BioC 3.1: CHECK report for Icens on petty

Package: Icens

Version: 1.40.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Icens_1.40.0.tar.gz

StartedAt: 2015-10-08 23:45:43 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:46:32 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 48.3 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 Icens_1.40.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/Icens.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.40.0’
* 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/6s] 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 ... [14s/14s] OK
Examples with CPU or elapsed time > 5s
     user system elapsed
ISDM 7.98   0.02   8.002
* 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-3.1-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	0.361	0.005	0.366
BVclmat	1.936	0.003	1.938
BVsupport	2.061	0.009	2.073
EM	0.118	0.005	0.123
EMICM	0.113	0.002	0.115
ISDM	7.980	0.020	8.002
MLEintvl	0.033	0.001	0.033
Maclist	0.019	0.001	0.020
Macmat	0.019	0.001	0.020
PGM	0.182	0.009	0.191
Plotboxes	0.060	0.003	0.064
VEM	0.144	0.001	0.146
cmv	0.003	0.000	0.003
cosmesis	0.003	0.001	0.003
hiv	0.009	0.001	0.011
plot.icsurv	0.438	0.005	0.447
pruitt	0.003	0.000	0.004