CRAN Package Check Results for Package penalizedSVM

Last updated on 2014-07-28 15:49:23.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1 0.98 24.81 25.80 NOTE
r-devel-linux-x86_64-debian-gcc 1.1 1.26 25.28 26.54 NOTE
r-devel-linux-x86_64-fedora-clang 1.1 54.46 NOTE
r-devel-linux-x86_64-fedora-gcc 1.1 48.53 NOTE
r-devel-osx-x86_64-clang 1.1 47.64 NOTE
r-devel-windows-ix86+x86_64 1.1 5.00 37.00 42.00 NOTE
r-patched-linux-x86_64 1.1 0.96 24.02 24.98 NOTE
r-patched-solaris-sparc 1.1 312.10 NOTE
r-patched-solaris-x86 1.1 61.90 NOTE
r-release-linux-ix86 1.1 1.52 32.76 34.28 NOTE
r-release-linux-x86_64 1.1 1.01 24.59 25.60 NOTE
r-release-osx-x86_64-mavericks 1.1 NOTE
r-release-osx-x86_64-snowleopard 1.1 NOTE
r-release-windows-ix86+x86_64 1.1 5.00 40.00 45.00 NOTE
r-oldrel-windows-ix86+x86_64 1.1 6.00 38.00 44.00 NOTE

Check Details

Version: 1.1
Check: package dependencies
Result: NOTE
    Depends: includes the non-default packages:
     e1071 MASS corpcor statmod tgp mlegp lhs
    Adding so many packages to the search path is excessive and importing
    selectively is preferable.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64

Version: 1.1
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls to packages already attached by Depends:
     MASS corpcor e1071 lhs mlegp statmod tgp
     Please remove these calls from your code.
    See the information on DESCRIPTION files in the chapter Creating R
    packages of the Writing R Extensions manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.1
Check: R code for possible problems
Result: NOTE
    .replaceinf: no visible global function definition for fcn_values<-
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.1
Check: Rd \usage sections
Result: NOTE
    S3 methods shown with full name in documentation object 'print':
     print.scad.svm print.1norm.svm
    
    The \usage entries for S3 methods should use the \method markup and not
    their full name.
    See the chapter Writing R documentation files in the Writing R
    Extensions manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.1
Check: Rd line widths
Result: NOTE
    Rd file 'EPSGO.Rd':
     \examples lines wider than 100 characters:
     # computation intensive; for demostration reasons only for the first 100 features
     system.time(fit<-EPSGO(Q.func, bounds=bounds, parms.coding="log2", fminlower=0,
     show='none', N=21, maxevals=500,
     pdf.name=NULL, seed=seed,
     # Q.func specific parameters:
     x.svm=t(train$x)[,1:100], y.svm=train$y, inner.val.method="cv" ... [TRUNCATED]
     cross.inner=5, maxIter=10 ))
     print(paste("minimal 5-fold cv error:", fit$fmin, "by log2(lambda1)=", fit$xmin))
    
    Rd file 'predict.Rd':
     \examples lines wider than 100 characters:
     # cross.outer= 0, grid.search = "discrete",
     # lambda1.set=lambda1.1norm, show="none",
     # parms.coding = "none",
     # maxIter = 700, inner.val.method = "cv", cross.inner= 5,
     # seed=seed, verbose=FALSE )
    
    Rd file 'svm.fs.Rd':
     \usage lines wider than 90 characters:
     # chose the search method for tuning lambda1,2: 'interval' or 'discrete'
     # method for the inner validation: cross validation, gacv
     \examples lines wider than 100 characters:
     system.time(scad.fix<- svm.fs(t(train$x)[,1:100], y=train$y, fs.method="scad",
     cross.outer= 0, grid.search = "discrete ... [TRUNCATED]
     lambda1.set=lambda1.scad,
     parms.coding = "none", show="none",
     maxIter = 10, inner.val.method = "cv", ... [TRUNCATED]
     seed=seed, verbose=FALSE) )
     #epsi.set<-vector(); for (num in (1:9)) epsi.set<-sort(c(epsi.set, c(num*10^seq(-5, -1, 1 ))) )
     # cross.outer= 0, grid.search = "discrete ... [TRUNCATED]
     # lambda1.set=lambda1.1norm,
     # parms.coding = "none", show="none",
     # maxIter = 700, inner.val.method = "cv", ... [TRUNCATED]
     # seed=seed, verbose=FALSE )
     system.time( scad<- svm.fs(t(train$x)[,1:100], y=train$y, fs.method="scad", bounds=bounds,
     cross.outer= 0, grid.search = "interval ... [TRUNCATED]
     inner.val.method = "cv", cross.inner= 5 ... [TRUNCATED]
     seed=seed, parms.coding = "log2", show ... [TRUNCATED]
    
    These lines will be truncated in the PDF manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc