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Package 456/609HostnameOS / ArchBUILDCHECKBUILD BIN
predictionet 1.4.0
Benjamin Haibe-Kains , Catharina Olsen
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/predictionet
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 N O T   S U P P O R T E D
perceval Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: predictionet
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch predictionet_1.4.0.tar.gz
StartedAt: 2013-03-25 00:53:32 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 00:54:36 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 63.8 seconds
RetCode: 0
Status:  OK 
CheckDir: predictionet.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/predictionet.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'predictionet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'predictionet' version '1.4.0'
* 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 whether package 'predictionet' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 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' ... 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 examples ... 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 was 1 note.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/predictionet.Rcheck/00check.log'
for details.

predictionet.Rcheck/00install.out:

* installing *source* package 'predictionet' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -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
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -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
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -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
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -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'
mrnet_ensemble_standalone.cpp: In function 'SEXPREC* mrmr_ensemble(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
mrnet_ensemble_standalone.cpp:726: warning: 'Rres' may be used uninitialized in this function
mrnet_ensemble_standalone.cpp:793: warning: 'res_old' may be used uninitialized in this function
mrnet_ensemble_standalone.cpp: In function 'SEXPREC* mrmr_ensemble_remove(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
mrnet_ensemble_standalone.cpp:1062: warning: 'res_old' may be used uninitialized in this function
mrnet_ensemble_standalone.cpp:996: warning: 'Rres' may be used uninitialized in this function
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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-2.11-bioc/meat/predictionet.Rcheck/predictionet/libs/i386
** R
** data
**  moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'predictionet.Rnw' 
** testing if installed package can be loaded

* DONE (predictionet)

predictionet.Rcheck/predictionet-Ex.timings:

nameusersystemelapsed
adj.get.hops0.0260.0020.029
adj.remove.cycles0.0010.0000.002
data.discretize0.3140.0200.342
expO.colon.ras0.0010.0010.010
jorissen.colon.ras0.0010.0010.001
net2pred0.1640.0170.196
netinf0.1950.0250.245
netinf.cv0.4220.0180.442
netinf.predict0.0840.0100.095
netinf2gml0.3460.0110.358
pred.score0.0060.0000.006
predictionet.press.statistic0.4270.0170.451
predictionet.stability.cv0.4290.0130.443