trio 3.7.1
Holger Schwender
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/trio | | Last Changed Rev: 103021 / Revision: 107696 | | Last Changed Date: 2015-04-23 16:03:18 -0700 (Thu, 23 Apr 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings trio_3.7.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/trio.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 ‘trio/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘trio’ version ‘3.7.1’
* 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 ... NOTE
'library' or 'require' calls in package code:
‘haplo.stats’ ‘logicFS’ ‘LogicReg’ ‘mcbiopi’ ‘siggenes’ ‘splines’
‘survival’ ‘VariantAnnotation’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
colGxEunstructured: no visible global function definition for ‘clogit’
colGxG: no visible global function definition for ‘clogit’
colGxGlrt: no visible global function definition for ‘clogit’
colTDTebam: no visible global function definition for ‘ebam’
colTDTepistatic: no visible global function definition for ‘clogit’
colTDTsam: no visible global function definition for ‘sam’
estimateRatioTDT: no visible global function definition for ‘ns’
freqmap.reconstruct: no visible global function definition for
‘haplo.em’
getOriginalStat: no visible global function definition for ‘clogit’
getPermStat: no visible global function definition for ‘clogit’
gtdt.null.approx2: no visible global function definition for ‘denspr’
printTrioTree: no visible global function definition for ‘getPImps’
tdt: no visible global function definition for ‘clogit’
tdtEpistatic: no visible global function definition for ‘clogit’
tdtGxG: no visible global function definition for ‘clogit’
trio.permTest: no visible global function definition for ‘evalTree’
trioFS.formula: no visible global function definition for ‘getXy’
trioLR.formula: no visible global function definition for ‘getXy’
trioPImp: no visible global function definition for ‘getPImps’
vimTrio: no visible global function definition for ‘clogit’
vimTrio.oneprime: no visible global function definition for ‘clogit’
* 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 ... [62s/63s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
trioFS 8.757 0.027 8.800
print.trioFS 8.727 0.043 8.824
trio.permTest 8.399 0.030 8.442
plot.trioLR 7.790 0.272 8.214
colGxGPerms 7.523 0.027 7.555
* 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
* DONE
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.2-bioc/meat/trio.Rcheck/00check.log’
for details.