Qian Liu
| Snapshot Date: 2025-09-22 13:40 -0400 (Mon, 22 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_21 |
| git_last_commit: 601a107 |
| git_last_commit_date: 2025-04-15 13:01:44 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-09-25 11:38 -0400 (Thu, 25 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4827 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4581 |
| 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 1758/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.8.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.8.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ReUseData_1.8.0.tar.gz |
| StartedAt: 2025-09-25 03:09:14 -0400 (Thu, 25 Sep 2025) |
| EndedAt: 2025-09-25 03:12:13 -0400 (Thu, 25 Sep 2025) |
| EllapsedTime: 179.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ReUseData_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.8.0’
* 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 6.373 0.427 6.801
* 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-3.21-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.8.0’ ** 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 4.5.1 (2025-06-13) -- "Great Square Root"
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...
2d8d272517d39f_GRCh38.primary_assembly.genome.fa.1.bt2 added
2d8d271807b0c4_GRCh38.primary_assembly.genome.fa.2.bt2 added
2d8d27d9b46c6_GRCh38.primary_assembly.genome.fa.3.bt2 added
2d8d2768c72377_GRCh38.primary_assembly.genome.fa.4.bt2 added
2d8d271e5ce2b7_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2d8d2763bcbf8c_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2d8d271214d141_outfile.txt added
2d8d276e5eb70f_GRCh37_to_GRCh38.chain added
2d8d274b9c7b02_GRCh37_to_NCBI34.chain added
2d8d2744786367_GRCh37_to_NCBI35.chain added
2d8d27265a76c3_GRCh37_to_NCBI36.chain added
2d8d2753d55d2b_GRCh38_to_GRCh37.chain added
2d8d272be78a62_GRCh38_to_NCBI34.chain added
2d8d2759769d60_GRCh38_to_NCBI35.chain added
2d8d27455ae604_GRCh38_to_NCBI36.chain added
2d8d276da23ce0_NCBI34_to_GRCh37.chain added
2d8d275c64cffd_NCBI34_to_GRCh38.chain added
2d8d2713e96fd_NCBI35_to_GRCh37.chain added
2d8d27180b8327_NCBI35_to_GRCh38.chain added
2d8d27e4af768_NCBI36_to_GRCh37.chain added
2d8d271540cb4_NCBI36_to_GRCh38.chain added
2d8d273e08ade8_GRCm38_to_NCBIM36.chain added
2d8d275fa4a9de_GRCm38_to_NCBIM37.chain added
2d8d2761914f50_NCBIM36_to_GRCm38.chain added
2d8d272b52b619_NCBIM37_to_GRCm38.chain added
2d8d2773701cfc_1000G_omni2.5.b37.vcf.gz added
2d8d272ebc6ade_1000G_omni2.5.b37.vcf.gz.tbi added
2d8d27a476816_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2d8d273ef7119e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2d8d27dcd5028_1000G_omni2.5.hg38.vcf.gz added
2d8d271b2193d1_1000G_omni2.5.hg38.vcf.gz.tbi added
2d8d27640ee53d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2d8d2725d500ec_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2d8d2728bcda97_af-only-gnomad.raw.sites.vcf added
2d8d274cd608b4_af-only-gnomad.raw.sites.vcf.idx added
2d8d274431e3a3_Mutect2-exome-panel.vcf.idx added
2d8d27c799a23_Mutect2-WGS-panel-b37.vcf added
2d8d275eead9f5_Mutect2-WGS-panel-b37.vcf.idx added
2d8d2732909ab3_small_exac_common_3.vcf added
2d8d2758161525_small_exac_common_3.vcf.idx added
2d8d2723633d5c_1000g_pon.hg38.vcf.gz added
2d8d2758eb1176_1000g_pon.hg38.vcf.gz.tbi added
2d8d272beb7250_af-only-gnomad.hg38.vcf.gz added
2d8d274f4ac7bf_af-only-gnomad.hg38.vcf.gz.tbi added
2d8d273261aed6_small_exac_common_3.hg38.vcf.gz added
2d8d2771465854_small_exac_common_3.hg38.vcf.gz.tbi added
2d8d273ced049f_gencode.v41.annotation.gtf added
2d8d27ec67ed3_gencode.v42.annotation.gtf added
2d8d277284ef52_gencode.vM30.annotation.gtf added
2d8d2754f887c6_gencode.vM31.annotation.gtf added
2d8d271d11763b_gencode.v41.transcripts.fa added
2d8d2773d8fc06_gencode.v41.transcripts.fa.fai added
2d8d27130135ae_gencode.v42.transcripts.fa added
