CRAN Package Check Results for Package rexpokit

Last updated on 2017-02-22 07:48:38.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.24.1 10.53 18.58 29.12 WARN
r-devel-linux-x86_64-debian-gcc 0.24.1 9.01 18.80 27.80 WARN
r-devel-linux-x86_64-fedora-clang 0.24.1 49.11 WARN --no-stop-on-test-error
r-devel-linux-x86_64-fedora-gcc 0.24.1 47.66 WARN --no-stop-on-test-error
r-devel-macos-x86_64-clang 0.24.1 41.16 WARN --no-stop-on-test-error
r-devel-windows-ix86+x86_64 0.24.1 55.00 111.00 166.00 ERROR
r-patched-linux-x86_64 0.24.1 7.99 15.65 23.64 NOTE
r-patched-solaris-sparc 0.24.1 255.70 WARN
r-patched-solaris-x86 0.24.1 54.00 WARN
r-release-linux-x86_64 0.24.1 8.21 15.79 23.99 NOTE
r-release-osx-x86_64-mavericks 0.24.1 NOTE
r-release-windows-ix86+x86_64 0.24.1 74.00 81.00 155.00 NOTE
r-oldrel-windows-ix86+x86_64 0.24.1 65.00 70.00 135.00 NOTE

Check Details

Version: 0.24.1
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Warning: GNU Extension: Non-default type object or sequence zz in EQUIVALENCE statement at (1) with objects of different type
     Warning: GNU Extension: Nonstandard type declaration REAL*4 at (1)
     Warning: GNU Extension: Symbol ‘n’ is used before it is typed at (1)
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64

Version: 0.24.1
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘SparseM’ which was already attached by Depends.
     Please remove these calls from your code.
    Packages in Depends field not imported from:
     ‘Rcpp’ ‘SparseM’ ‘methods’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.24.1
Check: R code for possible problems
Result: NOTE
    fermat.test: no visible global function definition for ‘runif’
    mat2coo: no visible global function definition for ‘as.matrix.coo’
    Undefined global functions or variables:
     as.matrix.coo runif
    Consider adding
     importFrom("stats", "runif")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64

Version: 0.24.1
Check: compiled code
Result: NOTE
    File ‘rexpokit/libs/rexpokit.so’:
     Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
    
    It is good practice to register native routines and to disable symbol
    search.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 0.24.1
Flags: --no-stop-on-test-error
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Warning: GNU Extension: Non-default type object or sequence zz in EQUIVALENCE statement at (1) with objects of different type
     Warning: GNU Extension: Nonstandard type declaration REAL*4 at (1)
     Warning: GNU Extension: Symbol ‘n’ is used before it is typed at (1)
     Warning: iteration 7 invokes undefined behavior [-Waggressive-loop-optimizations]
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.24.1
Flags: --no-stop-on-test-error
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘SparseM’ which was already attached by Depends.
     Please remove these calls from your code.
    Packages in Depends field not imported from:
     ‘Rcpp’ ‘SparseM’ ‘methods’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-x86_64-clang

Version: 0.24.1
Flags: --no-stop-on-test-error
Check: R code for possible problems
Result: NOTE
    fermat.test: no visible global function definition for ‘runif’
    mat2coo: no visible global function definition for ‘as.matrix.coo’
    Undefined global functions or variables:
     as.matrix.coo runif
    Consider adding
     importFrom("stats", "runif")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-x86_64-clang

Version: 0.24.1
Flags: --no-stop-on-test-error
Check: compiled code
Result: NOTE
    File ‘rexpokit/libs/rexpokit.so’:
     Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
    
    It is good practice to register native routines and to disable symbol
    search.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-x86_64-clang

Version: 0.24.1
Flags: --no-stop-on-test-error
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Warning: GNU Extension: Non-default type object or sequence zz in EQUIVALENCE statement at (1) with objects of different type
     Warning: GNU Extension: Nonstandard type declaration REAL*4 at (1)
     Warning: iteration 7 invokes undefined behavior [-Waggressive-loop-optimizations]
     Warning: GNU Extension: Symbol ‘n’ is used before it is typed at (1)
Flavors: r-devel-linux-x86_64-fedora-gcc, r-devel-macos-x86_64-clang

