pRoloc 0.99.17
Laurent Gatto
| Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pRoloc | | Last Changed Rev: 74764 / Revision: 74774 | | Last Changed Date: 2013-03-24 11:22:49 -0700 (Sun, 24 Mar 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | [ WARNINGS ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | ERROR | ERROR |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pRoloc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pRoloc’ version ‘0.99.17’
* 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 ‘pRoloc’ can be installed ... [51s/57s] OK
* checking installed package size ... OK
* checking package 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 ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated 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 ... WARNING
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck/00_pkg_src/pRoloc/man/MLearn-methods.Rd’:
‘MSnSet-class’
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck/00_pkg_src/pRoloc/man/exprsToRatios-methods.Rd’:
‘MSnSet-class’
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck/00_pkg_src/pRoloc/man/getMarkers.Rd’:
‘MSnSet-class’
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck/00_pkg_src/pRoloc/man/getPredictions.Rd’:
‘MSnSet-class’
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck/00_pkg_src/pRoloc/man/knnClassification.Rd’:
‘MSnSet-class’
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck/00_pkg_src/pRoloc/man/knnOptimisation.Rd’:
‘MSnSet-class’
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck/00_pkg_src/pRoloc/man/ksvmClassification.Rd’:
‘MSnSet-class’
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck/00_pkg_src/pRoloc/man/ksvmOptimisation.Rd’:
‘MSnSet-class’
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck/00_pkg_src/pRoloc/man/makeNaData.Rd’:
‘MSnSet-class’
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck/00_pkg_src/pRoloc/man/minClassScore.Rd’:
‘MSnSet-class’
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck/00_pkg_src/pRoloc/man/minMarkers.Rd’:
‘MSnSet-class’
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck/00_pkg_src/pRoloc/man/nbClassification.Rd’:
‘MSnSet-class’
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck/00_pkg_src/pRoloc/man/nbOptimisation.Rd’:
‘MSnSet-class’
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck/00_pkg_src/pRoloc/man/nnetClassification.Rd’:
‘MSnSet-class’
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck/00_pkg_src/pRoloc/man/nnetOptimisation.Rd’:
‘MSnSet-class’
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck/00_pkg_src/pRoloc/man/perTurboClassification.Rd’:
‘MSnSet-class’
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck/00_pkg_src/pRoloc/man/perTurboOptimisation.Rd’:
‘MSnSet-class’
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck/00_pkg_src/pRoloc/man/plsdaClassification.Rd’:
‘MSnSet-class’
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck/00_pkg_src/pRoloc/man/plsdaOptimisation.Rd’:
‘MSnSet-class’
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck/00_pkg_src/pRoloc/man/rfClassification.Rd’:
‘MSnSet-class’
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck/00_pkg_src/pRoloc/man/rfOptimisation.Rd’:
‘MSnSet-class’
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck/00_pkg_src/pRoloc/man/svmClassification.Rd’:
‘MSnSet-class’
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck/00_pkg_src/pRoloc/man/svmOptimisation.Rd’:
‘MSnSet-class’
See the information in section ‘Cross-references’ of 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [94s/97s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
perTurboClassification 22.221 0.028 22.690
rfClassification 8.777 0.076 9.059
svmClassification 8.448 0.032 8.661
nnetClassification 7.477 0.024 7.858
ksvmClassification 6.669 0.044 6.735
nbClassification 6.460 0.028 6.614
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘test-all.R’ [228s/233s]
[228s/233s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There was 1 warning.
See
‘/home/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck/00check.log’
for details.
* installing *source* package ‘pRoloc’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘scale’ from package ‘base’ in package ‘MSnbase’
Warning: replacing previous import ‘alpha’ when loading ‘scales’
** help
*** installing help indices
** building package indices
** installing vignettes
‘pRoloc-tutorial.Rnw’
processing file: pRoloc-tutorial.Rnw
output file: /home/biocbuild/bbs-2.12-bioc/meat/pRoloc.Rcheck/pRoloc/doc/pRoloc-tutorial.R
** testing if installed package can be loaded
Creating a generic function for ‘scale’ from package ‘base’ in package ‘MSnbase’
Warning: replacing previous import ‘alpha’ when loading ‘scales’
* DONE (pRoloc)