2d8d277cb62019_gencode.v42.transcripts.fa.fai added
2d8d27556a4b56_gencode.vM30.pc_transcripts.fa added
2d8d273e53ebc7_gencode.vM30.pc_transcripts.fa.fai added
2d8d2770263d15_gencode.vM31.pc_transcripts.fa added
2d8d27426b635_gencode.vM31.pc_transcripts.fa.fai added
2d8d27489b53dd_GRCh38.primary_assembly.genome.fa.1.ht2 added
2d8d272f1d4eb3_GRCh38.primary_assembly.genome.fa.2.ht2 added
2d8d2711f4065d_GRCh38.primary_assembly.genome.fa.3.ht2 added
2d8d2763bce7ae_GRCh38.primary_assembly.genome.fa.4.ht2 added
2d8d27132c33f0_GRCh38.primary_assembly.genome.fa.5.ht2 added
2d8d2737c90749_GRCh38.primary_assembly.genome.fa.6.ht2 added
2d8d27c79c245_GRCh38.primary_assembly.genome.fa.7.ht2 added
2d8d2760023ca4_GRCh38.primary_assembly.genome.fa.8.ht2 added
2d8d277bfaeaec_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2d8d2718f35c68_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2d8d273eed1699_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2d8d272e8b859f_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2d8d277109718d_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2d8d27625053f6_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2d8d277769715_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2d8d271cf4e3de_GRCh38.primary_assembly.genome.fa.fai added
2d8d27319b1bb5_GRCh38.primary_assembly.genome.fa.amb added
2d8d2739d845eb_GRCh38.primary_assembly.genome.fa.ann added
2d8d27e3b3c32_GRCh38.primary_assembly.genome.fa.bwt added
2d8d276e882054_GRCh38.primary_assembly.genome.fa.pac added
2d8d27489ec4be_GRCh38.primary_assembly.genome.fa.sa added
2d8d27c02b84_GRCh38.primary_assembly.genome.fa added
2d8d274380a81b_hs37d5.fa.fai added
2d8d2765b03af9_hs37d5.fa.amb added
2d8d277499278a_hs37d5.fa.ann added
2d8d275681ddc9_hs37d5.fa.bwt added
2d8d2762665b12_hs37d5.fa.pac added
2d8d274a0372e1_hs37d5.fa.sa added
2d8d2714d5c991_hs37d5.fa added
2d8d27528c9828_complete_ref_lens.bin added
2d8d274e2a2916_ctable.bin added
2d8d275d711d6e_ctg_offsets.bin added
2d8d271a9e6db_duplicate_clusters.tsv added
2d8d27601e2f73_info.json added
2d8d27412e051d_mphf.bin added
2d8d2714d61acc_pos.bin added
2d8d2717e736bc_pre_indexing.log added
2d8d274da7c762_rank.bin added
2d8d2774d85770_ref_indexing.log added
2d8d2713e221a8_refAccumLengths.bin added
2d8d27669b23cb_reflengths.bin added
2d8d2733c56e0a_refseq.bin added
2d8d27426da748_seq.bin added
2d8d2757a49558_versionInfo.json added
2d8d271615c200_salmon_index added
2d8d2749e43e5d_chrLength.txt added
2d8d2774997936_chrName.txt added
2d8d2747b0ddb5_chrNameLength.txt added
2d8d273bc8449_chrStart.txt added
2d8d272d4b569_exonGeTrInfo.tab added
2d8d273638fe09_exonInfo.tab added
2d8d274c5b4907_geneInfo.tab added
2d8d27394e0ed_Genome added
2d8d2779b9a624_genomeParameters.txt added
2d8d27320b8401_Log.out added
2d8d27782e0878_SA added
2d8d27503b83ee_SAindex added
2d8d271471df13_sjdbInfo.txt added
2d8d2742317b59_sjdbList.fromGTF.out.tab added
2d8d2765114d7f_sjdbList.out.tab added
2d8d2766fe773b_transcriptInfo.tab added
2d8d27105ba46f_GRCh38.GENCODE.v42_100 added
2d8d2742826aed_knownGene_hg38.sql added
2d8d2768a85e17_knownGene_hg38.txt added
2d8d277079d3e2_refGene_hg38.sql added
2d8d273b0700a_refGene_hg38.txt added
2d8d277d7e78e3_knownGene_mm39.sql added
2d8d278610a9e_knownGene_mm39.txt added
2d8d275158376d_refGene_mm39.sql added
2d8d277256d053_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/Rtmpe7dT4m/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
20.807 1.714 22.953
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.373 | 0.427 | 6.801 | |
| dataSearch | 1.226 | 0.061 | 1.286 | |
| dataUpdate | 0.000 | 0.001 | 0.001 | |
| getCloudData | 2.851 | 0.168 | 4.021 | |
| getData | 0.000 | 0.001 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.123 | 0.003 | 0.126 | |
| recipeLoad | 1.294 | 0.068 | 1.364 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.552 | 0.039 | 0.591 | |
| recipeUpdate | 0 | 0 | 0 | |