CorMut 1.0.0
Zhenpeng Li
| Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/CorMut | | Last Changed Rev: 70050 / Revision: 74773 | | Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | [ OK ] | OK |
* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/CorMut.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'CorMut/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CorMut' version '1.0.0'
* 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 whether package 'CorMut' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
biCompare-methods 23.326 0.119 24.011
miAA 17.194 4.127 22.100
plot-methods 8.102 0.040 8.171
ckaksAA 7.394 0.030 7.518
miCodon 5.658 0.036 5.742
ckaksCodon 5.393 0.019 5.519
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
* installing *source* package 'CorMut' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'CorMut'
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for 'seq_num' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for 'kaks' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for 'lod' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for 'q' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Creating a new generic function for 'q' in package 'CorMut'
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for 'ka' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for 'ks' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for 'mi' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for 'p.value' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for 'ckaks' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for 'method' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for 'positiveSite01' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for 'positiveSite02' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for 'state_1' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for 'statistic_1' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for 'state_2' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for 'statistic_2' calls 'standardGeneric' to dispatch on a different name ("aslot")!
** help
*** installing help indices
** building package indices
** installing vignettes
'CorMut.Rnw'
** testing if installed package can be loaded
* DONE (CorMut)