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This page was generated on 2024-07-12 17:41 -0400 (Fri, 12 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4741
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4461
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 1745/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReUseData 1.4.0  (landing page)
Qian Liu
Snapshot Date: 2024-07-10 14:00 -0400 (Wed, 10 Jul 2024)
git_url: https://git.bioconductor.org/packages/ReUseData
git_branch: RELEASE_3_19
git_last_commit: 801f620
git_last_commit_date: 2024-04-30 11:46:52 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for ReUseData on merida1

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.

raw results


Summary

Package: ReUseData
Version: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2024-07-11 10:21:42 -0400 (Thu, 11 Jul 2024)
EndedAt: 2024-07-11 10:27:02 -0400 (Thu, 11 Jul 2024)
EllapsedTime: 319.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ReUseData.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.4.0’
* 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 13.784  1.330  17.600
getCloudData   5.018  0.214   6.868
* 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-3.19-bioc/meat/ReUseData.Rcheck/00check.log’
for details.


Installation output

ReUseData.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ReUseData
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘ReUseData’ ...
** 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)

Tests output

ReUseData.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 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.)

}INFO Final process status is success

Updating data record...
outfile.txt added

Updating data record...
181991acd52a5_GRCh38.primary_assembly.genome.fa.1.bt2 added
181991decdc62_GRCh38.primary_assembly.genome.fa.2.bt2 added
181992978b547_GRCh38.primary_assembly.genome.fa.3.bt2 added
1819933c55d96_GRCh38.primary_assembly.genome.fa.4.bt2 added
1819962833d67_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
18199163467b8_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
181994a856c6b_outfile.txt added
181997d910b05_GRCh37_to_GRCh38.chain added
181993d6ab5aa_GRCh37_to_NCBI34.chain added
1819928bccb66_GRCh37_to_NCBI35.chain added
181992cdaa6f_GRCh37_to_NCBI36.chain added
18199c705ed9_GRCh38_to_GRCh37.chain added
181992562fef0_GRCh38_to_NCBI34.chain added
1819964f51bd_GRCh38_to_NCBI35.chain added
18199417f5287_GRCh38_to_NCBI36.chain added
18199e033ea9_NCBI34_to_GRCh37.chain added
181997706d06e_NCBI34_to_GRCh38.chain added
18199605e22ce_NCBI35_to_GRCh37.chain added
18199443f33cf_NCBI35_to_GRCh38.chain added
1819911627e0a_NCBI36_to_GRCh37.chain added
181995940cb70_NCBI36_to_GRCh38.chain added
181992cec53d7_GRCm38_to_NCBIM36.chain added
181994f745f4b_GRCm38_to_NCBIM37.chain added
18199611c5dad_NCBIM36_to_GRCm38.chain added
18199d4a3aaa_NCBIM37_to_GRCm38.chain added
1819945175b7_1000G_omni2.5.b37.vcf.gz added
1819974398_1000G_omni2.5.b37.vcf.gz.tbi added
181995ce6b02b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
181992d3806b3_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
18199393fe8f6_1000G_omni2.5.hg38.vcf.gz added
1819912d78bd7_1000G_omni2.5.hg38.vcf.gz.tbi added
1819951dd9eb_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
181996acdd5ec_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
181996f97afbb_af-only-gnomad.raw.sites.vcf added
181994f925739_af-only-gnomad.raw.sites.vcf.idx added
18199109c87ff_Mutect2-exome-panel.vcf.idx added
1819914a47ede_Mutect2-WGS-panel-b37.vcf added
181993b852b68_Mutect2-WGS-panel-b37.vcf.idx added
1819923e4d75f_small_exac_common_3.vcf added
181994f7b062_small_exac_common_3.vcf.idx added
18199215cf47a_1000g_pon.hg38.vcf.gz added
181995db686b2_1000g_pon.hg38.vcf.gz.tbi added
181997a45402e_af-only-gnomad.hg38.vcf.gz added
181995878cab8_af-only-gnomad.hg38.vcf.gz.tbi added
1819962452368_small_exac_common_3.hg38.vcf.gz added
181992917b33f_small_exac_common_3.hg38.vcf.gz.tbi added
1819952f9022c_gencode.v41.annotation.gtf added
