BioC 3.2: CHECK report for Icens on perceval

Package: Icens

Version: 1.42.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Icens_1.42.0.tar.gz

StartedAt: 2015-11-10 06:02:17 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 06:02:49 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 32.6 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 Icens_1.42.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/Icens.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘1.42.0’
* 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 ... [1s/1s] 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.
* 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 ... [10s/11s] OK
Examples with CPU or elapsed time > 5s
     user system elapsed
ISDM 5.93  0.012   5.948
* 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
 [1s/1s] OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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	0.226	0.003	0.230
BVclmat	1.498	0.002	1.501
BVsupport	1.462	0.006	1.469
EM	0.073	0.003	0.083
EMICM	0.077	0.002	0.079
ISDM	5.930	0.012	5.948
MLEintvl	0.026	0.000	0.027
Maclist	0.014	0.000	0.014
Macmat	0.015	0.001	0.015
PGM	0.139	0.007	0.146
Plotboxes	0.052	0.003	0.055
VEM	0.127	0.002	0.129
cmv	0.003	0.000	0.003
cosmesis	0.002	0.001	0.002
hiv	0.006	0.001	0.006
plot.icsurv	0.284	0.003	0.288
pruitt	0.001	0.001	0.003