BioC 2.12: CHECK report for Rtreemix on petty

Package: Rtreemix

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Rtreemix_1.22.0.tar.gz

StartedAt: 2013-10-08 23:51:27 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:53:56 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 149.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Rtreemix.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/Rtreemix.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 'Rtreemix/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rtreemix' version '1.22.0'
* 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 'Rtreemix' can be installed ... [58s/62s] 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 ... 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 for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... WARNING
File '/Users/biocbuild/bbs-2.12-bioc/meat/Rtreemix.Rcheck/Rtreemix/libs/Rtreemix.so':
  Found '__ZSt4cerr', possibly from 'std::cerr' (C++)
    Objects: 'Rtreemix.o', 'cfunctions.o', 'kmeans.o',
      'max_weight_branch.o', 'mtree.o', 'mtreemix.o', 'replaceleda.o'
  Found '_exit', possibly from 'exit' (C)
    Objects: 'cfunctions.o', 'kmeans.o', 'mtree.o', 'mtreemix.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [8s/8s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/Rtreemix.Rcheck/00check.log'
for details.

* installing *source* package 'Rtreemix' ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c Rtreemix.cc -o Rtreemix.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c WrapGraph.cc -o WrapGraph.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c cfunctions.cc -o cfunctions.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c kmeans.cc -o kmeans.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c max_weight_branch.cc -o max_weight_branch.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c mtree.cc -o mtree.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c mtreemix.cc -o mtreemix.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c replaceleda.cc -o replaceleda.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o Rtreemix.so Rtreemix.o WrapGraph.o cfunctions.o kmeans.o max_weight_branch.o mtree.o mtreemix.o replaceleda.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/Rtreemix.Rcheck/Rtreemix/libs
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'plot' when loading 'graphics'
Creating a generic function for 'print' from package 'base' in package 'Rtreemix'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'plot' when loading 'graphics'
* DONE (Rtreemix)

name	user	system	elapsed
L1.dist	0.016	0.002	0.017
L2.norm	0.008	0.000	0.008
Pval.dist	0.132	0.001	0.134
RtreemixData-class	0.079	0.006	0.084
RtreemixGPS-class	0.018	0.002	0.020
RtreemixModel-class	1.989	0.076	2.081
RtreemixSim-class	0.085	0.009	0.095
RtreemixStats-class	0.269	0.022	0.291
bootstrap-methods	0.014	0.001	0.014
comp.models	0.096	0.001	0.097
comp.trees	0.064	0.001	0.064
confIntGPS-methods	0.013	0.001	0.014
distribution-methods	0.088	0.017	0.104
fit-methods	1.365	0.007	1.375
generate-methods	0.021	0.001	0.022
get.tree.levels	0.017	0.001	0.018
gps-methods	0.013	0.001	0.014
hiv.data	0.019	0.004	0.024
kullback.leibler	0.013	0.000	0.014
likelihoods-methods	0.098	0.004	0.102
sim-methods	0.058	0.006	0.065
stability.sim	0.01	0.00	0.01