1819959fdc142_gencode.v42.annotation.gtf added
18199229b0236_gencode.vM30.annotation.gtf added
181996eae38f9_gencode.vM31.annotation.gtf added
18199701e9c33_gencode.v41.transcripts.fa added
1819969a111c6_gencode.v41.transcripts.fa.fai added
181994d961457_gencode.v42.transcripts.fa added
181993811838c_gencode.v42.transcripts.fa.fai added
181995d37916_gencode.vM30.pc_transcripts.fa added
181997eb29656_gencode.vM30.pc_transcripts.fa.fai added
181997eac2915_gencode.vM31.pc_transcripts.fa added
1819958bd62ab_gencode.vM31.pc_transcripts.fa.fai added
181997998f610_GRCh38.primary_assembly.genome.fa.1.ht2 added
181992942d2ce_GRCh38.primary_assembly.genome.fa.2.ht2 added
18199621de78b_GRCh38.primary_assembly.genome.fa.3.ht2 added
18199194c8900_GRCh38.primary_assembly.genome.fa.4.ht2 added
181996fb66bf9_GRCh38.primary_assembly.genome.fa.5.ht2 added
18199316ae1bb_GRCh38.primary_assembly.genome.fa.6.ht2 added
181996009d555_GRCh38.primary_assembly.genome.fa.7.ht2 added
181992594f0b5_GRCh38.primary_assembly.genome.fa.8.ht2 added
1819955470e59_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
181992bff20cc_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
181997ac247a4_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1819968ed9ef2_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
18199485e57af_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1819929cec747_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
18199467d1bc2_GRCh38_full_analysis_set_plus_decoy_hla.fa added
181993fa981b5_GRCh38.primary_assembly.genome.fa.fai added
181991182b2ba_GRCh38.primary_assembly.genome.fa.amb added
181991ba3da51_GRCh38.primary_assembly.genome.fa.ann added
1819922520a04_GRCh38.primary_assembly.genome.fa.bwt added
18199380f9e36_GRCh38.primary_assembly.genome.fa.pac added
1819995c07fb_GRCh38.primary_assembly.genome.fa.sa added
18199790ff489_GRCh38.primary_assembly.genome.fa added
1819967f8c77_hs37d5.fa.fai added
181991fdedbf6_hs37d5.fa.amb added
18199603b03d2_hs37d5.fa.ann added
1819942780159_hs37d5.fa.bwt added
1819954a09c26_hs37d5.fa.pac added
181997c6bae31_hs37d5.fa.sa added
1819917952c8_hs37d5.fa added
181994429c939_complete_ref_lens.bin added
181991359e025_ctable.bin added
18199718aa70f_ctg_offsets.bin added
1819945de0405_duplicate_clusters.tsv added
1819972da0818_info.json added
1819948499a90_mphf.bin added
1819958428903_pos.bin added
1819978315139_pre_indexing.log added
181996dcbb2d4_rank.bin added
181995849b49c_ref_indexing.log added
181994ef09b0c_refAccumLengths.bin added
1819916535951_reflengths.bin added
181993a0ce04a_refseq.bin added
181992359380c_seq.bin added
18199366eadf5_versionInfo.json added
181991c5ecbbe_salmon_index added
181991392357f_chrLength.txt added
1819963f62ee2_chrName.txt added
1819937802ab3_chrNameLength.txt added
181993f736a3c_chrStart.txt added
181993243a9af_exonGeTrInfo.tab added
18199783939f0_exonInfo.tab added
18199750af939_geneInfo.tab added
1819923704937_Genome added
1819920d6cc0e_genomeParameters.txt added
1819975eebbf9_Log.out added
18199c7714ec_SA added
181995dfe9858_SAindex added
1819975c3e99d_sjdbInfo.txt added
18199111e7ed2_sjdbList.fromGTF.out.tab added
18199691815c5_sjdbList.out.tab added
181992c3d6e6a_transcriptInfo.tab added
18199751c07d6_GRCh38.GENCODE.v42_100 added
18199346aeab_knownGene_hg38.sql added
1819915755e3b_knownGene_hg38.txt added
181994c7d7e7e_refGene_hg38.sql added
1819942fba96d_refGene_hg38.txt added
1819918305576_knownGene_mm39.sql added
18199d3ac262_knownGene_mm39.txt added
18199cafb6b7_refGene_mm39.sql added
181996404aee2_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/RtmpNdkz1M/test_gcpData/outfile.txt
}INFO 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 
 45.466   5.557  61.470 

Example timings

ReUseData.Rcheck/ReUseData-Ex.timings

nameusersystemelapsed
dataHub-class13.784 1.33017.600
dataSearch2.7380.0883.201
dataUpdate0.0010.0010.003
getCloudData5.0180.2146.868
getData0.0010.0010.001
meta_data0.0010.0000.002
recipeHub-class0.2950.0210.362
recipeLoad3.0560.1443.919
recipeMake0.0010.0010.003
recipeSearch1.2710.0571.633
recipeUpdate0.0000.0010.001