Qian Liu
| Snapshot Date: 2025-09-26 13:45 -0400 (Fri, 26 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: c5927b9 |
| git_last_commit_date: 2025-04-15 13:01:44 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-27 12:06 -0400 (Sat, 27 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4832 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4620 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4565 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
| 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 1752/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.9.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 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: 1.9.0 |
| 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_1.9.0.tar.gz |
| StartedAt: 2025-09-26 21:12:15 -0400 (Fri, 26 Sep 2025) |
| EndedAt: 2025-09-26 21:13:03 -0400 (Fri, 26 Sep 2025) |
| EllapsedTime: 48.5 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_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.9.0’
* 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
* 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-arm64/Resources/library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.9.0’ ** 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 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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...
42672eccb4f_GRCh38.primary_assembly.genome.fa.1.bt2 added
4261817ea7b_GRCh38.primary_assembly.genome.fa.2.bt2 added
4264a233d98_GRCh38.primary_assembly.genome.fa.3.bt2 added
4264fa0ec2e_GRCh38.primary_assembly.genome.fa.4.bt2 added
4264df1e8d9_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
42644ee2689_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
4266f240fb9_outfile.txt added
426288473b0_GRCh37_to_GRCh38.chain added
426fc73c98_GRCh37_to_NCBI34.chain added
426615b273f_GRCh37_to_NCBI35.chain added
426276dcb08_GRCh37_to_NCBI36.chain added
426192c8e71_GRCh38_to_GRCh37.chain added
4263c3ba9a0_GRCh38_to_NCBI34.chain added
42670fd6644_GRCh38_to_NCBI35.chain added
426c453450_GRCh38_to_NCBI36.chain added
426136d767b_NCBI34_to_GRCh37.chain added
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42654449a8e_NCBI35_to_GRCh37.chain added
42663ff0bda_NCBI35_to_GRCh38.chain added
4267d63487f_NCBI36_to_GRCh37.chain added
42612cca29_NCBI36_to_GRCh38.chain added
426238c4a59_GRCm38_to_NCBIM36.chain added
4264f652b4a_GRCm38_to_NCBIM37.chain added
4267afd2ffe_NCBIM36_to_GRCm38.chain added
42645a0bc7_NCBIM37_to_GRCm38.chain added
42633bb380c_1000G_omni2.5.b37.vcf.gz added
426485cb65c_1000G_omni2.5.b37.vcf.gz.tbi added
4263ec87721_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
4265b0537ba_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
426338dc305_1000G_omni2.5.hg38.vcf.gz added
4261ffe97b4_1000G_omni2.5.hg38.vcf.gz.tbi added
426399bad5_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
42661b8f7cb_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
4263694628c_af-only-gnomad.raw.sites.vcf added
42647d1f152_af-only-gnomad.raw.sites.vcf.idx added
426283a6354_Mutect2-exome-panel.vcf.idx added
426114f346e_Mutect2-WGS-panel-b37.vcf added
42666fb2aa2_Mutect2-WGS-panel-b37.vcf.idx added
42673ac267f_small_exac_common_3.vcf added
4262b13972d_small_exac_common_3.vcf.idx added
426132a2173_1000g_pon.hg38.vcf.gz added
42632fa0ed9_1000g_pon.hg38.vcf.gz.tbi added
4263ee4e2b4_af-only-gnomad.hg38.vcf.gz added
42624dfb7ae_af-only-gnomad.hg38.vcf.gz.tbi added
4265b94136b_small_exac_common_3.hg38.vcf.gz added
426568704c5_small_exac_common_3.hg38.vcf.gz.tbi added
4263a4a4de4_gencode.v41.annotation.gtf added
426643fd1a1_gencode.v42.annotation.gtf added
42619dbd472_gencode.vM30.annotation.gtf added
4262f5895a1_gencode.vM31.annotation.gtf added
42660c7954f_gencode.v41.transcripts.fa added
