Qian Liu
| Snapshot Date: 2025-12-01 13:45 -0500 (Mon, 01 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 2025-12-04 12:02 -0500 (Thu, 04 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" | 4878 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4624 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| 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 | | ||||||||
| 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: 2025-12-02 10:32:35 -0500 (Tue, 02 Dec 2025) |
| EndedAt: 2025-12-02 10:36:46 -0500 (Tue, 02 Dec 2025) |
| EllapsedTime: 252.0 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 11.338 1.200 13.519
recipeLoad 4.469 0.362 5.304
getCloudData 4.533 0.206 5.775
* 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...
3ef516fb97bd_GRCh38.primary_assembly.genome.fa.1.bt2 added
3ef55fa70514_GRCh38.primary_assembly.genome.fa.2.bt2 added
3ef54e3e951b_GRCh38.primary_assembly.genome.fa.3.bt2 added
3ef56eaf47be_GRCh38.primary_assembly.genome.fa.4.bt2 added
3ef5358f43b7_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3ef550a6bed9_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3ef5733bc1ec_outfile.txt added
3ef55838a80e_GRCh37_to_GRCh38.chain added
3ef56fa15c61_GRCh37_to_NCBI34.chain added
3ef54ab81d88_GRCh37_to_NCBI35.chain added
3ef57d9af20a_GRCh37_to_NCBI36.chain added
3ef54788aef2_GRCh38_to_GRCh37.chain added
3ef55e95b68e_GRCh38_to_NCBI34.chain added
3ef537045525_GRCh38_to_NCBI35.chain added
3ef57d720c5a_GRCh38_to_NCBI36.chain added
3ef54a89290d_NCBI34_to_GRCh37.chain added
3ef572e63ab5_NCBI34_to_GRCh38.chain added
3ef569187c01_NCBI35_to_GRCh37.chain added
3ef546755b8e_NCBI35_to_GRCh38.chain added
3ef542cdebc5_NCBI36_to_GRCh37.chain added
3ef55d31f4c6_NCBI36_to_GRCh38.chain added
3ef57abd22f6_GRCm38_to_NCBIM36.chain added
3ef51742836e_GRCm38_to_NCBIM37.chain added
3ef5fc2b6b0_NCBIM36_to_GRCm38.chain added
3ef53867e4e5_NCBIM37_to_GRCm38.chain added
3ef52ce49351_1000G_omni2.5.b37.vcf.gz added
3ef55283c1dd_1000G_omni2.5.b37.vcf.gz.tbi added
3ef5482cbe7d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3ef5718e258f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3ef52b440987_1000G_omni2.5.hg38.vcf.gz added
3ef57fcd9441_1000G_omni2.5.hg38.vcf.gz.tbi added
3ef511c078f4_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3ef57344e446_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3ef52fe6eac9_af-only-gnomad.raw.sites.vcf added
3ef561404ab0_af-only-gnomad.raw.sites.vcf.idx added
3ef543e79ab1_Mutect2-exome-panel.vcf.idx added
3ef51a5cfd4b_Mutect2-WGS-panel-b37.vcf added
3ef54ef95472_Mutect2-WGS-panel-b37.vcf.idx added
3ef5531730df_small_exac_common_3.vcf added
3ef51789ab17_small_exac_common_3.vcf.idx added
3ef54f3f7f13_1000g_pon.hg38.vcf.gz added
3ef551afe10a_1000g_pon.hg38.vcf.gz.tbi added
3ef571df816b_af-only-gnomad.hg38.vcf.gz added
3ef58a9d235_af-only-gnomad.hg38.vcf.gz.tbi added
3ef545279a04_small_exac_common_3.hg38.vcf.gz added
3ef52af0a014_small_exac_common_3.hg38.vcf.gz.tbi added
3ef51b9d9712_gencode.v41.annotation.gtf added
3ef57292ce8_gencode.v42.annotation.gtf added
3ef520433704_gencode.vM30.annotation.gtf added
3ef51cd0f828_gencode.vM31.annotation.gtf added
3ef55b5418df_gencode.v41.transcripts.fa added
3ef56e2d0750_gencode.v41.transcripts.fa.fai added
3ef54e3b4db2_gencode.v42.transcripts.fa added
3ef5176a093e_gencode.v42.transcripts.fa.fai added
3ef53284d174_gencode.vM30.pc_transcripts.fa added
3ef52dd33095_gencode.vM30.pc_transcripts.fa.fai added
3ef541a9db4_gencode.vM31.pc_transcripts.fa added
3ef56f679686_gencode.vM31.pc_transcripts.fa.fai added
