BioC 2.13: CHECK report for CellNOptR on perceval

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/CellNOptR.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 ‘CellNOptR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CellNOptR’ version ‘1.8.0’
* 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 ‘CellNOptR’ can be installed ... [12s/13s] 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
‘library’ or ‘require’ calls to packages already attached by Depends:
  ‘hash’ ‘RBGL’ ‘RCurl’ ‘Rgraphviz’ ‘XML’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘ggplot2’ ‘hash’ ‘methods’ ‘RCurl’ ‘Rgraphviz’ ‘XML’
  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 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 compilation flags in Makevars ... 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’:
  ‘CellNOptR-vignette.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [32s/35s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test_gaBinaryT1.R’ [7s/7s]
  Running ‘test_gaBinaryT2.R’ [10s/10s]
  Running ‘test_gaBinaryT3.R’ [12s/12s]
  Running ‘test_manySteadyStates.R’ [20s/20s]
  Running ‘test_priorBitString.R’ [4s/4s]
  Running ‘test_simulateTN.R’ [6s/6s]
 [58s/59s] OK
* 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/CellNOptR.Rcheck/00check.log’
for details.

* installing *source* package ‘CellNOptR’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -mtune=core2 -g -O2 -Wall  -c getFit.c -o getFit.o
getFit.c: In function ‘getFit’:
getFit.c:47: warning: unused variable ‘nReacs’
getFit.c:42: warning: unused variable ‘selCounter’
getFit.c:41: warning: unused variable ‘selection’
getFit.c:40: warning: unused variable ‘or_max’
getFit.c:39: warning: unused variable ‘curr_max’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -mtune=core2 -g -O2 -Wall  -c simulatorT1.c -o simulatorT1.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -I./include  -fPIC  -mtune=core2 -g -O2 -Wall  -c simulatorTN.c -o simulatorTN.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 CellNOptR.so getFit.o simulatorT1.o simulatorTN.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.13-bioc/meat/CellNOptR.Rcheck/CellNOptR/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 (CellNOptR)

name	user	system	elapsed
CNORbool	2.972	0.043	3.016

BioC 2.13: CHECK report for CellNOptR on perceval

Summary

Command output