BioC 3.4: CHECK report for MSGFplus on tokay1
This page was generated on 2017-04-15 16:19:12 -0400 (Sat, 15 Apr 2017).
MSGFplus 1.8.0
Thomas Lin Pedersen
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/MSGFplus | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
Summary
| Package: MSGFplus
|
| Version: 1.8.0
|
| Command: rm -rf MSGFplus.buildbin-libdir MSGFplus.Rcheck && mkdir MSGFplus.buildbin-libdir MSGFplus.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSGFplus.buildbin-libdir MSGFplus_1.8.0.tar.gz >MSGFplus.Rcheck\00install.out 2>&1 && cp MSGFplus.Rcheck\00install.out MSGFplus-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=MSGFplus.buildbin-libdir --install="check:MSGFplus-install.out" --force-multiarch --no-vignettes --timings MSGFplus_1.8.0.tar.gz
|
| StartedAt: 2017-04-14 23:41:29 -0400 (Fri, 14 Apr 2017)
|
| EndedAt: 2017-04-14 23:42:43 -0400 (Fri, 14 Apr 2017)
|
| EllapsedTime: 74.1 seconds
|
| RetCode: 0
|
| Status: OK
|
| CheckDir: MSGFplus.Rcheck
|
| Warnings: 0
|
Command output
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###
### Running command:
###
### rm -rf MSGFplus.buildbin-libdir MSGFplus.Rcheck && mkdir MSGFplus.buildbin-libdir MSGFplus.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSGFplus.buildbin-libdir MSGFplus_1.8.0.tar.gz >MSGFplus.Rcheck\00install.out 2>&1 && cp MSGFplus.Rcheck\00install.out MSGFplus-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=MSGFplus.buildbin-libdir --install="check:MSGFplus-install.out" --force-multiarch --no-vignettes --timings MSGFplus_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/MSGFplus.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.8.0'
* 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 ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
'library' or 'require' call to 'gWidgets' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getMSGFplus: no visible global function definition for 'download.file'
getMSGFplus: no visible global function definition for 'unzip'
msgfParGUI: no visible global function definition for 'gwindow'
msgfParGUI: no visible global function definition for 'glayout'
msgfParGUI: no visible global function definition for 'gfilebrowse'
msgfParGUI: no visible global function definition for 'ggroup'
msgfParGUI: no visible global function definition for 'gedit'
msgfParGUI: no visible global function definition for 'size'
msgfParGUI: no visible global function definition for 'size<-'
msgfParGUI: no visible global function definition for 'gcombobox'
msgfParGUI: no visible global function definition for 'gspinbutton'
msgfParGUI: no visible global function definition for 'svalue<-'
msgfParGUI: no visible global function definition for 'glabel'
msgfParGUI: no visible global function definition for 'gcheckbox'
msgfParGUI: no visible global function definition for 'gbutton'
msgfParGUI: no visible global function definition for 'addSpace'
msgfParGUI: no visible global function definition for 'gtable'
msgfParGUI: no visible global function definition for 'addSpring'
msgfParGUI: no visible global function definition for
'addHandlerClicked'
msgfParGUI : <anonymous>: no visible global function definition for
'gbasicdialog'
msgfParGUI : <anonymous> : <anonymous>: no visible binding for global
variable 'svalue'
msgfParGUI : <anonymous>: no visible global function definition for
'glayout'
msgfParGUI : <anonymous>: no visible global function definition for
'gedit'
msgfParGUI : <anonymous>: no visible global function definition for
'gcombobox'
msgfParGUI : <anonymous>: no visible global function definition for
'visible'
msgfParGUI : <anonymous>: no visible global function definition for
'svalue'
msgfParGUI : <anonymous>: no visible global function definition for
'dispose'
msgfParGUI: no visible global function definition for
'addHandlerUnrealize'
msgfParGUI: no visible global function definition for 'visible<-'
Undefined global functions or variables:
addHandlerClicked addHandlerUnrealize addSpace addSpring dispose
download.file gbasicdialog gbutton gcheckbox gcombobox gedit
gfilebrowse ggroup glabel glayout gspinbutton gtable gwindow size
size<- svalue svalue<- unzip visible visible<-
Consider adding
importFrom("utils", "download.file", "unzip")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 installed files from 'inst/doc' ... 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.4-bioc/meat/MSGFplus.Rcheck/00check.log'
for details.
