BioC 2.14: CHECK report for trio on morelia

Package: trio

Version: 3.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch trio_3.2.1.tar.gz

StartedAt: 2014-10-08 02:01:30 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 02:03:56 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 145.9 seconds

RetCode: 0

Status:  OK

CheckDir: trio.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch trio_3.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/trio.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘trio/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘trio’ version ‘3.2.1’
* 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 ‘trio’ can be installed ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Fortran("slogreg", ..., PACKAGE = "LogicReg")
See the chapter ‘System and foreign language interfaces’ of the
‘Writing R Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [53s/53s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
trioFS        7.954  0.014   7.974
print.trioFS  7.483  0.021   7.511
trio.permTest 7.088  0.023   7.117
colGxGPerms   6.397  0.028   6.429
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/trio.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
allelicTDT	0.038	0.002	0.040
colEMlrt	0.182	0.003	0.184
colGxE	0.010	0.001	0.012
colGxGPerms	6.397	0.028	6.429
colPOlrt	0.024	0.001	0.026
colTDTmaxTest	0.093	0.005	0.097
colTDTsam	1.064	0.018	1.083
findLDblocks	0.107	0.007	0.114
getLD	0.032	0.001	0.034
getMatPseudo	0.010	0.000	0.012
lrControl	0.001	0.000	0.000
ped2geno	0.001	0.000	0.001
plot.LDblocks	0.125	0.004	0.130
plot.getLD	0.047	0.002	0.049
plot.trioLR	4.482	0.021	4.577
poly4root	0.001	0.000	0.002
print.colGxE	0.086	0.003	0.089
print.trioFS	7.483	0.021	7.511
print.trioLR	4.392	0.012	4.406
probTDT	0.082	0.009	0.091
read.pedfile	0	0	0
removeSNPs	0.011	0.001	0.011
scoreTDT	0.014	0.001	0.015
tdt	0.064	0.002	0.066
tdtGxG	1.763	0.008	1.772
trio.check	1.113	0.009	1.125
trio.data	0.007	0.001	0.008
trio.permTest	7.088	0.023	7.117
trio.power	0.019	0.001	0.020
trio.prepare	4.383	0.009	4.394
trio.sim	0.205	0.001	0.207
trioFS	7.954	0.014	7.974
trioLR	4.750	0.010	4.764