BioC 2.13: CHECK report for trio on zin1

Package: trio

Version: 3.0.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings trio_3.0.0.tar.gz

StartedAt: 2014-04-05 04:26:14 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:28:17 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 123.6 seconds

RetCode: 0

Status:  OK

CheckDir: trio.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/trio.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (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 ‘3.0.0’
* 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 ‘trio’ can be installed ... [2s/2s] 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 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [59s/59s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
trioFS        9.333  0.004   9.411
print.trioFS  9.117  0.040   9.169
trio.permTest 8.989  0.000   9.093
colGxGPerms   6.876  0.008   6.898
* 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
  ‘/home/biocbuild/bbs-2.13-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	0.044	0.000	0.045
colGxE	0.036	0.000	0.037
colGxGPerms	6.876	0.008	6.898
colPOlrt	0.044	0.000	0.041
colTDTmaxTest	0.152	0.004	0.156
colTDTsam	1.004	0.024	1.028
findLDblocks	0.116	0.004	0.122
getLD	0.040	0.004	0.045
getMatPseudo	0.012	0.000	0.015
lrControl	0.004	0.000	0.003
ped2geno	0.004	0.000	0.005
plot.LDblocks	0.200	0.000	0.237
plot.getLD	0.056	0.004	0.061
plot.trioLR	4.664	0.000	4.681
poly4root	0.072	0.000	0.071
print.colGxE	0.072	0.004	0.077
print.trioFS	9.117	0.040	9.169
print.trioLR	4.800	0.008	4.830
probTDT	0.064	0.012	0.088
read.pedfile	0.004	0.000	0.006
removeSNPs	0.020	0.000	0.018
scoreTDT	0.028	0.000	0.031
tdt	0.056	0.004	0.061
tdtGxG	1.952	0.004	1.958
trio.check	1.112	0.004	1.115
trio.data	0.012	0.000	0.010
trio.permTest	8.989	0.000	9.093
trio.power	0.096	0.000	0.100
trio.prepare	4.420	0.000	4.511
trio.sim	0.208	0.000	0.206
trioFS	9.333	0.004	9.411
trioLR	4.584	0.008	4.598