Qian Liu
| Snapshot Date: 2025-12-18 13:45 -0500 (Thu, 18 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 2025-12-22 12:05 -0500 (Mon, 22 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" | 4883 |
| 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: 2025-12-19 10:02:10 -0500 (Fri, 19 Dec 2025) |
| EndedAt: 2025-12-19 10:06:49 -0500 (Fri, 19 Dec 2025) |
| EllapsedTime: 279.0 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 12.765 1.300 15.326
getCloudData 4.913 0.205 10.875
* 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...
17de148e9fb1c_GRCh38.primary_assembly.genome.fa.1.bt2 added
17de1796510a9_GRCh38.primary_assembly.genome.fa.2.bt2 added
17de15a290582_GRCh38.primary_assembly.genome.fa.3.bt2 added
17de13b28c80c_GRCh38.primary_assembly.genome.fa.4.bt2 added
17de17265aa2b_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
17de1708727b9_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
17de139411c66_outfile.txt added
17de161af89e7_GRCh37_to_GRCh38.chain added
17de14b86cecb_GRCh37_to_NCBI34.chain added
17de17f729829_GRCh37_to_NCBI35.chain added
17de13c63ed1d_GRCh37_to_NCBI36.chain added
17de1446429e4_GRCh38_to_GRCh37.chain added
17de1bfa5ad0_GRCh38_to_NCBI34.chain added
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17de16ab5f53d_GRCh38_to_NCBI36.chain added
17de14ff7ae86_NCBI34_to_GRCh37.chain added
17de1de3086e_NCBI34_to_GRCh38.chain added
17de1343e74e1_NCBI35_to_GRCh37.chain added
17de1706b7a92_NCBI35_to_GRCh38.chain added
17de1203c40e7_NCBI36_to_GRCh37.chain added
17de153c90e39_NCBI36_to_GRCh38.chain added
17de134c4eb28_GRCm38_to_NCBIM36.chain added
17de16c2aaa28_GRCm38_to_NCBIM37.chain added
17de165095f92_NCBIM36_to_GRCm38.chain added
17de14a619e10_NCBIM37_to_GRCm38.chain added
17de14ed05296_1000G_omni2.5.b37.vcf.gz added
17de14ede1e46_1000G_omni2.5.b37.vcf.gz.tbi added
17de15895ae1d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
17de14ada1f5a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
17de13640741a_1000G_omni2.5.hg38.vcf.gz added
17de1418672c9_1000G_omni2.5.hg38.vcf.gz.tbi added
17de161da0bba_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
17de132381286_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
17de17f48352b_af-only-gnomad.raw.sites.vcf added
17de15d9adb55_af-only-gnomad.raw.sites.vcf.idx added
17de161b5d975_Mutect2-exome-panel.vcf.idx added
17de169d7c270_Mutect2-WGS-panel-b37.vcf added
17de1541e7d59_Mutect2-WGS-panel-b37.vcf.idx added
17de11db78934_small_exac_common_3.vcf added
17de17c90c429_small_exac_common_3.vcf.idx added
17de143e9fa3_1000g_pon.hg38.vcf.gz added
17de12b628882_1000g_pon.hg38.vcf.gz.tbi added
17de151f0250e_af-only-gnomad.hg38.vcf.gz added
17de16d10e428_af-only-gnomad.hg38.vcf.gz.tbi added
17de16ff33608_small_exac_common_3.hg38.vcf.gz added
17de1486080a3_small_exac_common_3.hg38.vcf.gz.tbi added
17de1379d7274_gencode.v41.annotation.gtf added
17de141c53a32_gencode.v42.annotation.gtf added
17de17b6fca59_gencode.vM30.annotation.gtf added
17de1684dd85e_gencode.vM31.annotation.gtf added
17de14eb838d1_gencode.v41.transcripts.fa added
17de1209a49b7_gencode.v41.transcripts.fa.fai added
17de1715d9e19_gencode.v42.transcripts.fa added
17de13936b574_gencode.v42.transcripts.fa.fai added
17de136c2f004_gencode.vM30.pc_transcripts.fa added
17de1381bb2b2_gencode.vM30.pc_transcripts.fa.fai added
17de12270e0e5_gencode.vM31.pc_transcripts.fa added
17de120bcec0d_gencode.vM31.pc_transcripts.fa.fai added
17de1532d5a45_GRCh38.primary_assembly.genome.fa.1.ht2 added
17de1468192ac_GRCh38.primary_assembly.genome.fa.2.ht2 added
