BioC 2.13: CHECK report for flagme on perceval

Package: flagme

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flagme_1.18.0.tar.gz

StartedAt: 2014-04-05 01:12:10 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:14:36 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 145.8 seconds

RetCode: 0

Status:  OK

CheckDir: flagme.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/flagme.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flagme/DESCRIPTION’ ... OK
* this is package ‘flagme’ version ‘1.18.0’
* 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 ‘flagme’ can be installed ... [10s/10s] OK
* 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
* 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
Package in Depends field not imported from: ‘gcspikelite’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of 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 ... 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 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘flagme.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [43s/45s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
parseChromaTOF 6.207  0.051   6.495
parseELU       4.989  0.098   5.318
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/flagme.Rcheck/00check.log’
for details.

* installing *source* package ‘flagme’ ...
** 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 -Wall  -c dp.c -o dp.o
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 -Wall  -c init.c -o init.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 flagme.so dp.o init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.13-bioc/meat/flagme.Rcheck/flagme/libs
** R
** inst
** preparing package for lazy loading
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (0.11.0)
than is installed on your system (0.11.1). This might lead to errors
when loading mzR. If you encounter such issues, please send
a report, including the output of sessionInfo() to the Bioc
mailing list -- http://www.bioconductor.org/help/mailing-list.
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘flagme’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (0.11.0)
than is installed on your system (0.11.1). This might lead to errors
when loading mzR. If you encounter such issues, please send
a report, including the output of sessionInfo() to the Bioc
mailing list -- http://www.bioconductor.org/help/mailing-list.
* DONE (flagme)

name	user	system	elapsed
addAMDISPeaks	1.361	0.115	1.626
addChromaTOFPeaks	0.523	0.066	0.642
betweenAlignment	0.005	0.013	0.019
calcTimeDiffs	1.713	0.176	2.067
clusterAlignment	1.736	0.158	2.111
compress	1.972	0.169	2.512
dp	2.028	0.165	2.293
gatherInfo	2.125	0.156	2.346
imputePeaks	3.061	0.249	3.469
multipleAlignment	2.053	0.172	2.309
normDotProduct	1.854	0.162	2.085
parseChromaTOF	6.207	0.051	6.495
parseELU	4.989	0.098	5.318
peaksAlignment	0.007	0.007	0.014
peaksDataset	0.691	0.130	0.959
plot	1.296	0.212	1.602
plotImage	0.588	0.076	0.733
progressiveAlignment	1.737	0.172	1.973
rmaFitUnit	1.703	0.189	1.950