Package: nem

Version: 2.35.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch nem_2.35.1.tar.gz

StartedAt: 2013-03-24 08:08:02 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 08:10:12 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 129.7 seconds

RetCode: 0

Status:  OK

CheckDir: nem.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/nem.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'nem/DESCRIPTION' ... OK
* this is package 'nem' version '2.35.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking: 'doMC' 'Rglpk'
* 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 'nem' can be installed ... [9s/10s] 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 ... NOTE
get.insertions: warning in transitive.closure(Phinew, mat = TRUE, loop
  = TRUE): partial argument match of 'loop' to 'loops'
moduleNetwork: warning in transitive.closure(modeltotal, mat = TRUE,
  loop = TRUE): partial argument match of 'loop' to 'loops'
nem.calcSignificance : modify.rand: warning in
  transitive.closure(Phinew, mat = TRUE, loop = TRUE): partial argument
  match of 'loop' to 'loops'
sampleRndNetwork: warning in transitive.closure(S, mat = TRUE, loop =
  FALSE): partial argument match of 'loop' to 'loops'
nem.calcSignificance: no visible global function definition for
  'registerDoMC'
nem.calcSignificance: no visible global function definition for
  '%dopar%'
nem.calcSignificance: no visible global function definition for
  'foreach'
nem.featureselection: no visible global function definition for
  'registerDoMC'
nem.featureselection: no visible global function definition for
  '%dopar%'
nem.featureselection: no visible global function definition for
  'foreach'
nem.featureselection: no visible binding for global variable 'd'
nemModelSelection: no visible global function definition for
  'registerDoMC'
nemModelSelection: no visible global function definition for '%dopar%'
nemModelSelection: no visible global function definition for 'foreach'
nemModelSelection: no visible binding for global variable 'lam'
nemModelSelection: no visible binding for global variable 'r'
score.aux: no visible global function definition for 'registerDoMC'
score.aux: no visible global function definition for '%dopar%'
score.aux: no visible global function definition for 'foreach'
score.aux: no visible binding for global variable 'm'
transitive.reduction : solve.problem: no visible global function
  definition for 'Rglpk_solve_LP'
* 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 use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [14s/15s] 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

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/nem.Rcheck/00check.log'
for details.

* installing *source* package 'nem' ...
** 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  -c MCMC.c -o MCMC.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  -c netlearn.c -o netlearn.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  -c wrapper.c -o wrapper.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 -o nem.so MCMC.o netlearn.o wrapper.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/nem.Rcheck/nem/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'nem.Rnw' using 'latin1' 
** testing if installed package can be loaded
* DONE (nem)

name	user	system	elapsed
BFSlevel	0.007	0.001	0.007
BoutrosRNAi2002	0.167	0.005	0.171
Ivanova2006RNAiTimeSeries	0.018	0.002	0.020
NiederbergerMediator2012	0.042	0.003	0.044
SCCgraph	0.500	0.033	0.533
SahinRNAi2008	0.024	0.002	0.026
enumerate.models	0.029	0.001	0.030
generateNetwork	0.477	0.048	0.744
infer.edge.type	0.276	0.018	0.298
local.model.prior	0.009	0.001	0.009
nem	4.588	0.073	4.778
nem.bootstrap	0.018	0.001	0.019
nem.calcSignificance	0.006	0.006	0.012
nem.consensus	0.005	0.004	0.012
nem.cont.preprocess	0.253	0.019	0.278
nem.discretize	0.068	0.014	0.086
nem.jackknife	0.007	0.002	0.009
nemModelSelection	0.612	0.019	0.681
network.AIC	0.316	0.013	0.340
plotEffects	0.252	0.012	0.305
prior.EgeneAttach.EB	0.528	0.011	0.606
prune.graph	0.123	0.013	0.150
quicknem	0.014	0.006	0.020
selectEGenes	0.841	0.016	0.861
set.default.parameters	0.009	0.000	0.010
sim.intervention	0.336	0.009	0.346
subsets	0.014	0.005	0.019
transitive.closure	0.071	0.007	0.093
transitive.reduction	0.082	0.008	0.095