Qian Liu
| Snapshot Date: 2025-09-12 13:45 -0400 (Fri, 12 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 2025-09-13 12:06 -0400 (Sat, 13 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" | 4719 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4538 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4522 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4543 |
| 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 1747/2327 | 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: 2025-09-12 21:15:51 -0400 (Fri, 12 Sep 2025) |
| EndedAt: 2025-09-12 21:16:39 -0400 (Fri, 12 Sep 2025) |
| EllapsedTime: 48.6 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...
17374e554a65_GRCh38.primary_assembly.genome.fa.1.bt2 added
17374187343d_GRCh38.primary_assembly.genome.fa.2.bt2 added
1737453769193_GRCh38.primary_assembly.genome.fa.3.bt2 added
17374d4f74b4_GRCh38.primary_assembly.genome.fa.4.bt2 added
173745b76dc3f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
173745875db02_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
17374217d8dad_outfile.txt added
1737439e06a08_GRCh37_to_GRCh38.chain added
173743c5150e7_GRCh37_to_NCBI34.chain added
173747e968ca0_GRCh37_to_NCBI35.chain added
173744dea9d4d_GRCh37_to_NCBI36.chain added
1737465fd5231_GRCh38_to_GRCh37.chain added
173745a1f4346_GRCh38_to_NCBI34.chain added
173743a79d6e3_GRCh38_to_NCBI35.chain added
17374150aef13_GRCh38_to_NCBI36.chain added
17374d5d330_NCBI34_to_GRCh37.chain added
17374561bf4bd_NCBI34_to_GRCh38.chain added
173744560d075_NCBI35_to_GRCh37.chain added
173745715d4e8_NCBI35_to_GRCh38.chain added
173745a4cf802_NCBI36_to_GRCh37.chain added
17374732e799e_NCBI36_to_GRCh38.chain added
173747032af25_GRCm38_to_NCBIM36.chain added
17374f88dfaf_GRCm38_to_NCBIM37.chain added
1737463156220_NCBIM36_to_GRCm38.chain added
1737410dd55b2_NCBIM37_to_GRCm38.chain added
17374332521c4_1000G_omni2.5.b37.vcf.gz added
173744acbe517_1000G_omni2.5.b37.vcf.gz.tbi added
17374102d6f5e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1737416ea8c9e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
17374b5e4d3_1000G_omni2.5.hg38.vcf.gz added
1737425c1d902_1000G_omni2.5.hg38.vcf.gz.tbi added
17374598e25ab_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1737434b2b7c_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
173743c13db94_af-only-gnomad.raw.sites.vcf added
173743bb4f05c_af-only-gnomad.raw.sites.vcf.idx added
17374641046a3_Mutect2-exome-panel.vcf.idx added
17374688daaa7_Mutect2-WGS-panel-b37.vcf added
173742cbeef91_Mutect2-WGS-panel-b37.vcf.idx added
173742b622f8a_small_exac_common_3.vcf added
173743b1f2346_small_exac_common_3.vcf.idx added
173747944e6fc_1000g_pon.hg38.vcf.gz added
173741a98e897_1000g_pon.hg38.vcf.gz.tbi added
173742cce1f25_af-only-gnomad.hg38.vcf.gz added
17374105ecd1e_af-only-gnomad.hg38.vcf.gz.tbi added
173743fec74f7_small_exac_common_3.hg38.vcf.gz added
173743cf324ea_small_exac_common_3.hg38.vcf.gz.tbi added
173747efc9de8_gencode.v41.annotation.gtf added
173747ae32b79_gencode.v42.annotation.gtf added
17374583b53f6_gencode.vM30.annotation.gtf added
173741f0568bb_gencode.vM31.annotation.gtf added
173741c1edce6_gencode.v41.transcripts.fa added
173742e388e76_gencode.v41.transcripts.fa.fai added
17374310fcaf_gencode.v42.transcripts.fa added
17374503d46bb_gencode.v42.transcripts.fa.fai added
1737466eec824_gencode.vM30.pc_transcripts.fa added
173744695e847_gencode.vM30.pc_transcripts.fa.fai added
173741bc4b185_gencode.vM31.pc_transcripts.fa added
17374e62a101_gencode.vM31.pc_transcripts.fa.fai added
