Qian Liu
| Snapshot Date: 2025-12-18 13:40 -0500 (Thu, 18 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 2025-12-19 11:34 -0500 (Fri, 19 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" | 4593 |
| 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: 2025-12-19 02:45:36 -0500 (Fri, 19 Dec 2025) |
| EndedAt: 2025-12-19 02:48:21 -0500 (Fri, 19 Dec 2025) |
| EllapsedTime: 165.4 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 5.970 0.324 6.296
getCloudData 2.723 0.215 5.445
* 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...
e749a211b43e6_GRCh38.primary_assembly.genome.fa.1.bt2 added
e749a66f23a98_GRCh38.primary_assembly.genome.fa.2.bt2 added
e749a6d884b49_GRCh38.primary_assembly.genome.fa.3.bt2 added
e749a584be6b_GRCh38.primary_assembly.genome.fa.4.bt2 added
e749a197eb0bd_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
e749a72a67a60_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
e749a19b38546_outfile.txt added
e749a1d5708a2_GRCh37_to_GRCh38.chain added
e749a21faf827_GRCh37_to_NCBI34.chain added
e749a6248c734_GRCh37_to_NCBI35.chain added
e749a40eb776f_GRCh37_to_NCBI36.chain added
e749a486dc610_GRCh38_to_GRCh37.chain added
e749a580a8e1e_GRCh38_to_NCBI34.chain added
e749a51adaeb4_GRCh38_to_NCBI35.chain added
e749aa3da557_GRCh38_to_NCBI36.chain added
e749a7022c281_NCBI34_to_GRCh37.chain added
e749a668d9604_NCBI34_to_GRCh38.chain added
e749a5ea4b975_NCBI35_to_GRCh37.chain added
e749a13905c21_NCBI35_to_GRCh38.chain added
e749a7b3a14c7_NCBI36_to_GRCh37.chain added
e749a55e3d93_NCBI36_to_GRCh38.chain added
e749a34d9d200_GRCm38_to_NCBIM36.chain added
e749a1f599fea_GRCm38_to_NCBIM37.chain added
e749a65cf7049_NCBIM36_to_GRCm38.chain added
e749a2e0d09c4_NCBIM37_to_GRCm38.chain added
e749a66d68197_1000G_omni2.5.b37.vcf.gz added
e749a4ee0b1c9_1000G_omni2.5.b37.vcf.gz.tbi added
e749a48969187_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
e749a4dd1b61d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
e749a566a3d5a_1000G_omni2.5.hg38.vcf.gz added
e749a4c658167_1000G_omni2.5.hg38.vcf.gz.tbi added
e749a6eecfa03_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
e749a3d5c77f3_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
e749a39edccb0_af-only-gnomad.raw.sites.vcf added
e749a7471b86e_af-only-gnomad.raw.sites.vcf.idx added
e749a56db28b0_Mutect2-exome-panel.vcf.idx added
e749a2c944710_Mutect2-WGS-panel-b37.vcf added
e749ae253db5_Mutect2-WGS-panel-b37.vcf.idx added
e749a74323152_small_exac_common_3.vcf added
e749a4e8f3f37_small_exac_common_3.vcf.idx added
e749a706e04e9_1000g_pon.hg38.vcf.gz added
e749a351da8c2_1000g_pon.hg38.vcf.gz.tbi added
e749a16fd0547_af-only-gnomad.hg38.vcf.gz added
e749a48789307_af-only-gnomad.hg38.vcf.gz.tbi added
e749a6cb5776_small_exac_common_3.hg38.vcf.gz added
e749a213aaa9f_small_exac_common_3.hg38.vcf.gz.tbi added
e749a389b5588_gencode.v41.annotation.gtf added
e749a6d58ed7b_gencode.v42.annotation.gtf added
e749a7fdf6414_gencode.vM30.annotation.gtf added
e749a4c2bb1a9_gencode.vM31.annotation.gtf added
e749a68930242_gencode.v41.transcripts.fa added
e749a53da1a7_gencode.v41.transcripts.fa.fai added
e749a10583a9_gencode.v42.transcripts.fa added
e749a7eca22d_gencode.v42.transcripts.fa.fai added
e749a6b0d11f1_gencode.vM30.pc_transcripts.fa added
e749a2f128d6d_gencode.vM30.pc_transcripts.fa.fai added
e749a6ec323c4_gencode.vM31.pc_transcripts.fa added
e749a39edc3ba_gencode.vM31.pc_transcripts.fa.fai added
e749a77a91ef5_GRCh38.primary_assembly.genome.fa.1.ht2 added