4264f1ba72c_gencode.v41.transcripts.fa.fai added
426207c6247_gencode.v42.transcripts.fa added
426461833fa_gencode.v42.transcripts.fa.fai added
4265efc8609_gencode.vM30.pc_transcripts.fa added
42614c3e997_gencode.vM30.pc_transcripts.fa.fai added
4264a1cc327_gencode.vM31.pc_transcripts.fa added
42626505b74_gencode.vM31.pc_transcripts.fa.fai added
42665a43052_GRCh38.primary_assembly.genome.fa.1.ht2 added
4267e608b9f_GRCh38.primary_assembly.genome.fa.2.ht2 added
426746eb48a_GRCh38.primary_assembly.genome.fa.3.ht2 added
426100f0bbe_GRCh38.primary_assembly.genome.fa.4.ht2 added
4264bcbef2e_GRCh38.primary_assembly.genome.fa.5.ht2 added
42639c3dbe2_GRCh38.primary_assembly.genome.fa.6.ht2 added
4266998f00e_GRCh38.primary_assembly.genome.fa.7.ht2 added
42637b85d4b_GRCh38.primary_assembly.genome.fa.8.ht2 added
42628f50381_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
4266db91f28_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
42614acb35f_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
42656342c93_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
4267b5a931b_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
426777010e1_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
4265e646109_GRCh38_full_analysis_set_plus_decoy_hla.fa added
426101ec649_GRCh38.primary_assembly.genome.fa.fai added
426546beae3_GRCh38.primary_assembly.genome.fa.amb added
426790a0861_GRCh38.primary_assembly.genome.fa.ann added
4261ac565c_GRCh38.primary_assembly.genome.fa.bwt added
4265959b2df_GRCh38.primary_assembly.genome.fa.pac added
426fee7c4d_GRCh38.primary_assembly.genome.fa.sa added
4267222ab66_GRCh38.primary_assembly.genome.fa added
4264222f014_hs37d5.fa.fai added
4263bfd2f8_hs37d5.fa.amb added
42626b399b4_hs37d5.fa.ann added
42659300c45_hs37d5.fa.bwt added
4266175b3c1_hs37d5.fa.pac added
426766c75e3_hs37d5.fa.sa added
4264aafc6d2_hs37d5.fa added
4265a262b4c_complete_ref_lens.bin added
4267fe4b8d0_ctable.bin added
426121a149_ctg_offsets.bin added
42646e3c033_duplicate_clusters.tsv added
426125f78a1_info.json added
42639e89b73_mphf.bin added
4265635b8b8_pos.bin added
42660f2643f_pre_indexing.log added
426499395d2_rank.bin added
426785133ba_ref_indexing.log added
4261b1b360c_refAccumLengths.bin added
42617795bbb_reflengths.bin added
42620755e07_refseq.bin added
42679702e36_seq.bin added
42633ea1983_versionInfo.json added
4264e310215_salmon_index added
426737fd8cd_chrLength.txt added
4264e72b5f8_chrName.txt added
4264d08d504_chrNameLength.txt added
4267ed9211e_chrStart.txt added
426610d79a1_exonGeTrInfo.tab added
4263bac6ace_exonInfo.tab added
426349818fd_geneInfo.tab added
4266d90a504_Genome added
4263341e1ce_genomeParameters.txt added
4262a4fb5ac_Log.out added
426572044e7_SA added
42678bc661_SAindex added
426698d0e25_sjdbInfo.txt added
4262b9bd546_sjdbList.fromGTF.out.tab added
4263cefd08_sjdbList.out.tab added
426a461a2c_transcriptInfo.tab added
4266043f9_GRCh38.GENCODE.v42_100 added
426300e90a0_knownGene_hg38.sql added
426c391106_knownGene_hg38.txt added
426768ca72e_refGene_hg38.sql added
426c33f9d0_refGene_hg38.txt added
4262855ccf2_knownGene_mm39.sql added
4261902388e_knownGene_mm39.txt added
42660ceff75_refGene_mm39.sql added
42635e58bfa_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:
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpvnflZN/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
6.372 0.678 7.742
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 1.931 | 0.216 | 2.173 | |
| dataSearch | 0.330 | 0.015 | 0.346 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.836 | 0.054 | 1.988 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.038 | 0.006 | 0.043 | |
| recipeLoad | 0.384 | 0.027 | 0.413 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.157 | 0.010 | 0.167 | |
| recipeUpdate | 0 | 0 | 0 | |