trio 3.4.0
Holger Schwender
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/trio | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | 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 --no-multiarch trio_3.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/trio.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘3.4.0’
* 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 ... [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:
‘LogicReg’ ‘VariantAnnotation’ ‘haplo.stats’ ‘logicFS’ ‘mcbiopi’
‘siggenes’ ‘splines’ ‘survival’
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
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 ... [60s/61s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
trioFS 8.686 0.017 8.769
print.trioFS 8.621 0.030 9.335
trio.permTest 8.318 0.023 8.367
colGxGPerms 7.750 0.039 7.831
print.trioLR 5.174 0.015 5.203
plot.trioLR 5.065 0.023 5.259
trioLR 5.012 0.012 5.078
* 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
NOTE: There were 3 notes.
See
‘/Users/biocbuild/bbs-3.0-bioc/meat/trio.Rcheck/00check.log’
for details.