R Development Page

netmes log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2013-11-22-20-03/RF_PKG_CHECK/PKGS/netmes.Rcheck'
* using R version 3.0.2 Patched (2013-11-22 r64286)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'netmes/DESCRIPTION' ... OK
* this is package 'netmes' version '1.0'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Gokmen Altay '
New submission
Package has a FOSS license but eventually depends on the following
package which restricts use:
  minet
* 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 ... OK
* checking for portable file names ... NOTE
Found the following non-portable file paths:
  netmes/data/bio/1/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
  netmes/data/bio/2/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
  netmes/data/bio/3/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
  netmes/data/bio/4/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
  netmes/data/bio/5/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
  netmes/data/syn/1/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
  netmes/data/syn/2/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
  netmes/data/syn/3/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
  netmes/data/syn/4/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
  netmes/data/syn/5/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
  netmes/inst/extdata/bio/1/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
  netmes/inst/extdata/bio/2/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
  netmes/inst/extdata/bio/3/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
  netmes/inst/extdata/bio/4/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
  netmes/inst/extdata/bio/5/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
  netmes/inst/extdata/syn/1/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
  netmes/inst/extdata/syn/2/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
  netmes/inst/extdata/syn/3/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
  netmes/inst/extdata/syn/4/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
  netmes/inst/extdata/syn/5/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking whether package 'netmes' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file found at top level:
  'EXAMPLES.txt'
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Subdirectory 'data' contains no data sets.
* 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 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
plotDs: warning in postscript(file = "Ds.eps", horiz = FALSE, paper =
  "special", family = "Helvetica", encoding = "TeXtext.enc", width =
  10, height = 10): partial argument match of 'horiz' to 'horizontal'
* checking Rd files ... NOTE
prepare_Rd: plotMotifs.Rd:16-18: Dropping empty section \details
prepare_Rd: readNet.Rd:25: Dropping empty section \seealso
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'R:/run/building/build_2013-11-22-20-03/RF_PKG_CHECK/PKGS/netmes.Rcheck/00_pkg_src/netmes/man/motifcount3.Rd':
  \examples lines wider than 100 characters:
     # boxplot(y ~ xg, names = c("DAG"), ylab = expression(p), cex.lab = 1.7, cex.axis = 1.6, col = c("darkred") )

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'motifMI' 'motifrate' 'readMI' 'readNamesMI'
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ... WARNING
Files not of a type allowed in a 'data' directory:
  'bio' 'networkDAG.sif' 'networkEcoli.sif' 'syn'
Please use e.g. 'inst/extdata' for non-R data files
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
* checking PDF version of manual ... OK

WARNING: There were 3 warnings.
NOTE: There were 6 notes.
See
  'R:/run/building/build_2013-11-22-20-03/RF_PKG_CHECK/PKGS/netmes.Rcheck/00check.log'
for details.

Run time: 58.2 seconds.