Job van Riet
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/ProteoDisco |
| git_branch: master |
| git_last_commit: 24e9090 |
| git_last_commit_date: 2021-12-06 05:08:39 -0400 (Mon, 06 Dec 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:21 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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. |
| Package 1482/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ProteoDisco 1.1.3 (landing page) Job van Riet
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: ProteoDisco |
| Version: 1.1.3 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ProteoDisco.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ProteoDisco_1.1.3.tar.gz |
| StartedAt: 2022-03-17 19:56:42 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:04:08 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 445.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ProteoDisco.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ProteoDisco.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ProteoDisco_1.1.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/ProteoDisco.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ProteoDisco/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ProteoDisco' version '1.1.3'
* 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 whether package 'ProteoDisco' can be installed ... WARNING
Found the following significant warnings:
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::count' by 'plyr::count' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::desc' by 'plyr::desc' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::mutate' by 'plyr::mutate' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::arrange' by 'plyr::arrange' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::rename' by 'plyr::rename' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::summarise' by 'plyr::summarise' when loading 'ProteoDisco'
See 'D:/biocbuild/bbs-3.15-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 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 26.91 1.21 28.13
generateJunctionModels 9.05 0.67 23.85
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/ProteoDisco.Rcheck/00check.log'
for details.
ProteoDisco.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ProteoDisco
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'ProteoDisco' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
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::count' by 'plyr::count' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::desc' by 'plyr::desc' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::mutate' by 'plyr::mutate' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::arrange' by 'plyr::arrange' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::rename' by 'plyr::rename' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::summarise' by 'plyr::summarise' when loading 'ProteoDisco'
** help
*** installing help indices
converting help for package 'ProteoDisco'
finding HTML links ... done
ProteoDiscography html
ProteoDiscographyExample.hg19 html
checkProteotypicFragments html
dot-checkReferenceAnchor html
exportProteoDiscography html
generateJunctionModels html
generateProteoDiscography html
getDiscography html
importGenomicVariants.MAF html
importGenomicVariants html
importGenomicVariants.VCF html
importSpliceJunctions html
importTranscriptSequences html
incorporateGenomicVariants html
mutantTranscripts html
setGenomicSequences html
setMutantTranscripts html
setTxDb html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
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::count' by 'plyr::count' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::desc' by 'plyr::desc' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::mutate' by 'plyr::mutate' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::arrange' by 'plyr::arrange' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::rename' by 'plyr::rename' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::summarise' by 'plyr::summarise' when loading 'ProteoDisco'
** testing if installed package can be loaded from final location
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::count' by 'plyr::count' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::desc' by 'plyr::desc' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::mutate' by 'plyr::mutate' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::arrange' by 'plyr::arrange' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::rename' by 'plyr::rename' when loading 'ProteoDisco'
Warning: replacing previous import 'dplyr::summarise' by 'plyr::summarise' when loading 'ProteoDisco'
** testing if installed package keeps a record of temporary installation path
* DONE (ProteoDisco)
Making 'packages.html' ... done
ProteoDisco.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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::failwith' by 'plyr::failwith' when loading 'ProteoDisco'
2: replacing previous import 'dplyr::id' by 'plyr::id' when loading 'ProteoDisco'
3: replacing previous import 'dplyr::summarize' by 'plyr::summarize' when loading 'ProteoDisco'
4: replacing previous import 'dplyr::count' by 'plyr::count' when loading 'ProteoDisco'
5: replacing previous import 'dplyr::desc' by 'plyr::desc' when loading 'ProteoDisco'
6: replacing previous import 'dplyr::mutate' by 'plyr::mutate' when loading 'ProteoDisco'
7: replacing previous import 'dplyr::arrange' by 'plyr::arrange' when loading 'ProteoDisco'
8: replacing previous import 'dplyr::rename' by 'plyr::rename' when loading 'ProteoDisco'
9: replacing previous import 'dplyr::summarise' by 'plyr::summarise' 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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|======================================================================| 100%
ProteoDisco - Generating the annotation database (ProteoDiscography)
ProteoDisco - Importing genomic variants from 1 file(s) to the ProteoDiscography.
ProteoDisco - Importing 1 VCF file(s).
|
| | 0%
|
|======================================================================| 100%
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 5 | SKIP 0 | PASS 11 ]
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 11 ]
>
> proc.time()
user system elapsed
127.21 7.20 150.29
ProteoDisco.Rcheck/ProteoDisco-Ex.timings
| name | user | system | elapsed | |
| checkProteotypicFragments | 0.39 | 0.08 | 0.47 | |
| exportProteoDiscography | 0.24 | 0.09 | 0.33 | |
| generateJunctionModels | 9.05 | 0.67 | 23.85 | |
| generateProteoDiscography | 0.01 | 0.00 | 0.01 | |
| getDiscography | 0.24 | 0.07 | 0.30 | |
| importGenomicVariants.MAF | 2.53 | 0.09 | 2.62 | |
| importGenomicVariants | 1.78 | 0.12 | 1.91 | |
| importGenomicVariants.VCF | 1.88 | 0.02 | 1.89 | |
| importSpliceJunctions | 0.36 | 0.02 | 0.38 | |
| importTranscriptSequences | 0.21 | 0.00 | 0.21 | |
| incorporateGenomicVariants | 26.91 | 1.21 | 28.13 | |
| mutantTranscripts | 0.27 | 0.07 | 0.33 | |
| setGenomicSequences | 0.20 | 0.09 | 0.29 | |
| setMutantTranscripts | 0.28 | 0.08 | 0.36 | |
| setTxDb | 0.19 | 0.09 | 0.29 | |