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This page was generated on 2023-10-20 09:38:09 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 1575/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ProteoDisco 1.6.0  (landing page)
Job van Riet
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/ProteoDisco
git_branch: RELEASE_3_17
git_last_commit: ad361e5
git_last_commit_date: 2023-04-25 11:32:23 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for ProteoDisco on kjohnson2


To the developers/maintainers of the ProteoDisco package:
- 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: ProteoDisco
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ProteoDisco.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ProteoDisco_1.6.0.tar.gz
StartedAt: 2023-10-18 16:09:31 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 16:22:23 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 771.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ProteoDisco.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ProteoDisco.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ProteoDisco_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/ProteoDisco.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ProteoDisco/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ProteoDisco’ version ‘1.6.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘dplyr::rename’ by ‘plyr::rename’ when loading ‘ProteoDisco’
  Warning: replacing previous import ‘dplyr::count’ by ‘plyr::count’ when loading ‘ProteoDisco’
  Warning: replacing previous import ‘dplyr::failwith’ by ‘plyr::failwith’ when loading ‘ProteoDisco’
  Warning: replacing previous import ‘dplyr::id’ by ‘plyr::id’ when loading ‘ProteoDisco’
  Warning: replacing previous import ‘dplyr::summarize’ by ‘plyr::summarize’ when loading ‘ProteoDisco’
  Warning: replacing previous import ‘dplyr::summarise’ by ‘plyr::summarise’ when loading ‘ProteoDisco’
  Warning: replacing previous import ‘dplyr::mutate’ by ‘plyr::mutate’ when loading ‘ProteoDisco’
  Warning: replacing previous import ‘dplyr::desc’ by ‘plyr::desc’ when loading ‘ProteoDisco’
  Warning: replacing previous import ‘dplyr::arrange’ by ‘plyr::arrange’ when loading ‘ProteoDisco’
See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/ProteoDisco.Rcheck/00install.out’ for details.
* 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘ProteoDisco’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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 ... WARNING
Undocumented S4 methods:
  generic 'show' and siglist 'ProteoDiscography'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
incorporateGenomicVariants 42.997  1.023  67.137
generateJunctionModels     18.084  1.261  29.493
importGenomicVariants.MAF   4.217  0.282   6.864
importGenomicVariants       3.977  0.094   6.212
importGenomicVariants.VCF   3.824  0.099   5.938
* 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: 2 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/ProteoDisco.Rcheck/00check.log’
for details.



Installation output

ProteoDisco.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘ProteoDisco’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘dplyr::rename’ by ‘plyr::rename’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::count’ by ‘plyr::count’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::failwith’ by ‘plyr::failwith’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::id’ by ‘plyr::id’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::summarize’ by ‘plyr::summarize’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::summarise’ by ‘plyr::summarise’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::mutate’ by ‘plyr::mutate’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::desc’ by ‘plyr::desc’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::arrange’ by ‘plyr::arrange’ when loading ‘ProteoDisco’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘dplyr::rename’ by ‘plyr::rename’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::count’ by ‘plyr::count’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::failwith’ by ‘plyr::failwith’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::id’ by ‘plyr::id’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::summarize’ by ‘plyr::summarize’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::summarise’ by ‘plyr::summarise’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::mutate’ by ‘plyr::mutate’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::desc’ by ‘plyr::desc’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::arrange’ by ‘plyr::arrange’ when loading ‘ProteoDisco’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘dplyr::rename’ by ‘plyr::rename’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::count’ by ‘plyr::count’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::failwith’ by ‘plyr::failwith’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::id’ by ‘plyr::id’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::summarize’ by ‘plyr::summarize’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::summarise’ by ‘plyr::summarise’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::mutate’ by ‘plyr::mutate’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::desc’ by ‘plyr::desc’ when loading ‘ProteoDisco’
Warning: replacing previous import ‘dplyr::arrange’ by ‘plyr::arrange’ when loading ‘ProteoDisco’
** testing if installed package keeps a record of temporary installation path
* DONE (ProteoDisco)

Tests output

ProteoDisco.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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)
Warning messages:
1: replacing previous import 'dplyr::rename' by 'plyr::rename' when loading 'ProteoDisco' 
2: replacing previous import 'dplyr::count' by 'plyr::count' when loading 'ProteoDisco' 
3: replacing previous import 'dplyr::failwith' by 'plyr::failwith' when loading 'ProteoDisco' 
4: replacing previous import 'dplyr::id' by 'plyr::id' when loading 'ProteoDisco' 
5: replacing previous import 'dplyr::summarize' by 'plyr::summarize' when loading 'ProteoDisco' 
6: replacing previous import 'dplyr::summarise' by 'plyr::summarise' when loading 'ProteoDisco' 
7: replacing previous import 'dplyr::mutate' by 'plyr::mutate' when loading 'ProteoDisco' 
8: replacing previous import 'dplyr::desc' by 'plyr::desc' when loading 'ProteoDisco' 
9: replacing previous import 'dplyr::arrange' by 'plyr::arrange' when loading 'ProteoDisco' 
> 
> 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 3 | SKIP 0 | PASS 11 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
167.197  39.720 192.701 

Example timings

ProteoDisco.Rcheck/ProteoDisco-Ex.timings

nameusersystemelapsed
checkProteotypicFragments1.2810.0342.022
exportProteoDiscography0.4920.0150.773
generateJunctionModels18.084 1.26129.493
generateProteoDiscography0.0030.0010.005
getDiscography0.4600.0530.785
importGenomicVariants.MAF4.2170.2826.864
importGenomicVariants3.9770.0946.212
importGenomicVariants.VCF3.8240.0995.938
importSpliceJunctions0.4880.0420.807
importTranscriptSequences0.3470.0290.577
incorporateGenomicVariants42.997 1.02367.137
mutantTranscripts0.3810.0070.590
setGenomicSequences0.3630.0070.571
setMutantTranscripts0.4930.0090.775
setTxDb0.3570.0060.554