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Package 416/554HostnameOS / ArchBUILDCHECKBUILD BIN
predictionet 1.2.0
Benjamin Haibe-Kains , Catharina Olsen
Snapshot Date: 2012-03-31 17:01:49 -0700 (Sat, 31 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/predictionet
Last Changed Rev: 64678 / Revision: 64719
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK  OK 
puck5 Linux (Ubuntu 12.04) / 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 

Summary

Package: predictionet
Version: 1.2.0
Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings predictionet_1.2.0.tar.gz
StartedAt: 2012-04-01 02:48:09 -0700 (Sun, 01 Apr 2012)
EndedAt: 2012-04-01 02:48:52 -0700 (Sun, 01 Apr 2012)
EllapsedTime: 43.1 seconds
RetCode: 0
Status:  OK 
CheckDir: predictionet.Rcheck
Warnings: 0

Command output

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/predictionet.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-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 '1.2.0'
* 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 ... 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/hpages/test-puck5/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 ... 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 4 notes.
See
  '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/predictionet.Rcheck/00check.log'
for details.

predictionet.Rcheck/00install.out:

* installing *source* package 'predictionet' ...
** libs
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c foo_mrmr.cpp -o foo_mrmr.o
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c mrnet_adapted.cpp -o mrnet_adapted.o
g++ -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c mrnet_ensemble_standalone.cpp -o mrnet_ensemble_standalone.o
g++ -shared -L/usr/local/lib -o predictionet.so foo_mrmr.o mrnet_adapted.o mrnet_ensemble_standalone.o -L/home/hpages/test-puck5/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/hpages/test-puck5/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)

predictionet.Rcheck/predictionet-Ex.timings:

nameusersystemelapsed
adj.descent0.0040.0000.002
adj.remove.cycles0.0440.0000.043
data.discretize0.2320.0080.248
eval.network0.1120.0000.120
expO.colon.ras0.0040.0000.010
jorissen.colon.ras0.0000.0000.009
net2topo0.1000.0080.113
netinf2.4360.0762.204
netinf.cv8.0880.1526.491
netinf.predict0.0760.0040.087
netinf2gml0.4200.0080.445
pred.score0.0080.0000.007