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csSAM log file (check_x86_64_linux)

Thu Aug 18 14:07:17 2016: Checking package csSAM (SVN revision 12) ...
* using log directory ‘/mnt/building/build_2016-08-18-12-24/RF_PKG_CHECK/PKGS/csSAM.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 ‘csSAM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘csSAM’ version ‘1.2.4’
* checking CRAN incoming feasibility ... WARNING
Maintainer: ‘Shai Shen-Orr ’

Insufficient package version (submitted: 1.2.4, existing: 1.2.4)

The Title field starts with the package name.
The Title field should be in title case, current version then in title case:
‘csSAM - cell-specific Significance Analysis of Microarrays’
‘csSAM - Cell-Specific Significance Analysis of Microarrays’

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 ‘csSAM’ can be installed ... [1s/1s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Author field differs from that derived from Authors@R
  Author:    ‘Shai Shen-Orr, Rob Tibshirani, Narasimhan Balasubramanian, David Wang’
  Authors@R: ‘Shai Shen-Orr [aut, cre], Rob Tibshirani [aut], Narasimhan Balasubramanian [aut], David Wang [aut], Renaud Gaujoux [ctb] (roxygen/debug/CRAN-compliance)’

* 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
Package in Depends field not imported from: ‘compiler’
  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
csSAM: no visible binding for global variable ‘quantile’
csSAM: no visible global function definition for ‘median’
csfit: no visible global function definition for ‘lsfit’
csfit: no visible global function definition for ‘ls.diag’
plotCsSAM: no visible global function definition for ‘pdf’
plotCsSAM: no visible global function definition for ‘par’
plotCsSAM: no visible global function definition for ‘plot’
plotCsSAM: no visible global function definition for ‘title’
plotCsSAM: no visible global function definition for ‘dev.off’
runSAM: no visible binding for global variable ‘median’
runSAM: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  dev.off ls.diag lsfit median par pdf plot quantile title
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par", "plot", "title")
  importFrom("stats", "ls.diag", "lsfit", "median", "quantile")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'csSAM-package.Rd':
  \examples lines wider than 100 characters:
     deconvResults = csSamWrapper(G, cc, y, nperms = 50, alternative = "two.sided", standardize = TRUE, medianCenter = TRUE,fileName = fileN ... [TRUNCATED]
     # (e.g. useful if you want to perform only cell-specific expression without differential expression).

These lines will be truncated in the PDF manual.
* 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 examples ... [2s/2s] OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/mnt/building/build_2016-08-18-12-24/RF_PKG_CHECK/PKGS/csSAM.Rcheck/00check.log’
for details.


Run time: 24.98 seconds.