predictionet 1.2.2
Benjamin Haibe-Kains , Catharina Olsen
| Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/predictionet | | Last Changed Rev: 69073 / Revision: 69725 | | Last Changed Date: 2012-09-05 10:37:09 -0700 (Wed, 05 Sep 2012) |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | N O T S U P P O R T E D |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/predictionet.Rcheck’
* using R version 2.15.1 (2012-06-22)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.2.2’
* 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 ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/predictionet.Rcheck/predictionet/libs/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 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 ... 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
NOTE: There were 5 notes.
See
‘/loc/home/biocbuild/bbs-2.10-bioc/meat/predictionet.Rcheck/00check.log’
for details.
* installing *source* package ‘predictionet’ ...
** libs
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -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:13:28: 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/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -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:58:28: 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/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -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>&, 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: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
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
g++ -shared -L/usr/local/lib64 -o predictionet.so foo_mrmr.o mrnet_adapted.o mrnet_ensemble_standalone.o -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-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
‘predictionet.Rnw’
** testing if installed package can be loaded
* DONE (predictionet)