173746d385007_GRCh38.primary_assembly.genome.fa.1.ht2 added
17374c0e3396_GRCh38.primary_assembly.genome.fa.2.ht2 added
17374785cc308_GRCh38.primary_assembly.genome.fa.3.ht2 added
1737412087ff4_GRCh38.primary_assembly.genome.fa.4.ht2 added
173746c08756b_GRCh38.primary_assembly.genome.fa.5.ht2 added
173741f54fb36_GRCh38.primary_assembly.genome.fa.6.ht2 added
17374438a64c_GRCh38.primary_assembly.genome.fa.7.ht2 added
17374232dc9be_GRCh38.primary_assembly.genome.fa.8.ht2 added
173741317eafd_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1737474491d6_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1737426c27c54_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
173742a7082ad_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
173744093419f_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
173743b94ed8_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
173747ae748d0_GRCh38_full_analysis_set_plus_decoy_hla.fa added
17374665d8eb9_GRCh38.primary_assembly.genome.fa.fai added
173748454830_GRCh38.primary_assembly.genome.fa.amb added
173747c864b8d_GRCh38.primary_assembly.genome.fa.ann added
1737454ca55d9_GRCh38.primary_assembly.genome.fa.bwt added
173742fca450c_GRCh38.primary_assembly.genome.fa.pac added
1737487b2f57_GRCh38.primary_assembly.genome.fa.sa added
173744f60fd1a_GRCh38.primary_assembly.genome.fa added
173746888deac_hs37d5.fa.fai added
1737471d323d1_hs37d5.fa.amb added
173745cd4a8b8_hs37d5.fa.ann added
17374d90f7a5_hs37d5.fa.bwt added
1737428727898_hs37d5.fa.pac added
17374734b57e6_hs37d5.fa.sa added
173745777f82c_hs37d5.fa added
173745463d91_complete_ref_lens.bin added
173744673fd4b_ctable.bin added
1737468fa6b0f_ctg_offsets.bin added
17374108adba1_duplicate_clusters.tsv added
17374c592f83_info.json added
17374333e47ca_mphf.bin added
173743ddb390e_pos.bin added
1737437ee5dc_pre_indexing.log added
1737424d04f_rank.bin added
1737470e7f29b_ref_indexing.log added
17374be8d806_refAccumLengths.bin added
1737463be7805_reflengths.bin added
173746db9c36b_refseq.bin added
173743eccde14_seq.bin added
173747c081341_versionInfo.json added
1737476285004_salmon_index added
17374509d7336_chrLength.txt added
1737410f70793_chrName.txt added
173744a124c98_chrNameLength.txt added
173747762b525_chrStart.txt added
173747162cd5e_exonGeTrInfo.tab added
17374d99107a_exonInfo.tab added
173743c08c08f_geneInfo.tab added
17374629a0b13_Genome added
173746f4d3ef7_genomeParameters.txt added
1737438610337_Log.out added
17374691a2ccb_SA added
173743572f955_SAindex added
17374f4f56dd_sjdbInfo.txt added
1737421cfcf05_sjdbList.fromGTF.out.tab added
173745220629a_sjdbList.out.tab added
173744c299695_transcriptInfo.tab added
173743e5d3743_GRCh38.GENCODE.v42_100 added
1737459d72fb1_knownGene_hg38.sql added
173743e7c3b8b_knownGene_hg38.txt added
173744e2942b9_refGene_hg38.sql added
1737476dba7c5_refGene_hg38.txt added
173744ee3b379_knownGene_mm39.sql added
17374471bf565_knownGene_mm39.txt added
173747c8bde5b_refGene_mm39.sql added
1737442b3683e_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//RtmpaG5FWb/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
6.366 0.713 7.983
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 1.865 | 0.216 | 2.102 | |
| dataSearch | 0.316 | 0.013 | 0.330 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.817 | 0.059 | 1.763 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.037 | 0.005 | 0.043 | |
| recipeLoad | 0.406 | 0.028 | 0.436 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.166 | 0.010 | 0.176 | |
| recipeUpdate | 0.001 | 0.000 | 0.000 | |