Qian Liu
| Snapshot Date: 2025-12-11 13:45 -0500 (Thu, 11 Dec 2025) |
| 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 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-15 12:06 -0500 (Mon, 15 Dec 2025).
| 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" | 4882 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | 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: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReUseData_1.10.0.tar.gz |
| StartedAt: 2025-12-12 10:20:51 -0500 (Fri, 12 Dec 2025) |
| EndedAt: 2025-12-12 10:26:06 -0500 (Fri, 12 Dec 2025) |
| EllapsedTime: 315.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReUseData_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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 12.509 1.318 18.079
getCloudData 4.779 0.215 11.096
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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-apple-darwin20
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...
22aa68dc8f06_GRCh38.primary_assembly.genome.fa.1.bt2 added
22aa683208b2_GRCh38.primary_assembly.genome.fa.2.bt2 added
22aa2cd9138f_GRCh38.primary_assembly.genome.fa.3.bt2 added
22aa5f932849_GRCh38.primary_assembly.genome.fa.4.bt2 added
22aa363a01a4_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
22aa1a41d1cc_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
22aa5734b58b_outfile.txt added
22aa457ae567_GRCh37_to_GRCh38.chain added
22aa76af0d4_GRCh37_to_NCBI34.chain added
22aa7de8f219_GRCh37_to_NCBI35.chain added
22aa486e87e3_GRCh37_to_NCBI36.chain added
22aa509b6d3b_GRCh38_to_GRCh37.chain added
22aac2065d5_GRCh38_to_NCBI34.chain added
22aa22fd892b_GRCh38_to_NCBI35.chain added
22aa333877ff_GRCh38_to_NCBI36.chain added
22aa404e209e_NCBI34_to_GRCh37.chain added
22aa493f860d_NCBI34_to_GRCh38.chain added
22aa6979e50c_NCBI35_to_GRCh37.chain added
22aa41acaced_NCBI35_to_GRCh38.chain added
22aa2f8d1d4a_NCBI36_to_GRCh37.chain added
22aa597dfda9_NCBI36_to_GRCh38.chain added
22aa5e989025_GRCm38_to_NCBIM36.chain added
22aa721f9da7_GRCm38_to_NCBIM37.chain added
22aa79a77979_NCBIM36_to_GRCm38.chain added
22aa62183554_NCBIM37_to_GRCm38.chain added
22aa2355501c_1000G_omni2.5.b37.vcf.gz added
22aa35fe7063_1000G_omni2.5.b37.vcf.gz.tbi added
22aa53848f46_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
22aa23da6780_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
22aa57c116e3_1000G_omni2.5.hg38.vcf.gz added
22aa45c5be17_1000G_omni2.5.hg38.vcf.gz.tbi added
22aa3942fbca_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
22aa5ca0a824_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
22aa377f02fe_af-only-gnomad.raw.sites.vcf added
22aa739d8e28_af-only-gnomad.raw.sites.vcf.idx added
22aa6ce01f64_Mutect2-exome-panel.vcf.idx added
22aa6e2d1613_Mutect2-WGS-panel-b37.vcf added
22aa520471e7_Mutect2-WGS-panel-b37.vcf.idx added
22aa21d21ec2_small_exac_common_3.vcf added
22aa69e163e6_small_exac_common_3.vcf.idx added
22aa4c65c758_1000g_pon.hg38.vcf.gz added
22aa2e028997_1000g_pon.hg38.vcf.gz.tbi added
22aa2897301a_af-only-gnomad.hg38.vcf.gz added
22aa5dd70fc7_af-only-gnomad.hg38.vcf.gz.tbi added
22aa524d01f2_small_exac_common_3.hg38.vcf.gz added
22aa3dbae114_small_exac_common_3.hg38.vcf.gz.tbi added
22aa380f07b5_gencode.v41.annotation.gtf added
22aa62c318d3_gencode.v42.annotation.gtf added
22aa7692f74c_gencode.vM30.annotation.gtf added
22aa2aa9db65_gencode.vM31.annotation.gtf added
22aa7582d9c4_gencode.v41.transcripts.fa added
22aa61a70f21_gencode.v41.transcripts.fa.fai added
22aa1ed2719d_gencode.v42.transcripts.fa added
22aaa210a3a_gencode.v42.transcripts.fa.fai added
22aa7f266b07_gencode.vM30.pc_transcripts.fa added
22aa333cd9c8_gencode.vM30.pc_transcripts.fa.fai added
