Qian Liu
| Snapshot Date: 2025-09-02 13:45 -0400 (Tue, 02 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 2025-09-03 12:05 -0400 (Wed, 03 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4826 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4616 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4563 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
| 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 1742/2321 | 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: 2025-09-02 23:13:38 -0400 (Tue, 02 Sep 2025) |
| EndedAt: 2025-09-02 23:16:02 -0400 (Tue, 02 Sep 2025) |
| EllapsedTime: 144.6 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 (2025-06-13)
* 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 ‘1.9.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dataHub-class 7.523 0.895 8.522
* 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 ‘1.9.0’ ** 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 (2025-06-13) -- "Great Square Root"
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...
e0674c24be2e_GRCh38.primary_assembly.genome.fa.1.bt2 added
e06741e510_GRCh38.primary_assembly.genome.fa.2.bt2 added
e06766257d91_GRCh38.primary_assembly.genome.fa.3.bt2 added
e0672756eefb_GRCh38.primary_assembly.genome.fa.4.bt2 added
e0673c63b4ea_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
e06735fa8d9f_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
e0675467dd68_outfile.txt added
e0676ef90222_GRCh37_to_GRCh38.chain added
e0671dfb3f19_GRCh37_to_NCBI34.chain added
e06759eb91af_GRCh37_to_NCBI35.chain added
e06778a9a647_GRCh37_to_NCBI36.chain added
e06749e3bd34_GRCh38_to_GRCh37.chain added
e06769ac6d2_GRCh38_to_NCBI34.chain added
e0671b730861_GRCh38_to_NCBI35.chain added
e0671d2b265b_GRCh38_to_NCBI36.chain added
e0677be32f52_NCBI34_to_GRCh37.chain added
e06737f009_NCBI34_to_GRCh38.chain added
e067586fdefb_NCBI35_to_GRCh37.chain added
e06718985e19_NCBI35_to_GRCh38.chain added
e0673b49c7ec_NCBI36_to_GRCh37.chain added
e06768e4755c_NCBI36_to_GRCh38.chain added
e0676ed520d0_GRCm38_to_NCBIM36.chain added
e0676a5d7088_GRCm38_to_NCBIM37.chain added
e0671c872746_NCBIM36_to_GRCm38.chain added
e0676d23734b_NCBIM37_to_GRCm38.chain added
e067326678e7_1000G_omni2.5.b37.vcf.gz added
e067658b9f8a_1000G_omni2.5.b37.vcf.gz.tbi added
e0673197511b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
e067454ddd0c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
e0677aeb625f_1000G_omni2.5.hg38.vcf.gz added
e06773878a04_1000G_omni2.5.hg38.vcf.gz.tbi added
e067477647dd_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
e067266822d2_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
e0677ec61cb0_af-only-gnomad.raw.sites.vcf added
e06785a7d6_af-only-gnomad.raw.sites.vcf.idx added
e06746cdd2de_Mutect2-exome-panel.vcf.idx added
e06772cf1122_Mutect2-WGS-panel-b37.vcf added
e067786e0a10_Mutect2-WGS-panel-b37.vcf.idx added
e06756de35_small_exac_common_3.vcf added
e067471669bf_small_exac_common_3.vcf.idx added
e06710789f0f_1000g_pon.hg38.vcf.gz added
e0675f129a3b_1000g_pon.hg38.vcf.gz.tbi added
e0673e4bc840_af-only-gnomad.hg38.vcf.gz added
e067614801b3_af-only-gnomad.hg38.vcf.gz.tbi added
e0673e67c0aa_small_exac_common_3.hg38.vcf.gz added
e067d99f8e8_small_exac_common_3.hg38.vcf.gz.tbi added
e06777a44e51_gencode.v41.annotation.gtf added
e0674411e534_gencode.v42.annotation.gtf added
e06772dedbd5_gencode.vM30.annotation.gtf added
e067532b7de_gencode.vM31.annotation.gtf added
e06744c5527c_gencode.v41.transcripts.fa added
e06776aa6e29_gencode.v41.transcripts.fa.fai added
e0672f26829c_gencode.v42.transcripts.fa added
e067948e7f3_gencode.v42.transcripts.fa.fai added
e06711740748_gencode.vM30.pc_transcripts.fa added
