Package: iPAC

Version: 1.1.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch iPAC_1.1.3.tar.gz

StartedAt: 2013-03-25 03:12:40 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:23:20 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 640.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: iPAC.Rcheck

Warnings: 2

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/iPAC.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'iPAC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iPAC' version '1.1.3'
* 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 ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'iPAC' can be installed ... [13s/14s] WARNING
Found the following significant warnings:
  Warning: '.path.package' is deprecated.
  Warning: '.path.package' is deprecated.
See '/Users/biocbuild/bbs-2.12-bioc/meat/iPAC.Rcheck/00install.out' for details.
* 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 for unstated 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* 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 contents of 'data' directory ... OK
* 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 ... [513s/523s] WARNING
Found the following significant warnings:

  Warning: '.path.package' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                        user system elapsed
ClusterFind          303.068  2.991 307.691
get.Positions         51.644 34.956  90.641
nmc                   72.188  0.177  72.368
Plot.Protein.Linear   19.937  3.253  24.609
get.AlignedPositions   9.948  1.667  12.517
get.Remapped.Order     5.110  1.849   7.858
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 2 warnings.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/iPAC.Rcheck/00check.log'
for details.

* installing *source* package 'iPAC' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: '.path.package' is deprecated.
Use 'path.package' instead.
See help("Deprecated")
** help
*** installing help indices
** building package indices
** installing vignettes
   'iPAC.Rnw' 
** testing if installed package can be loaded
Warning: '.path.package' is deprecated.
Use 'path.package' instead.
See help("Deprecated")
* DONE (iPAC)

name	user	system	elapsed
ClusterFind	303.068	2.991	307.691
KRAS.Mutations	0.105	0.021	0.126
PIK3CA.Mutations	0.557	0.065	0.622
Plot.Protein.Linear	19.937	3.253	24.609
get.AASeq	0.007	0.008	0.573
get.AlignedPositions	9.948	1.667	12.517
get.Positions	51.644	34.956	90.641
get.Remapped.Order	5.110	1.849	7.858
get.SingleLetterCode	0.010	0.013	0.023
iPAC-package	0.011	0.015	0.027
nmc	72.188	0.177	72.368