BioC 2.12: CHECK report for MassSpecWavelet on petty

Package: MassSpecWavelet

Version: 1.26.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MassSpecWavelet_1.26.0.tar.gz

StartedAt: 2013-10-08 22:59:47 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:01:08 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 80.4 seconds

RetCode: 0

Status:  OK

CheckDir: MassSpecWavelet.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/MassSpecWavelet.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'MassSpecWavelet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MassSpecWavelet' version '1.26.0'
* 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 for sufficient/correct file permissions ... OK
* checking whether package 'MassSpecWavelet' can be installed ... [3s/3s] 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 ... NOTE
prepare_Rd: getRidgeValue.Rd:24-26: Dropping empty section \examples
prepare_Rd: sav.gol.Rd:28-29: Dropping empty section \examples
prepare_Rd: smoothDWT.Rd:22-25: Dropping empty section \details
prepare_Rd: smoothDWT.Rd:29: Dropping empty section \references
prepare_Rd: smoothDWT.Rd:32-34: Dropping empty section \examples
* 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 ... [44s/45s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
peakDetectionCWT        9.605  1.192  10.914
identifyMajorPeaks      7.686  0.548   8.307
tuneInPeakInfo          7.246  0.753   8.071
MassSpecWavelet.package 5.988  0.598   6.674
plotPeak                4.963  0.622   5.642
* 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/MassSpecWavelet.Rcheck/00check.log'
for details.

* installing *source* package 'MassSpecWavelet' ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c convolve2.c -o convolve2.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o MassSpecWavelet.so convolve2.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/MassSpecWavelet.Rcheck/MassSpecWavelet/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MassSpecWavelet)

name	user	system	elapsed
MassSpecWavelet.package	5.988	0.598	6.674
cwt	0.732	0.082	0.817
extendLength	0.003	0.005	0.007
extendNBase	0.003	0.004	0.006
getLocalMaximumCWT	0.610	0.101	0.771
getRidge	0.666	0.078	0.769
identifyMajorPeaks	7.686	0.548	8.307
localMaximum	0.106	0.009	0.118
peakDetectionCWT	9.605	1.192	10.914
plotLocalMax	0.450	0.067	0.521
plotPeak	4.963	0.622	5.642
plotRidgeList	0.818	0.077	0.906
tuneInPeakInfo	7.246	0.753	8.071