Thomas Lin Pedersen
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/MSGFplus |
| Branch: RELEASE_3_11 |
| Last Commit: 4504509 |
| Last Changed Date: 2020-10-07 04:05:57 -0400 (Wed, 07 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:12 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE MSGFplus PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1138/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MSGFplus 1.22.0 Thomas Lin Pedersen
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | ERROR | ERROR | skipped | skipped |
| Package: MSGFplus |
| Version: 1.22.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSGFplus.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings MSGFplus_1.22.0.tar.gz |
| StartedAt: 2020-10-17 06:16:11 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 06:17:37 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 86.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MSGFplus.Rcheck |
| Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSGFplus.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings MSGFplus_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/MSGFplus.Rcheck' * using R version 4.0.3 (2020-10-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'MSGFplus/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'MSGFplus' version '1.22.0' * 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 'MSGFplus' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp6Ry1Qr/R.INSTALL1b1c5ffb4057/MSGFplus/man/msgfPar-class.Rd:121: missing link 'msgfParGUI' Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp6Ry1Qr/R.INSTALL1b1c5ffb4057/MSGFplus/man/msgfPar-class.Rd:148: missing link 'msgfParGUI' See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/MSGFplus.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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... NOTE Namespace in Imports field not imported from: 'ProtGenerics' All declared Imports should be used. * 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 ... WARNING Missing link or links in documentation object 'msgfPar-class.Rd': 'msgfParGUI' See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'test-all.R' OK ** running tests for arch 'x64' ... Running 'test-all.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, 1 NOTE See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/MSGFplus.Rcheck/00check.log' for details.
MSGFplus.Rcheck/00install.out
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/MSGFplus_1.22.0.tar.gz && rm -rf MSGFplus.buildbin-libdir && mkdir MSGFplus.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSGFplus.buildbin-libdir MSGFplus_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL MSGFplus_1.22.0.zip && rm MSGFplus_1.22.0.tar.gz MSGFplus_1.22.0.zip
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install for i386
* installing *source* package 'MSGFplus' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'MSGFplus'
finding HTML links ... done
MSGFplus-package html
chargeRange html
db html
enzyme html
fragmentation html
getMSGFpar html
instrument html
isotopeError html
lengthRange html
matches html
mods html
msgfAsync-class html
msgfPar-class html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp6Ry1Qr/R.INSTALL1b1c5ffb4057/MSGFplus/man/msgfPar-class.Rd:121: missing link 'msgfParGUI'
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp6Ry1Qr/R.INSTALL1b1c5ffb4057/MSGFplus/man/msgfPar-class.Rd:148: missing link 'msgfParGUI'
msgfPar html
msgfParChargeRange-class html
msgfParEnzyme-class html
msgfParFragmentation-class html
msgfParFromID html
msgfParInstrument-class html
msgfParIsotopeError-class html
msgfParLengthRange-class html
msgfParMatches-class html
msgfParModification-class html
msgfParModificationList-class html
msgfParNtt-class html
msgfParProtocol-class html
msgfParTda-class html
msgfParTolerance-class html
ntt html
protocol html
runMSGF html
tda html
tolerance html
** 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
install for x64
* installing *source* package 'MSGFplus' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSGFplus' as MSGFplus_1.22.0.zip
* DONE (MSGFplus)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'MSGFplus' successfully unpacked and MD5 sums checked
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MSGFplus.Rcheck/tests_i386/test-all.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.
> library(testthat)
> test_check('MSGFplus')
Loading required package: MSGFplus
Attaching package: 'MSGFplus'
The following object is masked from 'package:testthat':
matches
== testthat results ===========================================================
[ OK: 169 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
2.78 0.09 3.60
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MSGFplus.Rcheck/tests_x64/test-all.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.
> library(testthat)
> test_check('MSGFplus')
Loading required package: MSGFplus
Attaching package: 'MSGFplus'
The following object is masked from 'package:testthat':
matches
== testthat results ===========================================================
[ OK: 169 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
3.50 0.14 4.29
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MSGFplus.Rcheck/examples_i386/MSGFplus-Ex.timings
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MSGFplus.Rcheck/examples_x64/MSGFplus-Ex.timings
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