e749a3c94d9e1_GRCh38.primary_assembly.genome.fa.2.ht2 added
e749a10580115_GRCh38.primary_assembly.genome.fa.3.ht2 added
e749a440ea05c_GRCh38.primary_assembly.genome.fa.4.ht2 added
e749a2b81d3e4_GRCh38.primary_assembly.genome.fa.5.ht2 added
e749a4db47908_GRCh38.primary_assembly.genome.fa.6.ht2 added
e749a7dfc6d0c_GRCh38.primary_assembly.genome.fa.7.ht2 added
e749a1ff38c53_GRCh38.primary_assembly.genome.fa.8.ht2 added
e749a248fa1b8_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
e749a2a90b41c_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
e749a2e18ca08_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
e749a18c1d30b_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
e749a791ff353_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
e749a1e86cef1_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
e749a4ddf7bcd_GRCh38_full_analysis_set_plus_decoy_hla.fa added
e749a101cf89a_GRCh38.primary_assembly.genome.fa.fai added
e749a66ff61f9_GRCh38.primary_assembly.genome.fa.amb added
e749a54aad343_GRCh38.primary_assembly.genome.fa.ann added
e749a3157a339_GRCh38.primary_assembly.genome.fa.bwt added
e749a1f9ab781_GRCh38.primary_assembly.genome.fa.pac added
e749a4203c0be_GRCh38.primary_assembly.genome.fa.sa added
e749a3137074e_GRCh38.primary_assembly.genome.fa added
e749a6bc6692b_hs37d5.fa.fai added
e749a2a96c301_hs37d5.fa.amb added
e749a3674a8f5_hs37d5.fa.ann added
e749a6ccbecd4_hs37d5.fa.bwt added
e749a3283652e_hs37d5.fa.pac added
e749a2181bae6_hs37d5.fa.sa added
e749a1bde7a42_hs37d5.fa added
e749a214688f2_complete_ref_lens.bin added
e749a5b6f7ea1_ctable.bin added
e749a13879937_ctg_offsets.bin added
e749a5ddb62d4_duplicate_clusters.tsv added
e749a6bc77fb6_info.json added
e749a57963993_mphf.bin added
e749a95d36b8_pos.bin added
e749a397bf8be_pre_indexing.log added
e749a5592a69f_rank.bin added
e749a2950c30b_ref_indexing.log added
e749a5e0b9a76_refAccumLengths.bin added
e749a235abb_reflengths.bin added
e749a57698d13_refseq.bin added
e749a76cd6d81_seq.bin added
e749a79434e0e_versionInfo.json added
e749a75f05c05_salmon_index added
e749a44ace94e_chrLength.txt added
e749a96046a8_chrName.txt added
e749a5cefbdfe_chrNameLength.txt added
e749a1957bc92_chrStart.txt added
e749a3ab7e9e2_exonGeTrInfo.tab added
e749a7c8a757f_exonInfo.tab added
e749a5b5b7d50_geneInfo.tab added
e749a6beef130_Genome added
e749a6850deaa_genomeParameters.txt added
e749a5f24051_Log.out added
e749a22639a25_SA added
e749a551ccb7f_SAindex added
e749a3875a57f_sjdbInfo.txt added
e749a43e5550c_sjdbList.fromGTF.out.tab added
e749a70fb45c1_sjdbList.out.tab added
e749a59bc2e72_transcriptInfo.tab added
e749a1f54d3ad_GRCh38.GENCODE.v42_100 added
e749a482def8_knownGene_hg38.sql added
e749a37979146_knownGene_hg38.txt added
e749ab1c5363_refGene_hg38.sql added
e749a5c19188b_refGene_hg38.txt added
e749a40f4c7fe_knownGene_mm39.sql added
e749a44984c21_knownGene_mm39.txt added
e749a31abbf2a_refGene_mm39.sql added
e749a6a458b0a_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/RtmpPVvJup/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
17.919 1.214 19.651
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.970 | 0.324 | 6.296 | |
| dataSearch | 1.152 | 0.018 | 1.171 | |
| dataUpdate | 0.001 | 0.000 | 0.001 | |
| getCloudData | 2.723 | 0.215 | 5.445 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.115 | 0.005 | 0.120 | |
| recipeLoad | 1.277 | 0.016 | 1.294 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.567 | 0.029 | 0.596 | |
| recipeUpdate | 0 | 0 | 0 | |