BioC 2.14: CHECK report for trio on petty

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 00:30:19 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:35:01 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 281.7 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-darwin10.8.0 (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 ... [4s/4s] 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 ... [101s/102s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
print.trioFS  15.136  0.058  15.527
trioFS        14.806  0.035  14.894
trio.permTest 14.287  0.046  14.377
colGxGPerms   12.149  0.037  12.302
plot.trioLR    8.670  0.051   8.808
print.trioLR   8.636  0.026   8.748
trioLR         8.545  0.019   8.587
trio.prepare   8.100  0.021   8.159
* 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	0.069	0.004	0.073
colEMlrt	0.294	0.004	0.299
colGxE	0.018	0.000	0.018
colGxGPerms	12.149	0.037	12.302
colPOlrt	0.066	0.002	0.068
colTDTmaxTest	0.179	0.011	0.190
colTDTsam	2.104	0.048	2.183
findLDblocks	0.184	0.007	0.191
getLD	0.055	0.002	0.057
getMatPseudo	0.017	0.002	0.019
lrControl	0.001	0.000	0.002
ped2geno	0.001	0.001	0.002
plot.LDblocks	0.215	0.004	0.221
plot.getLD	0.085	0.004	0.089
plot.trioLR	8.670	0.051	8.808
poly4root	0.003	0.000	0.003
print.colGxE	0.145	0.005	0.150
print.trioFS	15.136	0.058	15.527
print.trioLR	8.636	0.026	8.748
probTDT	0.162	0.018	0.179
read.pedfile	0.002	0.000	0.002
removeSNPs	0.018	0.001	0.018
scoreTDT	0.025	0.002	0.027
tdt	0.137	0.004	0.141
tdtGxG	3.001	0.006	3.011
trio.check	2.242	0.012	2.256
trio.data	0.012	0.001	0.013
trio.permTest	14.287	0.046	14.377
trio.power	0.033	0.001	0.033
trio.prepare	8.100	0.021	8.159
trio.sim	0.353	0.002	0.356
trioFS	14.806	0.035	14.894
trioLR	8.545	0.019	8.587