MSGFplus.Rcheck/00install.out:
install for i386
* installing *source* package 'MSGFplus' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'MSGFplus' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSGFplus' as MSGFplus_1.8.0.zip
* DONE (MSGFplus)
MSGFplus.Rcheck/examples_i386/MSGFplus-Ex.timings:
| name | user | system | elapsed
|
| chargeRange | 0 | 0 | 0 |
|
| db | 0 | 0 | 0 |
|
| enzyme | 0.02 | 0.00 | 0.02 |
|
| fragmentation | 0 | 0 | 0 |
|
| getMSGFpar | 0.02 | 0.00 | 0.01 |
|
| instrument | 0 | 0 | 0 |
|
| isotopeError | 0 | 0 | 0 |
|
| lengthRange | 0.01 | 0.00 | 0.02 |
|
| matches | 0 | 0 | 0 |
|
| mods | 0 | 0 | 0 |
|
| msgfAsync-class | 0 | 0 | 0 |
|
| msgfPar-class | 0 | 0 | 0 |
|
| msgfPar | 0.01 | 0.00 | 0.02 |
|
| msgfParChargeRange-class | 0 | 0 | 0 |
|
| msgfParEnzyme-class | 0.02 | 0.00 | 0.01 |
|
| msgfParFragmentation-class | 0 | 0 | 0 |
|
| msgfParFromID | 0 | 0 | 0 |
|
| msgfParGUI | 0 | 0 | 0 |
|
| msgfParInstrument-class | 0 | 0 | 0 |
|
| msgfParIsotopeError-class | 0 | 0 | 0 |
|
| msgfParLengthRange-class | 0 | 0 | 0 |
|
| msgfParMatches-class | 0 | 0 | 0 |
|
| msgfParModification-class | 0.01 | 0.00 | 0.02 |
|
| msgfParModificationList-class | 0 | 0 | 0 |
|
| msgfParNtt-class | 0 | 0 | 0 |
|
| msgfParProtocol-class | 0 | 0 | 0 |
|
| msgfParTda-class | 0 | 0 | 0 |
|
| msgfParTolerance-class | 0 | 0 | 0 |
|
| ntt | 0 | 0 | 0 |
|
| protocol | 0.02 | 0.00 | 0.02 |
|
| runMSGF | 0 | 0 | 0 |
|
| tda | 0 | 0 | 0 |
|
| tolerance | 0 | 0 | 0 |
|
MSGFplus.Rcheck/examples_x64/MSGFplus-Ex.timings:
| name | user | system | elapsed
|
| chargeRange | 0 | 0 | 0 |
|
| db | 0 | 0 | 0 |
|
| enzyme | 0.02 | 0.00 | 0.02 |
|
| fragmentation | 0.01 | 0.00 | 0.01 |
|
| getMSGFpar | 0.02 | 0.00 | 0.02 |
|
| instrument | 0.01 | 0.00 | 0.01 |
|
| isotopeError | 0 | 0 | 0 |
|
| lengthRange | 0.02 | 0.00 | 0.02 |
|
| matches | 0 | 0 | 0 |
|
| mods | 0.02 | 0.00 | 0.02 |
|
| msgfAsync-class | 0 | 0 | 0 |
|
| msgfPar-class | 0.00 | 0.01 | 0.01 |
|
| msgfPar | 0.03 | 0.00 | 0.03 |
|
| msgfParChargeRange-class | 0 | 0 | 0 |
|
| msgfParEnzyme-class | 0 | 0 | 0 |
|
| msgfParFragmentation-class | 0.01 | 0.00 | 0.02 |
|
| msgfParFromID | 0 | 0 | 0 |
|
| msgfParGUI | 0 | 0 | 0 |
|
| msgfParInstrument-class | 0 | 0 | 0 |
|
| msgfParIsotopeError-class | 0 | 0 | 0 |
|
| msgfParLengthRange-class | 0 | 0 | 0 |
|
| msgfParMatches-class | 0 | 0 | 0 |
|
| msgfParModification-class | 0.02 | 0.00 | 0.01 |
|
| msgfParModificationList-class | 0 | 0 | 0 |
|
| msgfParNtt-class | 0 | 0 | 0 |
|
| msgfParProtocol-class | 0.01 | 0.00 | 0.02 |
|
| msgfParTda-class | 0 | 0 | 0 |
|
| msgfParTolerance-class | 0 | 0 | 0 |
|
| ntt | 0 | 0 | 0 |
|
| protocol | 0.02 | 0.00 | 0.01 |
|
| runMSGF | 0 | 0 | 0 |
|
| tda | 0.02 | 0.00 | 0.02 |
|
| tolerance | 0 | 0 | 0 |
|