BioC 2.12: CHECK report for TSSi on petty

Package: TSSi

Version: 1.5.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch TSSi_1.5.0.tar.gz

StartedAt: 2013-03-25 05:01:37 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 05:03:59 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 141.3 seconds

RetCode: 0

Status: OK

CheckDir: TSSi.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/TSSi.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'TSSi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TSSi' version '1.5.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'multicore'
* 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 'TSSi' can be installed ... [10s/10s] 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 ... 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [30s/30s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
TSSi-package     6.711  0.063   6.779
plot-methods     5.946  0.034   5.981
identify-methods 5.539  0.024   5.597
* 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/TSSi.Rcheck/00check.log'
for details.

* installing *source* package 'TSSi' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c assess.c -o assess.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c init.c -o init.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o TSSi.so assess.o init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/TSSi.Rcheck/TSSi/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'start' from package 'stats' in package 'TSSi'
Creating a generic function for 'end' from package 'stats' in package 'TSSi'
Creating a new generic function for 'segments' in package 'TSSi'
Creating a generic function for 'plot' from package 'graphics' in package 'TSSi'
** help
*** installing help indices
** building package indices
** installing vignettes
   'TSSi.Rnw' using 'UTF-8' 
** testing if installed package can be loaded
* DONE (TSSi)

name	user	system	elapsed
TSSi-package	6.711	0.063	6.779
TssData-class	0.007	0.004	0.011
TssNorm-class	0.009	0.005	0.014
TssResult-class	0.006	0.005	0.011
asRangedData-methods	0.712	0.019	0.735
get-methods	0.100	0.024	0.125
identify-methods	5.539	0.024	5.597
normalize-methods	4.882	0.017	4.901
physcoCounts-data	0.007	0.005	0.012
plot-methods	5.946	0.034	5.981
segmentize-methods	0.054	0.013	0.067
subtract-functions	0.009	0.006	0.017

Summary

Command output