Qian Liu
| Snapshot Date: 2025-09-28 13:45 -0400 (Sun, 28 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 2025-09-29 12:06 -0400 (Mon, 29 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" | 4833 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4621 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4566 |
| 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: 2025-09-28 21:14:21 -0400 (Sun, 28 Sep 2025) |
| EndedAt: 2025-09-28 21:15:09 -0400 (Sun, 28 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...
8c717a172c0d_GRCh38.primary_assembly.genome.fa.1.bt2 added
8c7174d481a_GRCh38.primary_assembly.genome.fa.2.bt2 added
8c7162b8a6b4_GRCh38.primary_assembly.genome.fa.3.bt2 added
8c7148c8a60e_GRCh38.primary_assembly.genome.fa.4.bt2 added
8c716d0e0676_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
8c7133ca64e9_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
8c712ca7178f_outfile.txt added
8c71dfbc430_GRCh37_to_GRCh38.chain added
8c71c0d327c_GRCh37_to_NCBI34.chain added
8c71366d7112_GRCh37_to_NCBI35.chain added
8c714b1a70a8_GRCh37_to_NCBI36.chain added
8c7134da4c1d_GRCh38_to_GRCh37.chain added
8c7167bb1f06_GRCh38_to_NCBI34.chain added
8c712df1f81e_GRCh38_to_NCBI35.chain added
8c7168d89122_GRCh38_to_NCBI36.chain added
8c71622084f4_NCBI34_to_GRCh37.chain added
8c7144f8e180_NCBI34_to_GRCh38.chain added
8c712f9cbde0_NCBI35_to_GRCh37.chain added
8c715b75d58b_NCBI35_to_GRCh38.chain added
8c711516c796_NCBI36_to_GRCh37.chain added
8c71a8953ab_NCBI36_to_GRCh38.chain added
8c713dd404f4_GRCm38_to_NCBIM36.chain added
8c712a914ee2_GRCm38_to_NCBIM37.chain added
8c7129d1ed43_NCBIM36_to_GRCm38.chain added
8c71152fdf28_NCBIM37_to_GRCm38.chain added
8c7179e3c5f5_1000G_omni2.5.b37.vcf.gz added
8c7158d99657_1000G_omni2.5.b37.vcf.gz.tbi added
8c71351d5753_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
8c7119502563_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
8c715cc69390_1000G_omni2.5.hg38.vcf.gz added
8c7171020285_1000G_omni2.5.hg38.vcf.gz.tbi added
8c713af3a3b9_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
8c715181e4eb_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
8c7126dc2a1b_af-only-gnomad.raw.sites.vcf added
8c714050668b_af-only-gnomad.raw.sites.vcf.idx added
8c715e7c50a9_Mutect2-exome-panel.vcf.idx added
8c713393b7b5_Mutect2-WGS-panel-b37.vcf added
8c712701e687_Mutect2-WGS-panel-b37.vcf.idx added
8c716dc5bd12_small_exac_common_3.vcf added
8c715100210b_small_exac_common_3.vcf.idx added
8c715f7982b8_1000g_pon.hg38.vcf.gz added
8c7122752f00_1000g_pon.hg38.vcf.gz.tbi added
8c713b60baac_af-only-gnomad.hg38.vcf.gz added
8c714b7f90a8_af-only-gnomad.hg38.vcf.gz.tbi added
8c7123f22c51_small_exac_common_3.hg38.vcf.gz added
8c71703b8c46_small_exac_common_3.hg38.vcf.gz.tbi added
8c715576813a_gencode.v41.annotation.gtf added
8c71571e32ab_gencode.v42.annotation.gtf added
8c717f90a53b_gencode.vM30.annotation.gtf added
8c71715005ea_gencode.vM31.annotation.gtf added
8c713cb47fc4_gencode.v41.transcripts.fa added
8c716e303bfe_gencode.v41.transcripts.fa.fai added
8c7120b2d936_gencode.v42.transcripts.fa added
8c713dd278ff_gencode.v42.transcripts.fa.fai added
8c714505cd0e_gencode.vM30.pc_transcripts.fa added
8c717fd97588_gencode.vM30.pc_transcripts.fa.fai added
8c711db3754b_gencode.vM31.pc_transcripts.fa added
8c7170d99e28_gencode.vM31.pc_transcripts.fa.fai added
8c715f1e8df9_GRCh38.primary_assembly.genome.fa.1.ht2 added
