Package: CorMut

Version: 1.25.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CorMut.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CorMut_1.25.0.tar.gz

StartedAt: 2019-04-09 00:11:08 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:12:41 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 92.9 seconds

RetCode: 0

Status:  OK

CheckDir: CorMut.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CorMut.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CorMut_1.25.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CorMut.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.25.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
biCompare-methods 18.912  0.195  19.194
miAA               8.710  0.433   9.192
* 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: OK

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CorMut
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘CorMut’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
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)

name	user	system	elapsed
JI-class	0	0	0
MI-class	0	0	0
biCkaksCodon-class	0.000	0.001	0.000
biCompare-class	0	0	0
biCompare-methods	18.912	0.195	19.194
ckaks-class	0	0	0
ckaksAA	3.603	0.015	3.649
ckaksCodon	2.560	0.010	2.584
filterSites-methods	1.898	0.006	1.911
jiAA	3.968	0.045	4.032
kaksAA-class	0.001	0.000	0.000
kaksAA	2.511	0.005	2.526
kaksCodon-class	0.001	0.000	0.001
kaksCodon	1.782	0.005	1.791
miAA	8.710	0.433	9.192
miCodon	3.285	0.012	3.324
plot-methods	4.338	0.014	4.373
seqFormat-methods	0.663	0.002	0.668