BioC 2.12: CHECK report for nem on petty

Package: nem

Version: 2.36.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch nem_2.36.0.tar.gz

StartedAt: 2013-10-08 23:15:28 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:18:24 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 176.3 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 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'nem/DESCRIPTION' ... OK
* this is package 'nem' version '2.36.0'
* 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 ... [11s/12s] 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 sizes of PDF files under 'inst/doc' ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'markowetz-thesis-2006.pdf' from 1155Kb to 844Kb
  consider running tools::compactPDF() on these files
* checking installed files from 'inst/doc' ... OK
* checking examples ... [17s/19s] OK
Examples with CPU or elapsed time > 5s
     user system elapsed
nem 5.676  0.084   6.449
* 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 3 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 -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
** testing if installed package can be loaded
* DONE (nem)

name	user	system	elapsed
BFSlevel	0.005	0.001	0.006
BoutrosRNAi2002	0.168	0.006	0.174
Ivanova2006RNAiTimeSeries	0.020	0.001	0.021
NiederbergerMediator2012	0.036	0.002	0.039
SCCgraph	0.600	0.028	0.666
SahinRNAi2008	0.025	0.001	0.028
enumerate.models	0.021	0.002	0.028
generateNetwork	0.630	0.032	0.797
infer.edge.type	0.375	0.011	0.394
local.model.prior	0.018	0.001	0.019
nem	5.676	0.084	6.449
nem.bootstrap	0.005	0.001	0.006
nem.calcSignificance	0.009	0.001	0.012
nem.consensus	0.009	0.001	0.011
nem.cont.preprocess	0.444	0.009	0.462
nem.discretize	0.176	0.007	0.186
nem.jackknife	0.006	0.002	0.008
nemModelSelection	0.812	0.018	0.896
network.AIC	0.388	0.009	0.401
plotEffects	0.328	0.011	0.417
prior.EgeneAttach.EB	0.629	0.011	0.646
prune.graph	0.164	0.005	0.190
quicknem	0.146	0.006	0.153
selectEGenes	0.960	0.025	1.017
set.default.parameters	0.006	0.003	0.009
sim.intervention	0.266	0.009	0.277
subsets	0.005	0.002	0.007
transitive.closure	0.109	0.006	0.121
transitive.reduction	0.096	0.006	0.114