30.annotation.gtf added
331210285c6829_gencode.vM31.annotation.gtf added
33121020cc6499_gencode.v41.transcripts.fa added
33121077b60821_gencode.v41.transcripts.fa.fai added
33121014452fe9_gencode.v42.transcripts.fa added
3312101e2a9903_gencode.v42.transcripts.fa.fai added
33121012cffc44_gencode.vM30.pc_transcripts.fa added
33121027af2147_gencode.vM30.pc_transcripts.fa.fai added
3312105b74867_gencode.vM31.pc_transcripts.fa added
331210743a344e_gencode.vM31.pc_transcripts.fa.fai added
3312102ae497f3_GRCh38.primary_assembly.genome.fa.1.ht2 added
33121039791a5_GRCh38.primary_assembly.genome.fa.2.ht2 added
331210599f1e4c_GRCh38.primary_assembly.genome.fa.3.ht2 added
3312104b8547b7_GRCh38.primary_assembly.genome.fa.4.ht2 added
3312106238f2_GRCh38.primary_assembly.genome.fa.5.ht2 added
33121055abf7bc_GRCh38.primary_assembly.genome.fa.6.ht2 added
3312105b7ede79_GRCh38.primary_assembly.genome.fa.7.ht2 added
3312105ab05c4f_GRCh38.primary_assembly.genome.fa.8.ht2 added
331210c3185d1_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3312102db03604_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3312106066ad64_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3312107e06609d_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3312103a3b029a_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3312103cb7a019_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3312102505088e_GRCh38_full_analysis_set_plus_decoy_hla.fa added
33121042ce98f1_GRCh38.primary_assembly.genome.fa.fai added
33121040e76ca_GRCh38.primary_assembly.genome.fa.amb added
3312107d8e2694_GRCh38.primary_assembly.genome.fa.ann added
3312102d8b36c6_GRCh38.primary_assembly.genome.fa.bwt added
3312101075342e_GRCh38.primary_assembly.genome.fa.pac added
3312101e44a195_GRCh38.primary_assembly.genome.fa.sa added
33121018339217_GRCh38.primary_assembly.genome.fa added
33121038d19c57_hs37d5.fa.fai added
3312103f11062e_hs37d5.fa.amb added
331210fe99a38_hs37d5.fa.ann added
3312104d16cc40_hs37d5.fa.bwt added
3312105d3b9f31_hs37d5.fa.pac added
33121022b9967c_hs37d5.fa.sa added
33121074c5ed87_hs37d5.fa added
33121062f2e799_complete_ref_lens.bin added
33121016f3caca_ctable.bin added
3312101faa857a_ctg_offsets.bin added
331210668a793e_duplicate_clusters.tsv added
3312107092e916_info.json added
3312106b2fcd32_mphf.bin added
33121066ecb230_pos.bin added
331210463ee0d2_pre_indexing.log added
33121046aeabab_rank.bin added
331210419d0e7f_ref_indexing.log added
331210527066a4_refAccumLengths.bin added
331210745ee1af_reflengths.bin added
3312102203bbe4_refseq.bin added
3312105076c741_seq.bin added
3312102e99e449_versionInfo.json added
3312105ebb5bfd_salmon_index added
331210757bcfcf_chrLength.txt added
33121071687d3a_chrName.txt added
33121062c9d2c8_chrNameLength.txt added
3312107309f663_chrStart.txt added
3312101ef3b401_exonGeTrInfo.tab added
331210733f06f6_exonInfo.tab added
331210114e97f9_geneInfo.tab added
33121037274618_Genome added
3312102c10a34d_genomeParameters.txt added
331210505f9e27_Log.out added
3312104710e050_SA added
33121079276f8d_SAindex added
3312102d9b3d59_sjdbInfo.txt added
33121069ca76cd_sjdbList.fromGTF.out.tab added
3312106ded5d15_sjdbList.out.tab added
331210108e24f2_transcriptInfo.tab added
331210be4197_GRCh38.GENCODE.v42_100 added
331210d97e28f_knownGene_hg38.sql added
33121077189e30_knownGene_hg38.txt added
33121071512aae_refGene_hg38.sql added
33121078c7afc1_refGene_hg38.txt added
3312105e055061_knownGene_mm39.sql added
33121037900b80_knownGene_mm39.txt added
3312103f765b6c_refGene_mm39.sql added
3312101fa25ee0_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/RtmptbyvtI/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
18.965 1.890 21.185
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.837 | 0.288 | 6.130 | |
| dataSearch | 1.089 | 0.021 | 1.110 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.709 | 0.128 | 3.610 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.118 | 0.003 | 0.122 | |
| recipeLoad | 1.303 | 0.075 | 1.379 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.540 | 0.019 | 0.559 | |
| recipeUpdate | 0 | 0 | 0 | |