3ef579cb708d_GRCh38.primary_assembly.genome.fa.1.ht2 added
3ef51b4a7773_GRCh38.primary_assembly.genome.fa.2.ht2 added
3ef535e82d04_GRCh38.primary_assembly.genome.fa.3.ht2 added
3ef51de37d42_GRCh38.primary_assembly.genome.fa.4.ht2 added
3ef542348762_GRCh38.primary_assembly.genome.fa.5.ht2 added
3ef56a454e3_GRCh38.primary_assembly.genome.fa.6.ht2 added
3ef5ec1067d_GRCh38.primary_assembly.genome.fa.7.ht2 added
3ef52291001c_GRCh38.primary_assembly.genome.fa.8.ht2 added
3ef55d9e3ffe_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3ef5407b6cb6_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3ef5671e41cc_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3ef57371ecf7_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3ef53c7c8757_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3ef513997fc7_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3ef54293ebde_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3ef57d625df7_GRCh38.primary_assembly.genome.fa.fai added
3ef545074370_GRCh38.primary_assembly.genome.fa.amb added
3ef55fdc9177_GRCh38.primary_assembly.genome.fa.ann added
3ef59d24ccc_GRCh38.primary_assembly.genome.fa.bwt added
3ef54dafea1d_GRCh38.primary_assembly.genome.fa.pac added
3ef558333dc3_GRCh38.primary_assembly.genome.fa.sa added
3ef5c1bfa72_GRCh38.primary_assembly.genome.fa added
3ef5d75894_hs37d5.fa.fai added
3ef539f85cfa_hs37d5.fa.amb added
3ef560a03ed1_hs37d5.fa.ann added
3ef5387c3ce6_hs37d5.fa.bwt added
3ef564823d02_hs37d5.fa.pac added
3ef5227381db_hs37d5.fa.sa added
3ef54d526288_hs37d5.fa added
3ef55bc2f660_complete_ref_lens.bin added
3ef55cbd47b0_ctable.bin added
3ef5eada361_ctg_offsets.bin added
3ef529c13cce_duplicate_clusters.tsv added
3ef54d7f0dcc_info.json added
3ef55062f3d3_mphf.bin added
3ef51075cae0_pos.bin added
3ef5255a4091_pre_indexing.log added
3ef5484502bf_rank.bin added
3ef52ab76eaa_ref_indexing.log added
3ef570c270ce_refAccumLengths.bin added
3ef56d7c1e37_reflengths.bin added
3ef56fa3e508_refseq.bin added
3ef57111a97a_seq.bin added
3ef53e8dc294_versionInfo.json added
3ef54ce1a2a1_salmon_index added
3ef5717c1f75_chrLength.txt added
3ef5bf57488_chrName.txt added
3ef51fb592da_chrNameLength.txt added
3ef549bc3679_chrStart.txt added
3ef5639c67c0_exonGeTrInfo.tab added
3ef5315fa157_exonInfo.tab added
3ef57d597013_geneInfo.tab added
3ef57acd2faf_Genome added
3ef534f5c925_genomeParameters.txt added
3ef57468b74c_Log.out added
3ef56da1a49_SA added
3ef558f3b222_SAindex added
3ef5673403cd_sjdbInfo.txt added
3ef57e5bcaa_sjdbList.fromGTF.out.tab added
3ef57bc540f2_sjdbList.out.tab added
3ef5532b0f59_transcriptInfo.tab added
3ef52ffcc6b7_GRCh38.GENCODE.v42_100 added
3ef57c5a30fd_knownGene_hg38.sql added
3ef554671d3_knownGene_hg38.txt added
3ef553dad659_refGene_hg38.sql added
3ef5442e9811_refGene_hg38.txt added
3ef54f01a70f_knownGene_mm39.sql added
3ef5757ef24e_knownGene_mm39.txt added
3ef561561b25_refGene_mm39.sql added
3ef55c104c0f_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/RtmpkaEajY/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
37.906 3.467 43.478
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 11.338 | 1.200 | 13.519 | |
| dataSearch | 2.349 | 0.075 | 2.459 | |
| dataUpdate | 0.001 | 0.001 | 0.001 | |
| getCloudData | 4.533 | 0.206 | 5.775 | |
| getData | 0.001 | 0.001 | 0.002 | |
| meta_data | 0.002 | 0.001 | 0.002 | |
| recipeHub-class | 0.284 | 0.027 | 0.312 | |
| recipeLoad | 4.469 | 0.362 | 5.304 | |
| recipeMake | 0.000 | 0.002 | 0.002 | |
| recipeSearch | 1.129 | 0.054 | 1.194 | |
| recipeUpdate | 0.000 | 0.001 | 0.001 | |