predictionet 1.3.1
Benjamin Haibe-Kains , Catharina Olsen
| Snapshot Date: 2012-06-20 15:22:40 -0700 (Wed, 20 Jun 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/predictionet | | Last Changed Rev: 65534 / Revision: 66885 | | Last Changed Date: 2012-04-27 16:18:02 -0700 (Fri, 27 Apr 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | ERROR | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | N O T S U P P O R T E D |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | [ ERROR ] | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | ERROR | OK |
* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/predictionet.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* 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 '1.3.1'
* 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 ... NOTE
Non-standard license specification:
Artistic 2.0
Standardizable: TRUE
Standardized license specification:
Artistic-2.0
* 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 ... NOTE
.extract.adjacency.ensemble: warning in matrix(0, nc = ncol(data), nr =
ncol(data), dimnames = list(colnames(data), colnames(data))): partial
argument match of 'nr' to 'nrow'
.extract.adjacency.ensemble: warning in matrix(0, nc = ncol(data), nr =
ncol(data), dimnames = list(colnames(data), colnames(data))): partial
argument match of 'nc' to 'ncol'
.extract.all.parents: warning in matrix(0, nc = nsol, nr = (maxparents
+ 1)): partial argument match of 'nr' to 'nrow'
.extract.all.parents: warning in matrix(0, nc = nsol, nr = (maxparents
+ 1)): partial argument match of 'nc' to 'ncol'
.get.pairs: warning in matrix(0, nc = 2, nr = sum): partial argument
match of 'nr' to 'nrow'
.get.pairs: warning in matrix(0, nc = 2, nr = sum): partial argument
match of 'nc' to 'ncol'
.list2matrixens: warning in matrix(0, nc = length(myres$topology), nr =
length(myres$topology[[1]]), dimnames =
list(names(myres$topology[[1]]), names.target)): partial argument
match of 'nr' to 'nrow'
.list2matrixens: warning in matrix(0, nc = length(myres$topology), nr =
length(myres$topology[[1]]), dimnames =
list(names(myres$topology[[1]]), names.target)): partial argument
match of 'nc' to 'ncol'
.list2matrixens: warning in matrix(0, nc = length(myres$topology), nr =
length(myres$topology.coeff[[1]]), dimnames =
list(names(myres$topology.coeff[[1]]), names.target)): partial
argument match of 'nr' to 'nrow'
.list2matrixens: warning in matrix(0, nc = length(myres$topology), nr =
length(myres$topology.coeff[[1]]), dimnames =
list(names(myres$topology.coeff[[1]]), names.target)): partial
argument match of 'nc' to 'ncol'
.pred.onegene.regrnet.fs: warning in matrix(FALSE, nr = nrow(data), nc
= ncol(topo.coeff)): partial argument match of 'nr' to 'nrow'
.pred.onegene.regrnet.fs: warning in matrix(FALSE, nr = nrow(data), nc
= ncol(topo.coeff)): partial argument match of 'nc' to 'ncol'
.rank.genes.causal.ensemble: warning in matrix(Inf, nc = ncol(models),
nr = nrow(models)): partial argument match of 'nr' to 'nrow'
.rank.genes.causal.ensemble: warning in matrix(Inf, nc = ncol(models),
nr = nrow(models)): partial argument match of 'nc' to 'ncol'
.rank.genes.ensemble: warning in matrix(Inf, nc = ncol(models), nr =
nrow(models)): partial argument match of 'nr' to 'nrow'
.rank.genes.ensemble: warning in matrix(Inf, nc = ncol(models), nr =
nrow(models)): partial argument match of 'nc' to 'ncol'
.stab.cv2stab: warning in matrix(0, nc = length(tmp.names), nr =
nrow(topo), dimnames = list(rownames(topo), tmp.names)): partial
argument match of 'nr' to 'nrow'
.stab.cv2stab: warning in matrix(0, nc = length(tmp.names), nr =
nrow(topo), dimnames = list(rownames(topo), tmp.names)): partial
argument match of 'nc' to 'ncol'
.topo2stab: warning in matrix(0, nc = length(tmp.names), nr =
nrow(topo[[1]]), dimnames = list(rownames(topo[[1]]), tmp.names)):
partial argument match of 'nr' to 'nrow'
.topo2stab: warning in matrix(0, nc = length(tmp.names), nr =
nrow(topo[[1]]), dimnames = list(rownames(topo[[1]]), tmp.names)):
partial argument match of 'nc' to 'ncol'
