BioC 2.13: CHECK report for predictionet on perceval

Package: predictionet

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch predictionet_1.8.0.tar.gz

StartedAt: 2014-04-05 03:29:56 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:31:18 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 82.3 seconds

RetCode: 0

Status:  OK

CheckDir: predictionet.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/predictionet.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 ‘predictionet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘predictionet’ 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘predictionet’ can be installed ... [10s/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
Packages in Depends field not imported from:
  ‘catnet’ ‘igraph’
  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 for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ...sh: line 1: 98831 Abort trap              '/Library/Frameworks/R.framework/Resources/bin/qpdf' --stream-data=compress --object-streams=generate /tmp/RtmpzTRkvl/pdf17934461c70f/predictionet-cytoscape.pdf /tmp/RtmpzTRkvl/pdf179342f53ac08 > /dev/null 2> /dev/null
sh: line 1: 98863 Abort trap              '/Library/Frameworks/R.framework/Resources/bin/qpdf' --stream-data=compress --object-streams=generate /tmp/RtmpzTRkvl/pdf17934461c70f/predictionet-pn_webapp_ras.pdf /tmp/RtmpzTRkvl/pdf179342f53ac08 > /dev/null 2> /dev/null
 OK
* checking installed files from ‘inst/doc’ ... NOTE
The following files should probably not be installed:
  ‘Makefile’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘predictionet.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [6s/7s] 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 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/predictionet.Rcheck/00check.log’
for details.

