CorMut 1.15.0
Zhenpeng Li
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CorMut | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings CorMut_1.15.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/CorMut.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CorMut/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CorMut’ version ‘1.15.0’
* 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 ‘CorMut’ 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
* 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
Packages in Depends field not imported from:
‘igraph’ ‘seqinr’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
biCkaksAA: no visible global function definition for ‘new’
biCkaksCodon: no visible global function definition for ‘new’
biJIAA: no visible global function definition for ‘new’
biMIAA: no visible global function definition for ‘new’
biMICodon: no visible global function definition for ‘new’
ckaksAA: no visible global function definition for ‘s2c’
ckaksAA : <anonymous>: no visible global function definition for ‘s2c’
ckaksAA: no visible global function definition for ‘new’
ckaksCodon: no visible global function definition for ‘s2c’
ckaksCodon : <anonymous>: no visible global function definition for
‘s2c’
ckaksCodon: no visible global function definition for ‘new’
freqCompute: no visible global function definition for ‘s2c’
fvft: no visible global function definition for ‘s2c’
genericSlot: no visible global function definition for ‘isGeneric’
genericSlot: no visible global function definition for ‘setGeneric’
jiAA : <anonymous>: no visible global function definition for ‘s2c’
jiAA: no visible global function definition for ‘s2c’
jiAA: no visible global function definition for ‘fisher.test’
jiAA: no visible global function definition for ‘p.adjust’
jiAA: no visible global function definition for ‘new’
kaksAA : <anonymous>: no visible global function definition for ‘s2c’
kaksAA: no visible global function definition for ‘s2c’
kaksAA: no visible global function definition for ‘new’
kaksCodon : <anonymous>: no visible global function definition for
‘s2c’
kaksCodon: no visible global function definition for ‘s2c’
kaksCodon: no visible global function definition for ‘new’
miAA : <anonymous>: no visible global function definition for ‘s2c’
miAA: no visible global function definition for ‘s2c’
miAA: no visible global function definition for ‘fisher.test’
miAA: no visible global function definition for ‘p.adjust’
miAA: no visible global function definition for ‘new’
miCodon : <anonymous>: no visible global function definition for ‘s2c’
miCodon: no visible global function definition for ‘fisher.test’
miCodon: no visible global function definition for ‘p.adjust’
miCodon: no visible global function definition for ‘new’
rawreplace: no visible binding for global variable ‘s2c’
rawreplace: no visible global function definition for ‘s2c’
biCompare,biCkaksAA : <anonymous>: no visible global function
definition for ‘c2s’
biCompare,biCkaksAA : <anonymous>: no visible global function
definition for ‘s2c’
biCompare,biCkaksAA: no visible global function definition for ‘new’
biCompare,biCkaksCodon: no visible global function definition for ‘new’
biCompare,biJIAA: no visible global function definition for ‘new’
biCompare,biMIAA: no visible global function definition for ‘new’
biCompare,biMICodon: no visible global function definition for ‘new’
plot,JI: no visible global function definition for ‘graph.edgelist’
plot,JI: no visible global function definition for ‘E’
plot,JI: no visible global function definition for ‘E<-’
plot,JI: no visible global function definition for ‘V’
plot,JI: no visible binding for global variable
‘layout.fruchterman.reingold’
plot,MI: no visible global function definition for ‘graph.edgelist’
plot,MI: no visible global function definition for ‘E’
plot,MI: no visible global function definition for ‘E<-’
plot,MI: no visible global function definition for ‘V’
plot,MI: no visible binding for global variable
‘layout.fruchterman.reingold’
plot,biCompare: no visible global function definition for
‘graph.adjacency’
plot,biCompare: no visible global function definition for
‘layout.fruchterman.reingold’
plot,biCompare: no visible global function definition for ‘vcount’
plot,biCompare: no visible global function definition for ‘par’
plot,biCompare: no visible global function definition for ‘V’
plot,biCompare: no visible global function definition for ‘E’
plot,ckaks: no visible global function definition for ‘graph.edgelist’
plot,ckaks: no visible global function definition for ‘E’
plot,ckaks: no visible global function definition for ‘E<-’
plot,ckaks: no visible global function definition for ‘V’
plot,ckaks: no visible binding for global variable
‘layout.fruchterman.reingold’
Undefined global functions or variables:
E E<- V c2s fisher.test graph.adjacency graph.edgelist isGeneric
layout.fruchterman.reingold new p.adjust par s2c setGeneric vcount
Consider adding
importFrom("graphics", "par")
importFrom("methods", "isGeneric", "new", "setGeneric")
importFrom("stats", "fisher.test", "p.adjust")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
biCompare-methods 15.684 0.016 15.698
miAA 12.404 0.000 12.403
miCodon 6.496 0.000 6.495
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/CorMut.Rcheck/00check.log’
for details.
* 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.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for ‘kaks.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for ‘lod.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for ‘q.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for ‘ka.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for ‘ks.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for ‘mi.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for ‘p.value.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for ‘ckaks.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for ‘method.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for ‘positiveSite01.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for ‘positiveSite02.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for ‘state_1.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for ‘statistic_1.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for ‘state_2.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
the body of the generic function for ‘statistic_2.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CorMut)