BioC 2.14: CHECK report for trio on zin2

Package: trio

Version: 3.2.1

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings trio_3.2.1.tar.gz

StartedAt: 2014-10-08 03:24:57 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 03:27:10 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 133.9 seconds

RetCode: 0

Status:  OK

CheckDir: trio.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings trio_3.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/trio.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘3.2.1’
* 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 ... [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 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [54s/54s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
print.trioFS  8.625  0.008   8.648
trioFS        8.609  0.004   8.627
trio.permTest 8.429  0.004   8.447
colGxGPerms   6.416  0.000   6.432
* 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-2.14-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	0.032	0.000	0.032
colEMlrt	0.144	0.000	0.146
colGxE	0.012	0.000	0.012
colGxGPerms	6.416	0.000	6.432
colPOlrt	0.028	0.000	0.029
colTDTmaxTest	0.092	0.000	0.090
colTDTsam	0.900	0.028	0.931
findLDblocks	0.104	0.000	0.107
getLD	0.028	0.000	0.030
getMatPseudo	0.012	0.000	0.010
lrControl	0	0	0
ped2geno	0.004	0.000	0.001
plot.LDblocks	0.064	0.004	0.069
plot.getLD	0.100	0.000	0.097
plot.trioLR	4.224	0.016	4.255
poly4root	0.000	0.000	0.001
print.colGxE	0.080	0.004	0.083
print.trioFS	8.625	0.008	8.648
print.trioLR	4.208	0.008	4.222
probTDT	0.068	0.000	0.068
read.pedfile	0.000	0.000	0.001
removeSNPs	0.008	0.000	0.009
scoreTDT	0.016	0.000	0.016
tdt	0.052	0.000	0.052
tdtGxG	1.704	0.004	1.711
trio.check	1.140	0.004	1.145
trio.data	0.008	0.000	0.007
trio.permTest	8.429	0.004	8.447
trio.power	0.016	0.000	0.018
trio.prepare	4.020	0.000	4.029
trio.sim	0.180	0.000	0.183
trioFS	8.609	0.004	8.627
trioLR	4.184	0.008	4.200