Version: 0.24.1
Check: running examples for arch ‘i386’
Result: ERROR
    Running examples in 'rexpokit-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: expokit_dgexpv_Qmat
    > ### Title: EXPOKIT dgexpv matrix exponentiation on Q matrix
    > ### Aliases: expokit_dgexpv_Qmat
    >
    > ### ** Examples
    >
    > # Example:
    > # Make a square instantaneous rate matrix (Q matrix)
    > # This matrix is taken from Peter Foster's (2001) "The Idiot's Guide
    > # to the Zen of Likelihood in a Nutshell in Seven Days for Dummies,
    > # Unleashed" at:
    > # \url{http://www.bioinf.org/molsys/data/idiots.pdf}
    > #
    > # The Q matrix includes the stationary base freqencies, which Pmat
    > # converges to as t becomes large.
    > Qmat = matrix(c(-1.218, 0.504, 0.336, 0.378, 0.126, -0.882, 0.252, 0.504, 0.168,
    + 0.504, -1.05, 0.378, 0.126, 0.672, 0.252, -1.05), nrow=4, byrow=TRUE)
    >
    > # Make a series of t values
    > tvals = c(0.001, 0.005, 0.01, 0.05, 0.1, 0.5, 1, 2, 5, 14)
    >
    > # Exponentiate each with EXPOKIT's dgexpv (should be fast for large sparse matrices)
    > for (t in tvals)
    + {
    + Pmat = expokit_dgexpv_Qmat(Qmat=Qmat, t=t, transpose_needed=TRUE)
    + cat("\n\nTime=", t, "\n", sep="")
    + print(Pmat)
    + }
    At line 425 of file blas_mod.f
    Fortran runtime error: Index '2' of dimension 1 of array 'dy' above upper bound of 1
Flavor: r-devel-windows-ix86+x86_64

Version: 0.24.1
Check: running examples for arch ‘x64’
Result: ERROR
    Running examples in 'rexpokit-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: expokit_dgexpv_Qmat
    > ### Title: EXPOKIT dgexpv matrix exponentiation on Q matrix
    > ### Aliases: expokit_dgexpv_Qmat
    >
    > ### ** Examples
    >
    > # Example:
    > # Make a square instantaneous rate matrix (Q matrix)
    > # This matrix is taken from Peter Foster's (2001) "The Idiot's Guide
    > # to the Zen of Likelihood in a Nutshell in Seven Days for Dummies,
    > # Unleashed" at:
    > # \url{http://www.bioinf.org/molsys/data/idiots.pdf}
    > #
    > # The Q matrix includes the stationary base freqencies, which Pmat
    > # converges to as t becomes large.
    > Qmat = matrix(c(-1.218, 0.504, 0.336, 0.378, 0.126, -0.882, 0.252, 0.504, 0.168,
    + 0.504, -1.05, 0.378, 0.126, 0.672, 0.252, -1.05), nrow=4, byrow=TRUE)
    >
    > # Make a series of t values
    > tvals = c(0.001, 0.005, 0.01, 0.05, 0.1, 0.5, 1, 2, 5, 14)
    >
    > # Exponentiate each with EXPOKIT's dgexpv (should be fast for large sparse matrices)
    > for (t in tvals)
    + {
    + Pmat = expokit_dgexpv_Qmat(Qmat=Qmat, t=t, transpose_needed=TRUE)
    + cat("\n\nTime=", t, "\n", sep="")
    + print(Pmat)
    + }
    At line 425 of file blas_mod.f
    Fortran runtime error: Index '2' of dimension 1 of array 'dy' above upper bound of 1
Flavor: r-devel-windows-ix86+x86_64

Version: 0.24.1
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Warning: iteration 7 invokes undefined behavior [-Waggressive-loop-optimizations]
Flavors: r-patched-solaris-sparc, r-patched-solaris-x86

Version: 0.24.1
Check: R code for possible problems
Result: NOTE
    mat2coo: no visible global function definition for 'as.matrix.coo'
Flavor: r-oldrel-windows-ix86+x86_64