Qian Liu
| Snapshot Date: 2025-11-27 13:40 -0500 (Thu, 27 Nov 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 2025-11-28 11:38 -0500 (Fri, 28 Nov 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" | 4866 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4614 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4571 |
| 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 1751/2328 | 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 | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | TIMEOUT | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
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: 2025-11-28 03:13:35 -0500 (Fri, 28 Nov 2025) |
| EndedAt: 2025-11-28 03:16:24 -0500 (Fri, 28 Nov 2025) |
| EllapsedTime: 169.3 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) (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 6.049 0.369 6.433
* 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...
2eb0d812a3b36d_GRCh38.primary_assembly.genome.fa.1.bt2 added
2eb0d834cb578d_GRCh38.primary_assembly.genome.fa.2.bt2 added
2eb0d865afe907_GRCh38.primary_assembly.genome.fa.3.bt2 added
2eb0d86c057533_GRCh38.primary_assembly.genome.fa.4.bt2 added
2eb0d879730dae_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2eb0d8515d6106_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2eb0d8c564ed3_outfile.txt added
2eb0d819674fd2_GRCh37_to_GRCh38.chain added
2eb0d831329b2c_GRCh37_to_NCBI34.chain added
2eb0d83367afd0_GRCh37_to_NCBI35.chain added
2eb0d8184ffd2d_GRCh37_to_NCBI36.chain added
2eb0d84fff0b70_GRCh38_to_GRCh37.chain added
2eb0d84a6f1ad8_GRCh38_to_NCBI34.chain added
2eb0d8729e2fd5_GRCh38_to_NCBI35.chain added
2eb0d86f033c_GRCh38_to_NCBI36.chain added
2eb0d82419823d_NCBI34_to_GRCh37.chain added
2eb0d83be29e8d_NCBI34_to_GRCh38.chain added
2eb0d8718fc681_NCBI35_to_GRCh37.chain added
2eb0d86fd9e56c_NCBI35_to_GRCh38.chain added
2eb0d858117a92_NCBI36_to_GRCh37.chain added
2eb0d82b12ae33_NCBI36_to_GRCh38.chain added
2eb0d829cd735_GRCm38_to_NCBIM36.chain added
2eb0d85b6aff5d_GRCm38_to_NCBIM37.chain added
2eb0d837d54399_NCBIM36_to_GRCm38.chain added
2eb0d86afbe4cb_NCBIM37_to_GRCm38.chain added
2eb0d85e8bc4ee_1000G_omni2.5.b37.vcf.gz added
2eb0d877877041_1000G_omni2.5.b37.vcf.gz.tbi added
2eb0d826ffc18_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2eb0d85a58d16b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2eb0d83bd940bf_1000G_omni2.5.hg38.vcf.gz added
2eb0d831dd367a_1000G_omni2.5.hg38.vcf.gz.tbi added
2eb0d86cfc84d8_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2eb0d870a4984c_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2eb0d8178d1f81_af-only-gnomad.raw.sites.vcf added
2eb0d85901fa0b_af-only-gnomad.raw.sites.vcf.idx added
2eb0d86a17a5fa_Mutect2-exome-panel.vcf.idx added
2eb0d868ea8088_Mutect2-WGS-panel-b37.vcf added
2eb0d8655848de_Mutect2-WGS-panel-b37.vcf.idx added
2eb0d837ef5cc_small_exac_common_3.vcf added
2eb0d81a1d1bb4_small_exac_common_3.vcf.idx added
2eb0d818bff8af_1000g_pon.hg38.vcf.gz added
2eb0d81bcef2f9_1000g_pon.hg38.vcf.gz.tbi added
2eb0d86a1c2724_af-only-gnomad.hg38.vcf.gz added
2eb0d8632f1387_af-only-gnomad.hg38.vcf.gz.tbi added
2eb0d8e6d22ce_small_exac_common_3.hg38.vcf.gz added
2eb0d86a8b2a60_small_exac_common_3.hg38.vcf.gz.tbi added
2eb0d874895c4_gencode.v41.annotation.gtf added
2eb0d84a4fc15c_gencode.v42.annotation.gtf added
2eb0d85c1af0e1_gencode.vM30.annotation.gtf added
2eb0d877227b30_gencode.vM31.annotation.gtf added
2eb0d822613bee_gencode.v41.transcripts.fa added
2eb0d872d9f14_gencode.v41.transcripts.fa.fai added
2eb0d879bf5265_gencode.v42.transcripts.fa added
2eb0d87dcc3b4b_gencode.v42.transcripts.fa.fai added
2eb0d83f02e2ad_gencode.vM30.pc_transcripts.fa added
2eb0d864bb3731_gencode.vM30.pc_transcripts.fa.fai added
