BioC 2.14: CHECK report for Starr on petty

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Starr_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/Starr.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.20.0’
* 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 ‘Starr’ can be installed ... [35s/36s] 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 loading without being on the library search path ... OK
* checking 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 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 files in ‘vignettes’ ... OK
* checking examples ... [102s/103s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
plot.posBias 32.890  0.229  33.303
plot.gcBias  29.406  0.176  29.803
plot.ma       9.886  0.296  10.590
* 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 was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-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-2.14-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	0.001	0.000	0.001
cmarrt.ma	0.002	0.000	0.002
cmarrt.peak	0.001	0.001	0.002
correlationPlot	0.058	0.006	0.065
densityscatter	3.557	0.065	3.635
filterGenes	0.001	0.000	0.001
getMeans	0.002	0.001	0.003
getProfiles	0.002	0.001	0.002
getRatio	0.002	0.001	0.002
kde2dplot	0.683	0.061	0.746
makeSplines	0.002	0.000	0.002
normalize.Probes	0.001	0.000	0.002
plot.Density	0.843	0.039	0.900
plot.boxes	1.822	0.103	1.931
plot.cmarrt	0.002	0.000	0.002
plot.gcBias	29.406	0.176	29.803
plot.image	0.001	0.000	0.001
plot.ma	9.886	0.296	10.590
plot.posBias	32.890	0.229	33.303
plot.ratioScatter	2.016	0.099	2.289
plot.scatter	1.480	0.035	1.524
plotProfiles	0.362	0.010	0.377
profileplot	1.065	0.037	1.349
read.gffAnno	0.001	0.000	0.001
readCelFile	0.002	0.000	0.002
remap	0.001	0.000	0.002

BioC 2.14: CHECK report for Starr on petty

Summary

Command output