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BioC 2.12: CHECK report for predictionet on george2

This page was generated on 2013-10-09 09:37:49 -0700 (Wed, 09 Oct 2013).

Package 497/671HostnameOS / ArchBUILDCHECKBUILD BIN
predictionet 1.6.1
Benjamin Haibe-Kains , Catharina Olsen
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/predictionet
Last Changed Rev: 81065 / Revision: 81334
Last Changed Date: 2013-10-02 08:44:00 -0700 (Wed, 02 Oct 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / 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 Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: predictionet
Version: 1.6.1
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings predictionet_1.6.1.tar.gz
StartedAt: 2013-10-09 04:09:40 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 04:11:04 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 84.1 seconds
RetCode: 0
Status:  OK 
CheckDir: predictionet.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/predictionet.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.6.1’
* 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 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 ... [12s/12s] OK
* checking installed package size ... OK
* checking package 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 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 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 ... [7s/8s] 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 were 2 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/predictionet.Rcheck/00check.log’
for details.

predictionet.Rcheck/00install.out:

* installing *source* package ‘predictionet’ ...
** libs
g++ -I/home/biocbuild/bbs-2.12-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 [-Wsign-compare]
foo_mrmr.cpp:23:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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 [-Wsign-compare]
foo_mrmr.cpp:51:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr.cpp:57:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr.cpp:59:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -I/home/biocbuild/bbs-2.12-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(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mrnet_adapted.cpp:58:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mrnet_adapted.cpp:103:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mrnet_adapted.cpp:131:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c mrnet_adapted2.cpp -o mrnet_adapted2.o
mrnet_adapted2.cpp: In function ‘SEXPREC* mrnet_adapted2(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mrnet_adapted2.cpp:62:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mrnet_adapted2.cpp:121:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mrnet_adapted2.cpp:185:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -I/home/biocbuild/bbs-2.12-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 [-Wsign-compare]
mrnet_ensemble_standalone.cpp:42:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mrnet_ensemble_standalone.cpp:60:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mrnet_ensemble_standalone.cpp:65:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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’ [-Wunused-variable]
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:223:6: warning: variable ‘to_remove’ set but not used [-Wunused-but-set-variable]
mrnet_ensemble_standalone.cpp:283:6: warning: unused variable ‘rootdepth’ [-Wunused-variable]
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’ [-Wunused-variable]
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 [-Wsign-compare]
mrnet_ensemble_standalone.cpp:377:16: warning: unused variable ‘boot_val’ [-Wunused-variable]
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 [-Wsign-compare]
mrnet_ensemble_standalone.cpp:417:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mrnet_ensemble_standalone.cpp:426:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mrnet_ensemble_standalone.cpp:433:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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’ [-Wunused-variable]
mrnet_ensemble_standalone.cpp:442:7: warning: unused variable ‘nsub’ [-Wunused-variable]
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 [-Wsign-compare]
mrnet_ensemble_standalone.cpp:558:15: warning: variable ‘jmax’ set but not used [-Wunused-but-set-variable]
mrnet_ensemble_standalone.cpp:560:9: warning: unused variable ‘max_val’ [-Wunused-variable]
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 [-Wsign-compare]
