BioC 2.13: CHECK report for Starr on perceval

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/Starr.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 ‘Starr/DESCRIPTION’ ... OK
* this is package ‘Starr’ version ‘1.18.1’
* 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 ‘Starr’ can be installed ... [28s/29s] 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: ‘lattice’
  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 compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* 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’:
  ‘Starr.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [81s/82s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
plot.posBias 22.308  0.294  22.822
plot.gcBias  18.776  0.185  19.406
plot.ma       7.668  0.284   8.158
* 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 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/Starr.Rcheck/00check.log’
for details.

* installing *source* package ‘Starr’ ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ahocorasick.c -o ahocorasick.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c collect.c -o collect.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c rm_small_peak.c -o rm_small_peak.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c sort_by_genomic.c -o sort_by_genomic.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 Starr.so ahocorasick.o collect.o rm_small_peak.o sort_by_genomic.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.13-bioc/meat/Starr.Rcheck/Starr/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Starr)

name	user	system	elapsed
bpmapToProbeAnno	0.009	0.003	0.011
cmarrt.ma	0.485	0.008	0.506
cmarrt.peak	0.010	0.006	0.017
correlationPlot	0.050	0.009	0.059
densityscatter	4.145	0.101	4.292
filterGenes	0.002	0.003	0.006
getMeans	0.008	0.019	0.029
getProfiles	0.004	0.008	0.013
getRatio	0.007	0.010	0.017
kde2dplot	0.231	0.057	0.297
makeSplines	0.005	0.006	0.011
normalize.Probes	0.006	0.009	0.015
plot.Density	0.366	0.099	0.536
plot.boxes	4.147	0.175	4.570
plot.cmarrt	0.004	0.010	0.014
plot.gcBias	18.776	0.185	19.406
plot.image	0.019	0.009	0.027
plot.ma	7.668	0.284	8.158
plot.posBias	22.308	0.294	22.822
plot.ratioScatter	2.688	0.099	2.837
plot.scatter	1.957	0.066	2.075
plotProfiles	0.237	0.019	0.260
profileplot	0.993	0.057	1.073
read.gffAnno	0.002	0.004	0.006
readCelFile	0.003	0.006	0.009
remap	0.002	0.004	0.007

BioC 2.13: CHECK report for Starr on perceval

Summary

Command output