17de164c47e5d_GRCh38.primary_assembly.genome.fa.3.ht2 added
17de120443f5a_GRCh38.primary_assembly.genome.fa.4.ht2 added
17de1609b3e42_GRCh38.primary_assembly.genome.fa.5.ht2 added
17de17014909a_GRCh38.primary_assembly.genome.fa.6.ht2 added
17de15621a7f2_GRCh38.primary_assembly.genome.fa.7.ht2 added
17de13b992d0b_GRCh38.primary_assembly.genome.fa.8.ht2 added
17de1455c4bbe_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
17de12e70ca85_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
17de16efff994_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
17de1675a9c7a_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
17de16dd74298_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
17de14f55417e_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
17de1663edfe2_GRCh38_full_analysis_set_plus_decoy_hla.fa added
17de129dca2df_GRCh38.primary_assembly.genome.fa.fai added
17de15448f3f1_GRCh38.primary_assembly.genome.fa.amb added
17de11877e72_GRCh38.primary_assembly.genome.fa.ann added
17de1667e6f26_GRCh38.primary_assembly.genome.fa.bwt added
17de176b35c5b_GRCh38.primary_assembly.genome.fa.pac added
17de17974973e_GRCh38.primary_assembly.genome.fa.sa added
17de15575a5bd_GRCh38.primary_assembly.genome.fa added
17de11ed44720_hs37d5.fa.fai added
17de128995b0_hs37d5.fa.amb added
17de116c2571d_hs37d5.fa.ann added
17de130e53c97_hs37d5.fa.bwt added
17de119ecf695_hs37d5.fa.pac added
17de11430bd7f_hs37d5.fa.sa added
17de1be8e734_hs37d5.fa added
17de167a30d07_complete_ref_lens.bin added
17de11ac7bb9_ctable.bin added
17de162eeaf8a_ctg_offsets.bin added
17de12446bfc4_duplicate_clusters.tsv added
17de120d7ef77_info.json added
17de140aa7e79_mphf.bin added
17de179555b19_pos.bin added
17de152d0048a_pre_indexing.log added
17de156da2a7f_rank.bin added
17de1d1c2465_ref_indexing.log added
17de13299699c_refAccumLengths.bin added
17de175e49ab7_reflengths.bin added
17de17369a0d8_refseq.bin added
17de11bbf001a_seq.bin added
17de1189fb931_versionInfo.json added
17de11e374c98_salmon_index added
17de140859ea7_chrLength.txt added
17de14730709_chrName.txt added
17de11bd2e227_chrNameLength.txt added
17de131fd7cb6_chrStart.txt added
17de17906aa5d_exonGeTrInfo.tab added
17de1249afdbe_exonInfo.tab added
17de13b88d7b8_geneInfo.tab added
17de1150a8f91_Genome added
17de168578361_genomeParameters.txt added
17de149728acb_Log.out added
17de17ef63b18_SA added
17de157a1e5c6_SAindex added
17de145f4571c_sjdbInfo.txt added
17de12c831325_sjdbList.fromGTF.out.tab added
17de1515df8f7_sjdbList.out.tab added
17de1708449dc_transcriptInfo.tab added
17de17d0d4439_GRCh38.GENCODE.v42_100 added
17de171fa3a52_knownGene_hg38.sql added
17de1630b17f3_knownGene_hg38.txt added
17de16d518551_refGene_hg38.sql added
17de1307c0e9_refGene_hg38.txt added
17de1720a028c_knownGene_mm39.sql added
17de16f2d6fd1_knownGene_mm39.txt added
17de110083b5d_refGene_mm39.sql added
17de1c715ee4_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/RtmpEqsRxo/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
39.687 3.798 49.791
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 12.765 | 1.300 | 15.326 | |
| dataSearch | 2.559 | 0.085 | 2.771 | |
| dataUpdate | 0.001 | 0.001 | 0.001 | |
| getCloudData | 4.913 | 0.205 | 10.875 | |
| getData | 0.000 | 0.001 | 0.002 | |
| meta_data | 0.002 | 0.000 | 0.002 | |
| recipeHub-class | 0.271 | 0.018 | 0.313 | |
| recipeLoad | 2.957 | 0.141 | 3.504 | |
| recipeMake | 0.001 | 0.002 | 0.003 | |
| recipeSearch | 1.238 | 0.060 | 1.349 | |
| recipeUpdate | 0.000 | 0.001 | 0.001 | |