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Package 376/506HostnameOS / ArchBUILDCHECKBUILD BIN
predictionet 0.99.0
Benjamin Haibe-Kains , Catharina Olsen
Snapshot Date: 2011-10-16 18:22:53 -0700 (Sun, 16 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/predictionet
Last Changed Rev: 59264 / Revision: 59318
Last Changed Date: 2011-10-14 17:34:12 -0700 (Fri, 14 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  ERROR  skipped  skipped 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: predictionet
Version: 0.99.0
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch predictionet_0.99.0.tar.gz
StartedAt: 2011-10-17 05:05:19 -0700 (Mon, 17 Oct 2011)
EndedAt: 2011-10-17 05:07:33 -0700 (Mon, 17 Oct 2011)
EllapsedTime: 133.9 seconds
RetCode: 0
Status:  OK  
CheckDir: predictionet.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/predictionet.Rcheck'
* using R version 2.14.0 beta (2011-10-16 r57266)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'predictionet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'predictionet' version '0.99.0'
* 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 DESCRIPTION meta-information ... OK
* checking top-level 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 ... NOTE
File 'E:/biocbld/bbs-2.9-bioc/meat/predictionet.Rcheck/predictionet/libs/i386/predictionet.dll':
  Found '_assert', possibly from 'assert' (C)

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.  The detected symbols
are linked into the code but might come from libraries and not actually
be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
Warning: parse error in file 'predictionet.R':
1: unexpected input
5: ###################################################
6: % Benjamin Haibe-Kains
   ^
* 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

predictionet.Rcheck/00install.out:

* installing *source* package 'predictionet' ...
** libs
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c foo_mrmr.cpp -o foo_mrmr.o
foo_mrmr.cpp: In function 'double get_correlation(double*, int*, int, int, int)':
foo_mrmr.cpp:13:28: warning: comparison between signed and unsigned integer expressions
foo_mrmr.cpp:23:28: 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:50:27: warning: comparison between signed and unsigned integer expressions
foo_mrmr.cpp:51:28: warning: comparison between signed and unsigned integer expressions
foo_mrmr.cpp:57:27: warning: comparison between signed and unsigned integer expressions
foo_mrmr.cpp:59:30: warning: comparison between signed and unsigned integer expressions
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -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:58:28: warning: comparison between signed and unsigned integer expressions
mrnet_adapted.cpp:103:20: warning: comparison between signed and unsigned integer expressions
mrnet_adapted.cpp:131:28: warning: comparison between signed and unsigned integer expressions
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c mrnet_ensemble_standalone.cpp -o mrnet_ensemble_standalone.o
mrnet_ensemble_standalone.cpp: In function 'void remove_equiv_subtrees(tree<int>&, tree<double>&)':
mrnet_ensemble_standalone.cpp:24:26: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:42:28: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:60:30: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:65:30: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp: In function 'int verify_equivalentset_nparents(tree<int>&, tree<int>::pre_order_iterator, tree<int>::pre_order_iterator, tree<double>&, int)':
mrnet_ensemble_standalone.cpp:111:7: warning: unused variable 'found'
mrnet_ensemble_standalone.cpp: In function 'int verify_equivalentset(tree<int>&, tree<int>::pre_order_iterator, tree<int>::pre_order_iterator, int, int*, int*)':
mrnet_ensemble_standalone.cpp:283:6: warning: unused variable 'rootdepth'
mrnet_ensemble_standalone.cpp: In function 'void build_tree_int(tree<int>&, tree<int>::pre_order_iterator, tree<int>::pre_order_iterator, int*, int, int)':
mrnet_ensemble_standalone.cpp:304:6: 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:384:27: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:377:16: 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:414:27: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:417:28: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:426:26: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:433:26: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp: In function 'void bootstrap_tree(tree<int>&, tree<double>&, double*, int*, int, int, int)':
mrnet_ensemble_standalone.cpp:507:7: warning: unused variable 'cnt_back'
mrnet_ensemble_standalone.cpp:442:7: warning: unused variable 'nsub'
mrnet_ensemble_standalone.cpp: In function 'double mrnet_onegene(double*, int, int, int*, int, int)':
mrnet_ensemble_standalone.cpp:569:27: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:560:9: warning: unused variable 'max_val'
mrnet_ensemble_standalone.cpp: In function 'void mrmr_ensemble_one_gene(tree<int>&, tree<int>::pre_order_iterator, double*, int*, int, int, int, int, int, int, double)':
mrnet_ensemble_standalone.cpp:600:26: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:658:47: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:665:29: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:668:28: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:672:29: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:689:30: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:586:48: 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:760:27: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:799:27: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:813:26: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:822:27: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:777:13: warning: unused variable 'cnt2'
mrnet_ensemble_standalone.cpp:780:7: warning: unused variable 'rootdepth'
mrnet_ensemble_standalone.cpp:794:7: warning: unused variable 'ind'
mrnet_ensemble_standalone.cpp:722:30: warning: unused variable 'res_all'
mrnet_ensemble_standalone.cpp:722:39: warning: unused variable 'res_all2'
mrnet_ensemble_standalone.cpp:723:6: warning: unused variable 'vec_tmp'
mrnet_ensemble_standalone.cpp: In function 'void mrmr_ensemble_one_gene_remove(tree<int>&, tree<int>::pre_order_iterator, double*, int*, int, int, int, int, int, int, double)':
mrnet_ensemble_standalone.cpp:860:26: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:904:29: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:912:28: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:915:69: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:919:28: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:848:48: warning: unused variable 'tmp_val_max_ind'
mrnet_ensemble_standalone.cpp:848:66: warning: unused variable 'prev_sel_tmp'
mrnet_ensemble_standalone.cpp:849:21: 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:1029:27: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:1066:27: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:1080:26: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:1089:27: warning: comparison between signed and unsigned integer expressions
mrnet_ensemble_standalone.cpp:1046:13: warning: unused variable 'cnt2'
mrnet_ensemble_standalone.cpp:1049:7: warning: unused variable 'rootdepth'
mrnet_ensemble_standalone.cpp:1063:7: warning: unused variable 'ind'
mrnet_ensemble_standalone.cpp:992:30: warning: unused variable 'res_all'
mrnet_ensemble_standalone.cpp:992:39: warning: unused variable 'res_all2'
mrnet_ensemble_standalone.cpp:993:6: 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:726:7: warning: 'Rres' may be used uninitialized in this function
mrnet_ensemble_standalone.cpp:793:18: 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:996:7: warning: 'Rres' may be used uninitialized in this function
mrnet_ensemble_standalone.cpp:1062:18: warning: 'res_old' may be used uninitialized in this function
g++ -shared -s -static-libgcc -o predictionet.dll tmp.def foo_mrmr.o mrnet_adapted.o mrnet_ensemble_standalone.o -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-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 ...
*** tangling vignette sources ...
   'predictionet.Rnw' 
** testing if installed package can be loaded

* DONE (predictionet)

predictionet.Rcheck/predictionet-Ex.timings:

nameusersystemelapsed
adj.descent000
adj.remove.cycles0.020.000.01
data.discretize0.220.000.22
eval.network0.120.000.13
expO.colon.ras000
jorissen.colon.ras0.020.000.04
net2topo0.080.000.16
netinf 2.56 0.1015.53
netinf.cv 5.33 0.1757.39
netinf.predict0.090.000.09
netinf2gml0.440.000.49
pred.score000