e067588a10eb_gencode.vM30.pc_transcripts.fa.fai added
e067505ce1b6_gencode.vM31.pc_transcripts.fa added
e0671e69cf2_gencode.vM31.pc_transcripts.fa.fai added
e0674b49d4d7_GRCh38.primary_assembly.genome.fa.1.ht2 added
e0675c3495de_GRCh38.primary_assembly.genome.fa.2.ht2 added
e0675b511d_GRCh38.primary_assembly.genome.fa.3.ht2 added
e0676b2a4719_GRCh38.primary_assembly.genome.fa.4.ht2 added
e06724a1f146_GRCh38.primary_assembly.genome.fa.5.ht2 added
e0673e73d74_GRCh38.primary_assembly.genome.fa.6.ht2 added
e06742738cac_GRCh38.primary_assembly.genome.fa.7.ht2 added
e06730189249_GRCh38.primary_assembly.genome.fa.8.ht2 added
e0671d2c0f4a_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
e067379fd23c_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
e0675da37dab_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
e067188f9594_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
e0677aa53424_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
e06774026663_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
e06749902915_GRCh38_full_analysis_set_plus_decoy_hla.fa added
e0671779476e_GRCh38.primary_assembly.genome.fa.fai added
e0671b4092cc_GRCh38.primary_assembly.genome.fa.amb added
e0672c659d0e_GRCh38.primary_assembly.genome.fa.ann added
e067432a18e7_GRCh38.primary_assembly.genome.fa.bwt added
e067c90824_GRCh38.primary_assembly.genome.fa.pac added
e067e3573e3_GRCh38.primary_assembly.genome.fa.sa added
e067574b435e_GRCh38.primary_assembly.genome.fa added
e067e33fd18_hs37d5.fa.fai added
e067772d39f0_hs37d5.fa.amb added
e0673a36f8b0_hs37d5.fa.ann added
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e0672ce04b7c_hs37d5.fa.pac added
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e0675463e9fe_complete_ref_lens.bin added
e0676b974dfa_ctable.bin added
e0671a808f45_ctg_offsets.bin added
e0676e3e089a_duplicate_clusters.tsv added
e0672aa6ef01_info.json added
e06735954087_mphf.bin added
e06759bf7a8c_pos.bin added
e0672a06ab5c_pre_indexing.log added
e0671bdc3a92_rank.bin added
e06717895588_ref_indexing.log added
e067394e5fca_refAccumLengths.bin added
e0674872e42a_reflengths.bin added
e0676ee1a68e_refseq.bin added
e067207ded81_seq.bin added
e0672b73c0d1_versionInfo.json added
e0673c77efa0_salmon_index added
e06766151063_chrLength.txt added
e06770e707f0_chrName.txt added
e0674fba5778_chrNameLength.txt added
e06752c4b02c_chrStart.txt added
e0676f0a4327_exonGeTrInfo.tab added
e067abeee65_exonInfo.tab added
e0677d152e65_geneInfo.tab added
e0677999290a_Genome added
e06736558de4_genomeParameters.txt added
e0672ad68f9a_Log.out added
e0676c6ddd6e_SA added
e06720e4985f_SAindex added
e0677fcf95d7_sjdbInfo.txt added
e067157697cf_sjdbList.fromGTF.out.tab added
e0671ce8a20b_sjdbList.out.tab added
e0676ce68f00_transcriptInfo.tab added
e06714b680db_GRCh38.GENCODE.v42_100 added
e06759c5b47c_knownGene_hg38.sql added
e06742cc66ef_knownGene_hg38.txt added
e0677979f72b_refGene_hg38.sql added
e0673652665b_refGene_hg38.txt added
e0675bbdfc39_knownGene_mm39.sql added
e06715fa313d_knownGene_mm39.txt added
e0675cb6a710_refGene_mm39.sql added
e0675b923afd_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/RtmpQrclma/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
21.672 2.387 24.941
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 7.523 | 0.895 | 8.522 | |
| dataSearch | 1.386 | 0.063 | 1.459 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.913 | 0.169 | 4.364 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.001 | 0.001 | |
| recipeHub-class | 0.165 | 0.015 | 0.182 | |
| recipeLoad | 1.625 | 0.104 | 1.747 | |
| recipeMake | 0.000 | 0.002 | 0.002 | |
| recipeSearch | 0.649 | 0.042 | 0.697 | |
| recipeUpdate | 0 | 0 | 0 | |