Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-12-03 13:04:57 -0500 (Fri, 03 Dec 2021).

CHECK results for ProteoDisco on nebbiolo2

To the developers/maintainers of the ProteoDisco package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ProteoDisco.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1475/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ProteoDisco 1.0.0  (landing page)
Job van Riet
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/ProteoDisco
git_branch: RELEASE_3_14
git_last_commit: efdf16d
git_last_commit_date: 2021-10-26 13:12:13 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ProteoDisco
Version: 1.0.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ProteoDisco.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ProteoDisco_1.0.0.tar.gz
StartedAt: 2021-12-02 08:32:43 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 08:39:30 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 406.3 seconds
RetCode: 0
Status:   OK  
CheckDir: ProteoDisco.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ProteoDisco.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ProteoDisco_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/ProteoDisco.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ProteoDisco/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ProteoDisco’ version ‘1.0.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ProteoDisco’ 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 R 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... NOTE
  Error loading dataset 'ProteoDiscographyExample.hg19':
   Error in h(simpleError(msg, call)) : 
    error in evaluating the argument 'x' in selecting a method for function 'seqlevels': UCSC library operation failed
  
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
incorporateGenomicVariants 28.535  0.576  29.111
generateJunctionModels     12.940  0.255  16.068
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/ProteoDisco.Rcheck/00check.log’
for details.



Installation output

ProteoDisco.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL ProteoDisco
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘ProteoDisco’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘print’ in package ‘ProteoDisco’
Creating a new generic function for ‘summary’ in package ‘ProteoDisco’
** 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 (ProteoDisco)

Tests output

ProteoDisco.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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.

> Sys.setenv("R_TESTS" = "")
> 
> library(testthat)
> library(ProteoDisco)

Attaching package: 'ProteoDisco'

The following object is masked from 'package:methods':

    show

The following objects are masked from 'package:base':

    print, summary

> 
> testthat::test_check("ProteoDisco")
ProteoDisco - Importing manual transcript sequences to the ProteoDiscography.
ProteoDisco - Importing splice-junctions to the ProteoDiscography.
ProteoDisco - Generating splice-junctions models based on 9 unique (sample-specific or aggregated) splice-junctions.

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ProteoDisco - Generating the annotation database (ProteoDiscography)
ProteoDisco - Importing genomic variants from 1 file(s) to the ProteoDiscography.
ProteoDisco - Importing 1 VCF file(s).

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	ProteoDisco - Calculating a prelim. overlap of genomic mutations with given annotations
ProteoDisco - Adding SNV/MNV and InDel mutations to transcript sequences.
	ProteoDisco - Incorporating mutations within the CDS sequence(s).

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	ProteoDisco - Generating mutant transcript sequence(s) by replacing wild-type to mutant CDS.
		Working on sample: validationSet_hg19.vcf (33 mutant CDS; 4 threads)

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	ProteoDisco - Adding mutant transcripts to the ProteoDiscography.
ProteoDisco - Adding SNV/MNV and InDel mutations to transcript sequences.
	ProteoDisco - Incorporating mutations within the CDS sequence(s).

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	ProteoDisco - Generating mutant transcript sequence(s) by replacing wild-type to mutant CDS.
		Working on sample: validationSet_hg19.vcf (34 mutant CDS; 4 threads)

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	ProteoDisco - Adding mutant transcripts to the ProteoDiscography.
	Exporting 99 mutant protein sequences.
	Writing to test.FASTA.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
142.548  82.986 113.200 

Example timings

ProteoDisco.Rcheck/ProteoDisco-Ex.timings

nameusersystemelapsed
checkProteotypicFragments1.2550.0961.351
exportProteoDiscography0.3260.0040.330
generateJunctionModels12.940 0.25516.068
generateProteoDiscography0.0020.0000.002
getDiscography2.9190.2830.293
importGenomicVariants.MAF2.8490.1643.014
importGenomicVariants2.5810.0082.590
importGenomicVariants.VCF2.5240.0002.525
importSpliceJunctions0.6030.0000.604
importTranscriptSequences0.3240.0000.323
incorporateGenomicVariants28.535 0.57629.111
mutantTranscripts0.1950.0080.203
organism0.1390.0000.139
print0.2040.0000.204
seqinfo0.1490.0040.153
seqlevels0.1430.0000.143
setGenomicSequences0.1620.0000.161
setMutantTranscripts0.2760.0000.277
setTxDb0.1710.0000.171
show0.1720.0000.172
summary0.1710.0000.171