8c714efb0738_GRCh38.primary_assembly.genome.fa.2.ht2 added
8c714297160a_GRCh38.primary_assembly.genome.fa.3.ht2 added
8c714d280cad_GRCh38.primary_assembly.genome.fa.4.ht2 added
8c7158596e_GRCh38.primary_assembly.genome.fa.5.ht2 added
8c71285744ef_GRCh38.primary_assembly.genome.fa.6.ht2 added
8c71796ebb99_GRCh38.primary_assembly.genome.fa.7.ht2 added
8c7154de7817_GRCh38.primary_assembly.genome.fa.8.ht2 added
8c71599e5988_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
8c712b081daf_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
8c7121d4e23b_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
8c711f50a0d7_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
8c71666f9350_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
8c7127309dba_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
8c7168c3326f_GRCh38_full_analysis_set_plus_decoy_hla.fa added
8c7167244b24_GRCh38.primary_assembly.genome.fa.fai added
8c717fc15d62_GRCh38.primary_assembly.genome.fa.amb added
8c716fda0e74_GRCh38.primary_assembly.genome.fa.ann added
8c7154eb1b0a_GRCh38.primary_assembly.genome.fa.bwt added
8c71173c5914_GRCh38.primary_assembly.genome.fa.pac added
8c717afc3bf6_GRCh38.primary_assembly.genome.fa.sa added
8c7145c4d28e_GRCh38.primary_assembly.genome.fa added
8c717cdb8c6a_hs37d5.fa.fai added
8c7131dfc330_hs37d5.fa.amb added
8c7159879de4_hs37d5.fa.ann added
8c71568f11a7_hs37d5.fa.bwt added
8c714ad01756_hs37d5.fa.pac added
8c7123ac3579_hs37d5.fa.sa added
8c717eeaad3a_hs37d5.fa added
8c716112fbee_complete_ref_lens.bin added
8c712559f80c_ctable.bin added
8c7135abeefc_ctg_offsets.bin added
8c712ad6fdeb_duplicate_clusters.tsv added
8c718b86546_info.json added
8c71200db23_mphf.bin added
8c71632d7dc_pos.bin added
8c7173f9afb1_pre_indexing.log added
8c71d7dc8f3_rank.bin added
8c713d13d070_ref_indexing.log added
8c715fd98863_refAccumLengths.bin added
8c7142894cbe_reflengths.bin added
8c71440d7012_refseq.bin added
8c714e38d0a5_seq.bin added
8c71740a28c1_versionInfo.json added
8c7146f9d26b_salmon_index added
8c713b659334_chrLength.txt added
8c719a35963_chrName.txt added
8c7143417786_chrNameLength.txt added
8c717f0e20e8_chrStart.txt added
8c717892a082_exonGeTrInfo.tab added
8c716267f4a5_exonInfo.tab added
8c7116eeaf1c_geneInfo.tab added
8c71102a6307_Genome added
8c714ecb68db_genomeParameters.txt added
8c71c512a47_Log.out added
8c7124aea1a2_SA added
8c7144f5a57e_SAindex added
8c715b441690_sjdbInfo.txt added
8c71532576bf_sjdbList.fromGTF.out.tab added
8c714097203e_sjdbList.out.tab added
8c711c5e793_transcriptInfo.tab added
8c7167e664cd_GRCh38.GENCODE.v42_100 added
8c7146e40405_knownGene_hg38.sql added
8c7123c4089f_knownGene_hg38.txt added
8c711b121111_refGene_hg38.sql added
8c713f1e80f9_refGene_hg38.txt added
8c716ba57bce_knownGene_mm39.sql added
8c713d634898_knownGene_mm39.txt added
8c71413312a4_refGene_mm39.sql added
8c71cee6d_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//Rtmpe4xlBi/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
6.304 0.691 7.661
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 1.837 | 0.213 | 2.060 | |
| dataSearch | 0.327 | 0.013 | 0.340 | |
| dataUpdate | 0.000 | 0.001 | 0.001 | |
| getCloudData | 0.902 | 0.054 | 2.208 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.041 | 0.005 | 0.046 | |
| recipeLoad | 0.398 | 0.026 | 0.428 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.161 | 0.009 | 0.176 | |
| recipeUpdate | 0 | 0 | 0 | |