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This page was generated on 2024-03-28 11:36:54 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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Package 1602/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ProteoDisco 1.9.0  (landing page)
Job van Riet
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/ProteoDisco
git_branch: devel
git_last_commit: 1285cb1
git_last_commit_date: 2023-10-24 11:36:01 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for ProteoDisco on nebbiolo1


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: 1.9.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ProteoDisco.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ProteoDisco_1.9.0.tar.gz
StartedAt: 2024-03-28 01:38:21 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 01:47:43 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 561.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ProteoDisco.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ProteoDisco.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ProteoDisco_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ProteoDisco.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* 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 ‘1.9.0’
* 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 ... 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-3.19-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 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 ... 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 ... NOTE
checkRd: (-1) checkProteotypicFragments.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{x}{({ProteoDiscography}): ProteoDiscography object which stores the annotation and genomic sequences.}
       |           ^
checkRd: (-1) checkProteotypicFragments.Rd:39: Lost braces; missing escapes or markup?
    39 | {ProteoDiscography} with an additional column specifying the number of proteotypic fragments per record.
       | ^
checkRd: (-1) generateJunctionModels.Rd:36: Lost braces; missing escapes or markup?
    36 | of the given {ProteoDiscography}; strand-information is taken into account. If no strand-information is given, the nearest (or overlapping) known
       |              ^
checkRd: (-1) importGenomicVariants.MAF.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{ProteoDiscography}{({ProteoDiscography}): ProteoDiscography object which stores the annotation and genomic sequences.}
       |                           ^
checkRd: (-1) importGenomicVariants.Rd:40: Lost braces; missing escapes or markup?
    40 | into the {ProteoDiscography} as a {VRanges}. This genomic variants can later be incorporated within transcript 
       |          ^
checkRd: (-1) importGenomicVariants.Rd:40: Lost braces; missing escapes or markup?
    40 | into the {ProteoDiscography} as a {VRanges}. This genomic variants can later be incorporated within transcript 
       |                                   ^
checkRd: (-1) importGenomicVariants.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{ProteoDiscography}{({ProteoDiscography}): ProteoDiscography object which stores the annotation and genomic sequences.}
       |                           ^
checkRd: (-1) importGenomicVariants.VCF.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{ProteoDiscography}{({ProteoDiscography}): ProteoDiscography object which stores the annotation and genomic sequences.}
       |                           ^
checkRd: (-1) importSpliceJunctions.Rd:39: Lost braces; missing escapes or markup?
    39 | Input should be a {tibble} containing the following columns:
       |                   ^
checkRd: (-1) importSpliceJunctions.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{ProteoDiscography}{({ProteoDiscography}): ProteoDiscography object which stores the annotation and genomic sequences.}
       |                           ^
checkRd: (-1) importTranscriptSequences.Rd:15: Lost braces; missing escapes or markup?
    15 | \item{ProteoDiscography}{({ProteoDiscography}): ProteoDiscography object which stores the annotation and genomic sequences.}
       |                           ^
checkRd: (-1) incorporateGenomicVariants.Rd:34: Lost braces; missing escapes or markup?
    34 | \code{incorporateMutations} Incorporates SNV, MNV and InDels present in the {ProteoDiscography} on the transcripts.
       |                                                                             ^
checkRd: (-1) incorporateGenomicVariants.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{ProteoDiscography}{({ProteoDiscography}): ProteoDiscography object which stores the annotation and genomic sequences.}
       |                           ^
* 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 33.700  1.320  35.021
generateJunctionModels     13.172  1.257  19.201
getDiscography              4.092  1.008   0.261
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/ProteoDisco.Rcheck/00check.log’
for details.


Installation output

ProteoDisco.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ProteoDisco
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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 Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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-3.19-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 
131.780  51.024 109.213 

Example timings

ProteoDisco.Rcheck/ProteoDisco-Ex.timings

nameusersystemelapsed
checkProteotypicFragments0.2710.0160.285
exportProteoDiscography0.2040.0200.224
generateJunctionModels13.172 1.25719.201
generateProteoDiscography0.0020.0000.002
getDiscography4.0921.0080.261
importGenomicVariants.MAF3.3050.3243.630
importGenomicVariants3.0950.0763.171
importGenomicVariants.VCF3.0700.1043.174
importSpliceJunctions0.3430.0320.376
importTranscriptSequences0.1980.0200.219
incorporateGenomicVariants33.700 1.32035.021
mutantTranscripts0.1950.0080.203
setGenomicSequences0.1910.0040.194
setMutantTranscripts0.2830.0000.283
setTxDb0.1740.0110.186