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This page was generated on 2024-03-27 11:36:08 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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 1603/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ProteoDisco 1.8.0  (landing page)
Job van Riet
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/ProteoDisco
git_branch: RELEASE_3_18
git_last_commit: 678154a
git_last_commit_date: 2023-10-24 11:36:01 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for ProteoDisco on nebbiolo2


To the developers/maintainers of the ProteoDisco package:
- 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 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: ProteoDisco
Version: 1.8.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:ProteoDisco.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings ProteoDisco_1.8.0.tar.gz
StartedAt: 2024-03-26 01:22:59 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 01:32:23 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 564.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ProteoDisco.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:ProteoDisco.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings ProteoDisco_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ProteoDisco.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘ProteoDisco/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ProteoDisco’ version ‘1.8.0’
* 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 ‘/home/biocbuild/bbs-3.18-bioc/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 loading without being on the library search path ... 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 34.277  0.900  35.177
generateJunctionModels     13.106  1.143  18.783
* 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 ...
  ‘Overview_ProteoDisco.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/ProteoDisco.Rcheck/00check.log’
for details.



Installation output

ProteoDisco.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL ProteoDisco
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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)
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.
Retrieving all CDS-records from the TxDb.

  |                                                                            
  |                                                                      |   0%Retrieving overlapping or adjacent CDS for each splice-junction: testSJ
Retrieving 5'-adjacent or overlapping CDS.
Retrieving 3'-adjacent or overlapping CDS.

  |                                                                            
  |======================================================================| 100%

ProteoDisco - Ignoring subsetting on shared seqlevels as a BSgenome was given.
ProteoDisco - Generating the annotation database (ProteoDiscography)
ProteoDisco - Importing genomic variants from 1 file(s) to the ProteoDiscography.
ProteoDisco - Importing 1 VCF file(s).

  |                                                                            
  |                                                                      |   0%ProteoDisco - Importing /home/biocbuild/bbs-3.18-bioc/R/site-library/ProteoDisco/extdata/validationSet_hg19.vcf
ProteoDisco - Checking sanity of reference anchors for validationSet_hg19.vcf.
ProteoDisco - Checking sanity of reference anchors in chr1 (using 1 threads)
ProteoDisco - Checking sanity of reference anchors in chr2 (using 1 threads)
ProteoDisco - Checking sanity of reference anchors in chr3 (using 1 threads)
ProteoDisco - Checking sanity of reference anchors in chr6 (using 1 threads)
ProteoDisco - Checking sanity of reference anchors in chr7 (using 1 threads)
ProteoDisco - Checking sanity of reference anchors in chr10 (using 1 threads)
ProteoDisco - Checking sanity of reference anchors in chr11 (using 1 threads)
ProteoDisco - Checking sanity of reference anchors in chr13 (using 1 threads)
ProteoDisco - Checking sanity of reference anchors in chr14 (using 1 threads)
ProteoDisco - Checking sanity of reference anchors in chr17 (using 1 threads)
ProteoDisco - Checking sanity of reference anchors in chr19 (using 1 threads)
ProteoDisco - Checking sanity of reference anchors in chrX (using 1 threads)

  |                                                                            
  |======================================================================| 100%

	ProteoDisco - Calculating a prelim. overlap of genomic mutations with given annotations
ProteoDisco - Adding SNV/MNV and InDel mutations to transcript sequences.
	ProteoDisco - Finding overlap of mutations with CDS within the TxDb.
	ProteoDisco - Incorporating mutations within the CDS sequence(s).
		Working on sample: validationSet_hg19.vcf (28 overlapping CDS; 4 threads)

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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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Retrieving 3' UTR
	ProteoDisco - Adding mutant transcripts to the ProteoDiscography.
ProteoDisco - Adding SNV/MNV and InDel mutations to transcript sequences.
	ProteoDisco - Finding overlap of mutations with CDS within the TxDb.
	ProteoDisco - Incorporating mutations within the CDS sequence(s).
		Working on sample: validationSet_hg19.vcf (28 overlapping CDS; 4 threads)

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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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Retrieving 3' UTR
	ProteoDisco - Adding mutant transcripts to the ProteoDiscography.
ProteoDisco - Exporting mutant protein isoforms.
	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 
133.459  47.767 108.055 

Example timings

ProteoDisco.Rcheck/ProteoDisco-Ex.timings

nameusersystemelapsed
checkProteotypicFragments0.2800.0040.284
exportProteoDiscography0.2600.0070.268
generateJunctionModels13.106 1.14318.783
generateProteoDiscography0.0020.0010.002
getDiscography3.9670.8990.258
importGenomicVariants.MAF3.5750.2763.852
importGenomicVariants3.2350.1723.408
importGenomicVariants.VCF3.1060.1523.258
importSpliceJunctions0.3790.0120.391
importTranscriptSequences0.2270.0080.235
incorporateGenomicVariants34.277 0.90035.177
mutantTranscripts0.2120.0000.212
setGenomicSequences0.2190.0000.219
setMutantTranscripts0.3020.0000.302
setTxDb0.1720.0000.172