* installing *source* package ‘predictionet’ ...
** 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 -Wall  -c foo_mrmr.cpp -o foo_mrmr.o
foo_mrmr.cpp: In function ‘double get_correlation(double*, int*, int, int, int)’:
foo_mrmr.cpp:13: warning: comparison between signed and unsigned integer expressions
foo_mrmr.cpp:23: warning: comparison between signed and unsigned integer expressions
foo_mrmr.cpp: In function ‘void build_mim_subset(double*, double*, int*, int, int, int*, int)’:
foo_mrmr.cpp:50: warning: comparison between signed and unsigned integer expressions
foo_mrmr.cpp:51: warning: comparison between signed and unsigned integer expressions
foo_mrmr.cpp:57: warning: comparison between signed and unsigned integer expressions
foo_mrmr.cpp:59: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c mrnet_adapted.cpp -o mrnet_adapted.o
mrnet_adapted.cpp: In function ‘SEXPREC* mrnet_adapted(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
mrnet_adapted.cpp:58: warning: comparison between signed and unsigned integer expressions
mrnet_adapted.cpp:103: warning: comparison between signed and unsigned integer expressions
mrnet_adapted.cpp:131: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c mrnet_adapted2.cpp -o mrnet_adapted2.o
mrnet_adapted2.cpp: In function ‘SEXPREC* mrnet_adapted2(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
mrnet_adapted2.cpp:62: warning: comparison between signed and unsigned integer expressions
mrnet_adapted2.cpp:121: warning: comparison between signed and unsigned integer expressions
mrnet_adapted2.cpp:185: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c mrnet_ensemble_standalone.cpp -o mrnet_ensemble_standalone.o
mrnet_ensemble_standalone.cpp: In function ‘void remove_equiv_subtrees(tree<int, std::allocator<tree_node_<int> > >&, tree<double, std::allocator<tree_node_<double> > >&)’:
mrnet_ensemble_standalone.cpp:24: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:42: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:47: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:60: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:65: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp: In function ‘int verify_equivalentset_nparents(tree<int, std::allocator<tree_node_<int> > >&, tree<int, std::allocator<tree_node_<int> > >::pre_order_iterator, tree<int, std::allocator<tree_node_<int> > >::pre_order_iterator, tree<double, std::allocator<tree_node_<double> > >&, int)’:
mrnet_ensemble_standalone.cpp:111: warning: unused variable ‘found’
mrnet_ensemble_standalone.cpp: In function ‘int verify_equivalentset(tree<int, std::allocator<tree_node_<int> > >&, tree<int, std::allocator<tree_node_<int> > >::pre_order_iterator, tree<int, std::allocator<tree_node_<int> > >::pre_order_iterator, int, int*, int*)’:
mrnet_ensemble_standalone.cpp:283: warning: unused variable ‘rootdepth’
mrnet_ensemble_standalone.cpp: In function ‘void build_tree_int(tree<int, std::allocator<tree_node_<int> > >&, tree<int, std::allocator<tree_node_<int> > >::pre_order_iterator, tree<int, std::allocator<tree_node_<int> > >::pre_order_iterator, int*, int, int)’:
mrnet_ensemble_standalone.cpp:304: warning: unused variable ‘rootdepth’
mrnet_ensemble_standalone.cpp: In function ‘void bootstrap_mrmr_fix(double&, double&, double*, int*, int, int, int, int, int, int, int, int*)’:
mrnet_ensemble_standalone.cpp:384: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:377: warning: unused variable ‘boot_val’
mrnet_ensemble_standalone.cpp: In function ‘void bootstrap_mrmr(double&, double&, double*, int*, int, int, int, int, int, int, int, int*)’:
mrnet_ensemble_standalone.cpp:414: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:417: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:426: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:433: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp: In function ‘void bootstrap_tree(tree<int, std::allocator<tree_node_<int> > >&, tree<double, std::allocator<tree_node_<double> > >&, double*, int*, int, int, int)’:
mrnet_ensemble_standalone.cpp:507: warning: unused variable ‘cnt_back’
mrnet_ensemble_standalone.cpp:442: warning: unused variable ‘nsub’
mrnet_ensemble_standalone.cpp: In function ‘double mrnet_onegene(double*, int, int, int*, int, int)’:
mrnet_ensemble_standalone.cpp:569: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:560: warning: unused variable ‘max_val’
mrnet_ensemble_standalone.cpp: In function ‘void mrmr_ensemble_one_gene(tree<int, std::allocator<tree_node_<int> > >&, tree<int, std::allocator<tree_node_<int> > >::pre_order_iterator, double*, int*, int, int, int, int, int, int, double)’:
mrnet_ensemble_standalone.cpp:600: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:658: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:665: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:668: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:672: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:677: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:689: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:586: warning: unused variable ‘nprev_sel’
mrnet_ensemble_standalone.cpp: In function ‘SEXPREC* mrmr_ensemble(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
mrnet_ensemble_standalone.cpp:760: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:799: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:813: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:819: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:822: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:777: warning: unused variable ‘cnt2’
mrnet_ensemble_standalone.cpp:780: warning: unused variable ‘rootdepth’
mrnet_ensemble_standalone.cpp:794: warning: unused variable ‘ind’
mrnet_ensemble_standalone.cpp:722: warning: unused variable ‘res_all’
mrnet_ensemble_standalone.cpp:722: warning: unused variable ‘res_all2’
mrnet_ensemble_standalone.cpp:723: warning: unused variable ‘vec_tmp’
mrnet_ensemble_standalone.cpp: In function ‘void mrmr_ensemble_one_gene_remove(tree<int, std::allocator<tree_node_<int> > >&, tree<int, std::allocator<tree_node_<int> > >::pre_order_iterator, double*, int*, int, int, int, int, int, int, double)’:
mrnet_ensemble_standalone.cpp:860: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:904: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:912: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:915: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:919: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:848: warning: unused variable ‘tmp_val_max_ind’
mrnet_ensemble_standalone.cpp:848: warning: unused variable ‘prev_sel_tmp’
mrnet_ensemble_standalone.cpp:849: warning: unused variable ‘vec_sort’
mrnet_ensemble_standalone.cpp: In function ‘SEXPREC* mrmr_ensemble_remove(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
mrnet_ensemble_standalone.cpp:1029: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:1066: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:1080: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:1085: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:1089: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:1046: warning: unused variable ‘cnt2’
mrnet_ensemble_standalone.cpp:1049: warning: unused variable ‘rootdepth’
mrnet_ensemble_standalone.cpp:1063: warning: unused variable ‘ind’
mrnet_ensemble_standalone.cpp:992: warning: unused variable ‘res_all’
mrnet_ensemble_standalone.cpp:992: warning: unused variable ‘res_all2’
mrnet_ensemble_standalone.cpp:993: warning: unused variable ‘vec_tmp’
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 predictionet.so foo_mrmr.o mrnet_adapted.o mrnet_adapted2.o mrnet_ensemble_standalone.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.13-bioc/meat/predictionet.Rcheck/predictionet/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (predictionet)

name	user	system	elapsed
adj.get.hops	0.027	0.001	0.029
adj.remove.cycles	0.010	0.001	0.011
data.discretize	0.538	0.017	0.558
expO.colon.ras	0.008	0.001	0.010
jorissen.colon.ras	0.010	0.000	0.012
net2pred	0.349	0.009	0.359
netinf	0.344	0.015	0.370
netinf.cv	0.596	0.020	0.623
netinf.predict	0.117	0.009	0.127
netinf2gml	0.524	0.014	0.561
pred.score	0.018	0.002	0.030
predictionet.press.statistic	0.431	0.018	0.484
predictionet.stability.cv	0.703	0.013	0.726