2eb0d85c58003a_gencode.vM31.pc_transcripts.fa added
2eb0d8368a52ee_gencode.vM31.pc_transcripts.fa.fai added
2eb0d8672b3349_GRCh38.primary_assembly.genome.fa.1.ht2 added
2eb0d836b0d1a5_GRCh38.primary_assembly.genome.fa.2.ht2 added
2eb0d8726393ae_GRCh38.primary_assembly.genome.fa.3.ht2 added
2eb0d8190869c4_GRCh38.primary_assembly.genome.fa.4.ht2 added
2eb0d823ad567d_GRCh38.primary_assembly.genome.fa.5.ht2 added
2eb0d863082bfa_GRCh38.primary_assembly.genome.fa.6.ht2 added
2eb0d830958945_GRCh38.primary_assembly.genome.fa.7.ht2 added
2eb0d87caf5088_GRCh38.primary_assembly.genome.fa.8.ht2 added
2eb0d84d1fd1f5_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2eb0d8198009cd_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2eb0d862079967_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2eb0d8509ec7c1_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2eb0d8339d2582_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2eb0d87ac79216_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2eb0d86c6dbabb_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2eb0d81db94ca6_GRCh38.primary_assembly.genome.fa.fai added
2eb0d85df6a59d_GRCh38.primary_assembly.genome.fa.amb added
2eb0d87adadd89_GRCh38.primary_assembly.genome.fa.ann added
2eb0d88447707_GRCh38.primary_assembly.genome.fa.bwt added
2eb0d8653f3b61_GRCh38.primary_assembly.genome.fa.pac added
2eb0d8452a9ee5_GRCh38.primary_assembly.genome.fa.sa added
2eb0d8645f67e8_GRCh38.primary_assembly.genome.fa added
2eb0d85c61b691_hs37d5.fa.fai added
2eb0d8678bdad3_hs37d5.fa.amb added
2eb0d86b8d06fd_hs37d5.fa.ann added
2eb0d8562108f6_hs37d5.fa.bwt added
2eb0d86558161f_hs37d5.fa.pac added
2eb0d82a8fe9aa_hs37d5.fa.sa added
2eb0d83adc4027_hs37d5.fa added
2eb0d841b01659_complete_ref_lens.bin added
2eb0d8611a3c99_ctable.bin added
2eb0d822077371_ctg_offsets.bin added
2eb0d87860e7fe_duplicate_clusters.tsv added
2eb0d8537dd047_info.json added
2eb0d83b0fdd35_mphf.bin added
2eb0d81c0e3e7b_pos.bin added
2eb0d83685fc41_pre_indexing.log added
2eb0d86ba5667a_rank.bin added
2eb0d818bd8f03_ref_indexing.log added
2eb0d83a5ce36_refAccumLengths.bin added
2eb0d85257048_reflengths.bin added
2eb0d87ac5286a_refseq.bin added
2eb0d8544495f8_seq.bin added
2eb0d838c295ca_versionInfo.json added
2eb0d8758cba80_salmon_index added
2eb0d840b250b3_chrLength.txt added
2eb0d8567be270_chrName.txt added
2eb0d85383601d_chrNameLength.txt added
2eb0d83b8d2e3c_chrStart.txt added
2eb0d85ec05977_exonGeTrInfo.tab added
2eb0d838c29b7e_exonInfo.tab added
2eb0d8b7cd22_geneInfo.tab added
2eb0d8431fc160_Genome added
2eb0d81524520f_genomeParameters.txt added
2eb0d86843a7f5_Log.out added
2eb0d82eacc85d_SA added
2eb0d86b455b06_SAindex added
2eb0d84d9bbe14_sjdbInfo.txt added
2eb0d8593cb207_sjdbList.fromGTF.out.tab added
2eb0d826219b2d_sjdbList.out.tab added
2eb0d8f4bd46d_transcriptInfo.tab added
2eb0d83a56eea0_GRCh38.GENCODE.v42_100 added
2eb0d848290e9e_knownGene_hg38.sql added
2eb0d87acbc6b_knownGene_hg38.txt added
2eb0d8dd4bee7_refGene_hg38.sql added
2eb0d8338ebd3_refGene_hg38.txt added
2eb0d823bafae6_knownGene_mm39.sql added
2eb0d8445abb29_knownGene_mm39.txt added
2eb0d86ede524e_refGene_mm39.sql added
2eb0d83c7889ea_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/RtmpctDYVN/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
18.588 1.046 20.291
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.049 | 0.369 | 6.433 | |
| dataSearch | 1.091 | 0.044 | 1.135 | |
| dataUpdate | 0.000 | 0.001 | 0.000 | |
| getCloudData | 2.686 | 0.169 | 3.692 | |
| getData | 0.000 | 0.001 | 0.000 | |
| meta_data | 0.000 | 0.001 | 0.001 | |
| recipeHub-class | 0.125 | 0.003 | 0.129 | |
| recipeLoad | 1.275 | 0.077 | 1.353 | |
| recipeMake | 0.000 | 0.001 | 0.000 | |
| recipeSearch | 0.545 | 0.012 | 0.558 | |
| recipeUpdate | 0 | 0 | 0 | |