22aa5ffdf3bf_gencode.vM31.pc_transcripts.fa added
22aa198db1d5_gencode.vM31.pc_transcripts.fa.fai added
22aa2596240e_GRCh38.primary_assembly.genome.fa.1.ht2 added
22aa24192669_GRCh38.primary_assembly.genome.fa.2.ht2 added
22aa6f28ca02_GRCh38.primary_assembly.genome.fa.3.ht2 added
22aa5ee68251_GRCh38.primary_assembly.genome.fa.4.ht2 added
22aa6f75c483_GRCh38.primary_assembly.genome.fa.5.ht2 added
22aa1cb8ada0_GRCh38.primary_assembly.genome.fa.6.ht2 added
22aa208ef21b_GRCh38.primary_assembly.genome.fa.7.ht2 added
22aa8b8db50_GRCh38.primary_assembly.genome.fa.8.ht2 added
22aa204665a9_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
22aa6dbc4acc_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
22aa64d2cf5c_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
22aa4c2bd4ba_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
22aa519b2667_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
22aa20f65e0c_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
22aae9876bc_GRCh38_full_analysis_set_plus_decoy_hla.fa added
22aa3b9b3820_GRCh38.primary_assembly.genome.fa.fai added
22aa4b81db72_GRCh38.primary_assembly.genome.fa.amb added
22aa3a6e4018_GRCh38.primary_assembly.genome.fa.ann added
22aa1c3205a0_GRCh38.primary_assembly.genome.fa.bwt added
22aa180f59d6_GRCh38.primary_assembly.genome.fa.pac added
22aa17d2fcf1_GRCh38.primary_assembly.genome.fa.sa added
22aa1cdc3e6f_GRCh38.primary_assembly.genome.fa added
22aa3f86f836_hs37d5.fa.fai added
22aa3611c1cf_hs37d5.fa.amb added
22aa47cb18c4_hs37d5.fa.ann added
22aa66c710ae_hs37d5.fa.bwt added
22aa17184439_hs37d5.fa.pac added
22aa3a270607_hs37d5.fa.sa added
22aa57fcd364_hs37d5.fa added
22aa179a775d_complete_ref_lens.bin added
22aa1e1286c6_ctable.bin added
22aa524e4096_ctg_offsets.bin added
22aaf726211_duplicate_clusters.tsv added
22aa1e845203_info.json added
22aa124529c_mphf.bin added
22aa77ab8059_pos.bin added
22aa1c779070_pre_indexing.log added
22aa6dabb7a9_rank.bin added
22aa24a6f07f_ref_indexing.log added
22aa4bf734a5_refAccumLengths.bin added
22aa52a16399_reflengths.bin added
22aa6191fc30_refseq.bin added
22aa3743e55b_seq.bin added
22aa4a86d5b5_versionInfo.json added
22aa5a38844c_salmon_index added
22aa3475c7da_chrLength.txt added
22aa2093d41e_chrName.txt added
22aa494b0e47_chrNameLength.txt added
22aa5e967ce8_chrStart.txt added
22aa69e293db_exonGeTrInfo.tab added
22aa1a59452c_exonInfo.tab added
22aa5acc5937_geneInfo.tab added
22aa1df55873_Genome added
22aa5681f562_genomeParameters.txt added
22aa6e15214c_Log.out added
22aa2d3d3d0a_SA added
22aaf7272ba_SAindex added
22aa22ca1942_sjdbInfo.txt added
22aa2404de6_sjdbList.fromGTF.out.tab added
22aa4bba3831_sjdbList.out.tab added
22aa2ebf3fce_transcriptInfo.tab added
22aadf6055c_GRCh38.GENCODE.v42_100 added
22aa12d9e22d_knownGene_hg38.sql added
22aa1e900206_knownGene_hg38.txt added
22aa74e797_refGene_hg38.sql added
22aa7b106abc_refGene_hg38.txt added
22aa72cf9bc2_knownGene_mm39.sql added
22aa1bfb1871_knownGene_mm39.txt added
22aa201b111_refGene_mm39.sql added
22aa3d0fd41e_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/RtmpGFoq73/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
38.928 3.837 56.740
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 12.509 | 1.318 | 18.079 | |
| dataSearch | 2.546 | 0.082 | 3.293 | |
| dataUpdate | 0.001 | 0.001 | 0.003 | |
| getCloudData | 4.779 | 0.215 | 11.096 | |
| getData | 0.000 | 0.001 | 0.004 | |
| meta_data | 0.002 | 0.000 | 0.002 | |
| recipeHub-class | 0.266 | 0.020 | 0.356 | |
| recipeLoad | 2.882 | 0.152 | 4.307 | |
| recipeMake | 0.000 | 0.001 | 0.002 | |
| recipeSearch | 1.138 | 0.061 | 1.540 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |