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rexpokit log file (check_x86_64_linux)

Thu Aug 18 15:44:17 2016: Checking package rexpokit (SVN revision 19) ...
* using log directory ‘/mnt/building/build_2016-08-18-12-24/RF_PKG_CHECK/PKGS/rexpokit.Rcheck’
* using R version 3.3.1 Patched (2016-08-17 r71112)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘rexpokit/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rexpokit’ version ‘0.24’
* checking CRAN incoming feasibility ... WARNING
Maintainer: ‘Nicholas J. Matzke ’

Insufficient package version (submitted: 0.24, existing: 0.24.1)

Found the following (possibly) invalid URLs:
  URL: http://pyprop.googlecode.com/svn/trunk/core/krylov/expokit/expokitpropagator.cpp
    From: man/rexpokit-package.Rd
    Status: 404
    Message: Not Found

The Title field should be in title case, current version then in title case:
‘R wrappers for EXPOKIT; other matrix functions’
‘R Wrappers for EXPOKIT; Other Matrix Functions’

The Description field should not start with the package name,
  'This package' or similar.

The Date field is over a month old.
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rexpokit’ can be installed ... [10s/10s] 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 loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... 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.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'SparseM_coo_to_REXPOKIT_coo.Rd':
  \examples lines wider than 100 characters:
     tmpmat = 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), nr ... [TRUNCATED]

Rd file 'coo2mat.Rd':
  \examples lines wider than 100 characters:
     a  = c(-1.218, 0.126, 0.168, 0.126, 0.504, -0.882, 0.504, 0.672, 0.336, 0.252, -1.050, 0.252, 0.378, 0.504, 0.378, -1.050)

Rd file 'expokit_dgexpv_Qmat.Rd':
  \examples lines wider than 100 characters:
     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 ... [TRUNCATED]
     list_of_P_matrices_dgexpv = expokit_wrapalldgexpv_tvals(Qmat=Qmat, tvals=tvals, transpose_needed=TRUE)

Rd file 'expokit_dgexpv_wrapper.Rd':
  \examples lines wider than 100 characters:
     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 ... [TRUNCATED]
     tmpoutmat = expokit_dgexpv_wrapper(n, m, timeval, v, w, tol, anorm, wsp, lwsp, iwsp, liwsp, itrace, iflag, ia, ja, a, nz, res)

Rd file 'expokit_dgpadm_Qmat.Rd':
  \examples lines wider than 100 characters:
     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 ... [TRUNCATED]

Rd file 'expokit_dmexpv_Qmat.Rd':
  \examples lines wider than 100 characters:
     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 ... [TRUNCATED]

Rd file 'expokit_dmexpv_wrapper.Rd':
  \examples lines wider than 100 characters:
     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 ... [TRUNCATED]
     list_of_P_matrices_dmexpv = expokit_wrapalldmexpv_tvals(Qmat=Qmat, tvals=tvals, transpose_needed=TRUE)

Rd file 'expokit_mydgexpv_wrapper.Rd':
  \examples lines wider than 100 characters:
     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 ... [TRUNCATED]
     list_of_P_matrices_dgexpv = expokit_wrapalldgexpv_tvals(Qmat=Qmat, tvals=tvals, transpose_needed=TRUE)

Rd file 'expokit_mydmexpv_wrapper.Rd':
  \examples lines wider than 100 characters:
     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 ... [TRUNCATED]
     list_of_P_matrices_dmexpv = expokit_wrapalldmexpv_tvals(Qmat=Qmat, tvals=tvals, transpose_needed=TRUE)

Rd file 'expokit_wrapalldgexpv_tvals.Rd':
  \examples lines wider than 100 characters:
     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 ... [TRUNCATED]
     list_of_P_matrices_dgexpv = expokit_wrapalldgexpv_tvals(Qmat=Qmat, tvals=tvals, transpose_needed=TRUE)

Rd file 'expokit_wrapalldmexpv_tvals.Rd':
  \examples lines wider than 100 characters:
     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 ... [TRUNCATED]
     list_of_P_matrices_dgexpv = expokit_wrapalldgexpv_tvals(Qmat=Qmat, tvals=tvals, transpose_needed=TRUE)

Rd file 'findrows_w_all_zeros.Rd':
  \examples lines wider than 100 characters:
     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 ... [TRUNCATED]
     list_of_P_matrices_dgexpv = expokit_wrapalldgexpv_tvals(Qmat=Qmat, tvals=tvals, transpose_needed=TRUE)

Rd file 'mat2coo_forloop.Rd':
  \examples lines wider than 100 characters:
     tmpmat = 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), nr ... [TRUNCATED]

Rd file 'rexpokit-package.Rd':
  \examples lines wider than 100 characters:
     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 ... [TRUNCATED]
     list_of_P_matrices_dmexpv = expokit_wrapalldmexpv_tvals(Qmat=Qmat, tvals=tvals, transpose_needed=TRUE)
     list_of_P_matrices_dgexpv = expokit_wrapalldgexpv_tvals(Qmat=Qmat, tvals=tvals, transpose_needed=TRUE)

Rd file 'row_allzero_TF.Rd':
  \examples lines wider than 100 characters:
     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 ... [TRUNCATED]
     list_of_P_matrices_dgexpv = expokit_wrapalldgexpv_tvals(Qmat=Qmat, tvals=tvals, transpose_needed=TRUE)

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... WARNING
Packages unavailable to check Rd xrefs: ‘diversitree’, ‘expoRkit’
Unknown package ‘ctarma’ in Rd xrefs
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking examples ... [1s/1s] OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/mnt/building/build_2016-08-18-12-24/RF_PKG_CHECK/PKGS/rexpokit.Rcheck/00check.log’
for details.


Run time: 55.71 seconds.