mcc: warning in matrix(1, nc = nbcat, nr = nbcat): partial argument
match of 'nr' to 'nrow'
mcc: warning in matrix(1, nc = nbcat, nr = nbcat): partial argument
match of 'nc' to 'ncol'
pred.score: warning in matrix(0, nc = ncol(pred), nr = nrow(data),
dimnames = list(rownames(data), colnames(pred))): partial argument
match of 'nr' to 'nrow'
pred.score: warning in matrix(0, nc = ncol(pred), nr = nrow(data),
dimnames = list(rownames(data), colnames(pred))): partial argument
match of 'nc' to 'ncol'
* 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 '/Users/biocbuild/bbs-2.11-bioc/meat/predictionet.Rcheck/predictionet/libs/i386/predictionet.so':
Found '__ZSt4cout', possibly from 'std::cout' (C++)
Object: 'mrnet_ensemble_standalone.o'
Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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 ... ERROR
Running examples in 'predictionet-Ex.R' failed
The error most likely occurred in:
> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: netinf.cv
> ### Title: Function performing network inference by combining priors and
> ### genomic data
> ### Aliases: netinf.cv
> ### Keywords: graphs
>
> ### ** Examples
>
> ## load gene expression data for colon cancer data, list of genes related to RAS signaling pathway and the corresponding priors
> data(expO.colon.ras)
> ## create matrix of perturbations (no perturbations in this dataset)
> pert <- matrix(0, nrow=nrow(data.ras), ncol=ncol(data.ras), dimnames=dimnames(data.ras))
>
> ## number of genes to select for the analysis
> genen <- 10
> ## select only the top genes
> goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fold.change"])), decreasing=TRUE)[1:genen]]
> mydata <- data.ras[ , goi, drop=FALSE]
> myannot <- annot.ras[goi, , drop=FALSE]
> mypriors <- priors.ras[goi, goi, drop=FALSE]
> mydemo <- demo.ras
> mypert <- pert[ , goi, drop=FALSE]
>
> ########################
> ## regression-based network inference
> ########################
> ## number of fold for cross-validation
> res <- netinf.cv(data=mydata, categories=3, perturbations=mypert, priors=mypriors, priors.weight=0.5, method="regrnet", nfold=3, seed=54321)
>
> ## MCC for predictions in cross-validation
> print(res$prediction.score.cv)
$r2
FOS CCL20 PPBP HRAS DUSP1 GAS1 CXCL3
fold.1 0.5335351 0.5082363 0.00000000 0.02018532 0.0000000 0.2427078 0.5145974
fold.2 0.4771753 0.1865518 0.09129329 0.02783777 0.5833812 0.2915766 0.5014927
fold.3 0.5178571 0.0000000 0.10158726 0.14751513 0.0000000 0.3912777 0.2514120
IL13RA2 PTGS2 TFPI2
fold.1 0.3608951 0.4392476 0.0000000
fold.2 0.1834522 0.4960721 0.3867194
fold.3 0.3193965 0.2822637 0.3135704
$nrmse
FOS CCL20 PPBP HRAS DUSP1 GAS1 CXCL3
fold.1 0.1694785 0.1920147 Inf 1.545934 Inf 0.3669145 0.1949637
fold.2 0.2036071 0.4746500 0.6094423 1.303681 0.1744127 0.3597342 0.1948309
fold.3 0.1733124 Inf 0.6182272 0.506450 Inf 0.2762540 0.3488444
IL13RA2 PTGS2 TFPI2
fold.1 0.2899066 0.2063793 Inf
fold.2 0.4325765 0.1977033 0.2581543
fold.3 0.2924706 0.3154415 0.2981617
$mcc
FOS CCL20 PPBP HRAS DUSP1 GAS1 CXCL3
fold.1 0.7355625 0.7483319 0.5131898 0.5024938 0.4980132 0.6613108 0.7269849
fold.2 0.6995451 0.5909191 0.5747988 0.5012957 0.6714865 0.6510897 0.6579002
fold.3 0.6804252 0.4901607 0.5538250 0.5265658 0.5034288 0.5858961 0.6358583
IL13RA2 PTGS2 TFPI2
fold.1 0.6769016 0.6271571 0.4980130
fold.2 0.6136563 0.6888178 0.6597640
fold.3 0.5713158 0.6152310 0.6060594
>
> ## export network as a 'gml' file that you can import into Cytoscape
> rr <- netinf2gml(object=res, file=paste(tempdir(),"predictionet_regrnet",sep=""))
Error in edge.info[[i]][igraph::get.edges(graph = net.igraph, es = ee) + :
subscript out of bounds
Calls: netinf2gml
Execution halted
* installing *source* package 'predictionet' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/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: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
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
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_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)