BioC 2.14: CHECK report for Icens on petty

Package: Icens

Version: 1.36.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Icens_1.36.0.tar.gz

StartedAt: 2014-10-07 22:33:58 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:34:56 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 58.3 seconds

RetCode: 0

Status:  OK

CheckDir: Icens.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Icens_1.36.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/Icens.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Icens/DESCRIPTION’ ... OK
* this is package ‘Icens’ version ‘1.36.0’
* 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 ‘Icens’ can be installed ... [2s/2s] 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 dependencies in R code ... NOTE
Package in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
VEMICMmac: no visible binding for global variable ‘EMstep’
* 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 examples ... [21s/21s] OK
Examples with CPU or elapsed time > 5s
       user system elapsed
ISDM 11.517  0.021  11.771
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘testbv.R’ [1s/1s]
  Comparing ‘testbv.Rout’ to ‘testbv.Rout.save’ ...117c117
<  [6]  1.461001e+00  1.207129e+00  1.000000e+00  4.748624e-01 -2.640501e-16
---
>  [6]  1.461001e+00  1.207129e+00  1.000000e+00  4.748624e-01 -2.480201e-16
 [2s/2s] OK
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/Icens.Rcheck/00check.log’
for details.

* installing *source* package ‘Icens’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (Icens)

name	user	system	elapsed
BVcliques	0.439	0.006	0.447
BVclmat	3.156	0.007	3.171
BVsupport	3.269	0.010	3.295
EM	0.159	0.008	0.168
EMICM	0.169	0.002	0.171
ISDM	11.517	0.021	11.771
MLEintvl	0.060	0.001	0.069
Maclist	0.031	0.001	0.034
Macmat	0.034	0.002	0.038
PGM	0.275	0.009	0.298
Plotboxes	0.104	0.005	0.116
VEM	0.255	0.002	0.274
cmv	0.007	0.002	0.013
cosmesis	0.004	0.001	0.005
hiv	0.017	0.003	0.023
plot.icsurv	0.594	0.007	0.607
pruitt	0.003	0.001	0.005