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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### rm -rf trio.buildbin-libdir trio.Rcheck && mkdir trio.buildbin-libdir trio.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=trio.buildbin-libdir trio_3.4.0.tar.gz >trio.Rcheck\00install.out 2>&1 && cp trio.Rcheck\00install.out trio-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=trio.buildbin-libdir --install="check:trio-install.out" --force-multiarch --no-vignettes --timings trio_3.4.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/trio.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 whether package 'trio' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [69s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
print.trioFS 13.46 0.02 13.48
trio.permTest 12.90 0.00 12.90
trioFS 11.35 0.00 11.34
colGxGPerms 6.44 0.02 6.46
** running examples for arch 'x64' ... [84s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
trio.permTest 14.57 0.01 14.59
trioFS 14.33 0.02 14.34
print.trioFS 12.23 0.00 12.23
colGxGPerms 11.71 0.03 11.75
trioLR 6.97 0.00 6.97
trio.prepare 6.31 0.00 6.30
print.trioLR 5.64 0.01 5.64
plot.trioLR 5.26 0.04 5.32
* 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
'D:/biocbld/bbs-3.0-bioc/meat/trio.Rcheck/00check.log'
for details.
install for i386
* 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
install for x64
* installing *source* package 'trio' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'trio' as trio_3.4.0.zip
* DONE (trio)