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BioC 3.0: CHECK report for CorMut on oaxaca

This page was generated on 2015-04-10 10:06:12 -0700 (Fri, 10 Apr 2015).

Package 201/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CorMut 1.8.0
Zhenpeng Li
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/CorMut
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 

Summary

Package: CorMut
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CorMut_1.8.0.tar.gz
StartedAt: 2015-04-09 22:37:54 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 22:39:38 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 104.2 seconds
RetCode: 0
Status:  OK 
CheckDir: CorMut.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CorMut_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/CorMut.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 ‘CorMut/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CorMut’ version ‘1.8.0’
* 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 ... [2s/2s] 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
ckaksAA: no visible global function definition for ‘s2c’
ckaksAA : <anonymous>: no visible global function definition for ‘s2c’
ckaksCodon: no visible global function definition for ‘s2c’
ckaksCodon : <anonymous>: no visible global function definition for
  ‘s2c’
freqCompute: no visible global function definition for ‘s2c’
fvft: no visible global function definition for ‘s2c’
jiAA : <anonymous>: no visible global function definition for ‘s2c’
jiAA: no visible global function definition for ‘s2c’
kaksAA : <anonymous>: no visible global function definition for ‘s2c’
kaksAA: no visible global function definition for ‘s2c’
kaksCodon : <anonymous>: no visible global function definition for
  ‘s2c’
kaksCodon: no visible global function definition for ‘s2c’
miAA : <anonymous>: no visible global function definition for ‘s2c’
miAA: no visible global function definition for ‘s2c’
miCodon : <anonymous>: no visible global function definition for ‘s2c’
rawreplace: no visible binding for global variable ‘s2c’
rawreplace: no visible global function definition for ‘s2c’
* 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 ... [71s/75s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
biCompare-methods 23.003  0.088  23.202
miAA              10.354  0.172  11.098
plot-methods       6.100  0.016   6.186
ckaksAA            5.738  0.018   5.784
jiAA               5.262  0.044   5.898
* 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 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/CorMut.Rcheck/00check.log’
for details.

CorMut.Rcheck/00install.out:

* 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)

CorMut.Rcheck/CorMut-Ex.timings:

nameusersystemelapsed
JI-class0.0010.0000.001
MI-class0.0010.0000.000
biCkaksCodon-class0.0000.0000.001
biCompare-class0.0010.0000.001
biCompare-methods23.003 0.08823.202
ckaks-class0.0010.0000.001
ckaksAA5.7380.0185.784
ckaksCodon4.3490.0194.968
filterSites-methods3.0110.0063.347
jiAA5.2620.0445.898
kaksAA-class0.0000.0000.003
kaksAA3.9410.0114.398
kaksCodon-class0.0000.0000.001
kaksCodon3.0130.0083.273
miAA10.354 0.17211.098
miCodon4.2880.0154.467
plot-methods6.1000.0166.186
seqFormat-methods1.2510.0021.255