mrnet_ensemble_standalone.cpp:658:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mrnet_ensemble_standalone.cpp:665:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mrnet_ensemble_standalone.cpp:668:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mrnet_ensemble_standalone.cpp:672:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mrnet_ensemble_standalone.cpp:689:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mrnet_ensemble_standalone.cpp:586:48: warning: unused variable ‘nprev_sel’ [-Wunused-variable]
mrnet_ensemble_standalone.cpp:587:10: warning: variable ‘res_vec’ set but not used [-Wunused-but-set-variable]
mrnet_ensemble_standalone.cpp: In function ‘SEXPREC* mrmr_ensemble(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mrnet_ensemble_standalone.cpp:760:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mrnet_ensemble_standalone.cpp:799:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mrnet_ensemble_standalone.cpp:813:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mrnet_ensemble_standalone.cpp:822:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mrnet_ensemble_standalone.cpp:777:13: warning: unused variable ‘cnt2’ [-Wunused-variable]
mrnet_ensemble_standalone.cpp:780:7: warning: unused variable ‘rootdepth’ [-Wunused-variable]
mrnet_ensemble_standalone.cpp:794:7: warning: unused variable ‘ind’ [-Wunused-variable]
mrnet_ensemble_standalone.cpp:722:30: warning: unused variable ‘res_all’ [-Wunused-variable]
mrnet_ensemble_standalone.cpp:722:39: warning: unused variable ‘res_all2’ [-Wunused-variable]
mrnet_ensemble_standalone.cpp:723:6: warning: unused variable ‘vec_tmp’ [-Wunused-variable]
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 [-Wsign-compare]
mrnet_ensemble_standalone.cpp:904:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mrnet_ensemble_standalone.cpp:912:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mrnet_ensemble_standalone.cpp:915:69: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mrnet_ensemble_standalone.cpp:919:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mrnet_ensemble_standalone.cpp:848:48: warning: unused variable ‘tmp_val_max_ind’ [-Wunused-variable]
mrnet_ensemble_standalone.cpp:848:66: warning: unused variable ‘prev_sel_tmp’ [-Wunused-variable]
mrnet_ensemble_standalone.cpp:849:21: warning: unused variable ‘vec_sort’ [-Wunused-variable]
mrnet_ensemble_standalone.cpp:849:63: warning: variable ‘vec_local_max_sd’ set but not used [-Wunused-but-set-variable]
mrnet_ensemble_standalone.cpp: In function ‘SEXPREC* mrmr_ensemble_remove(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mrnet_ensemble_standalone.cpp:1029:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mrnet_ensemble_standalone.cpp:1066:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mrnet_ensemble_standalone.cpp:1080:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mrnet_ensemble_standalone.cpp:1089:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
mrnet_ensemble_standalone.cpp:1046:13: warning: unused variable ‘cnt2’ [-Wunused-variable]
mrnet_ensemble_standalone.cpp:1049:7: warning: unused variable ‘rootdepth’ [-Wunused-variable]
mrnet_ensemble_standalone.cpp:1063:7: warning: unused variable ‘ind’ [-Wunused-variable]
mrnet_ensemble_standalone.cpp:992:30: warning: unused variable ‘res_all’ [-Wunused-variable]
mrnet_ensemble_standalone.cpp:992:39: warning: unused variable ‘res_all2’ [-Wunused-variable]
mrnet_ensemble_standalone.cpp:993:6: warning: unused variable ‘vec_tmp’ [-Wunused-variable]
mrnet_ensemble_standalone.cpp: In function ‘SEXPREC* mrmr_ensemble(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mrnet_ensemble_standalone.cpp:840:9: warning: ‘Rres’ may be used uninitialized in this function [-Wuninitialized]
mrnet_ensemble_standalone.cpp:800:25: warning: ‘res_old’ may be used uninitialized in this function [-Wuninitialized]
mrnet_ensemble_standalone.cpp: In function ‘SEXPREC* mrmr_ensemble_remove(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mrnet_ensemble_standalone.cpp:1105:9: warning: ‘Rres’ may be used uninitialized in this function [-Wuninitialized]
mrnet_ensemble_standalone.cpp:1067:25: warning: ‘res_old’ may be used uninitialized in this function [-Wuninitialized]
g++ -shared -L/usr/local/lib -o predictionet.so foo_mrmr.o mrnet_adapted.o mrnet_adapted2.o mrnet_ensemble_standalone.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-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)

predictionet.Rcheck/predictionet-Ex.timings:

nameusersystemelapsed
adj.get.hops0.0360.0080.052
adj.remove.cycles0.0120.0040.015
data.discretize0.5520.0000.591
expO.colon.ras0.0120.0000.013
jorissen.colon.ras0.0120.0000.014
net2pred0.2080.0040.213
netinf0.2360.0080.257
netinf.cv0.8000.0200.922
netinf.predict0.1720.0000.176
netinf2gml0.5200.0040.524
pred.score0.0480.0000.048
predictionet.press.statistic0.5320.0120.548
predictionet.stability.cv0.7680.0080.911