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BioC 3.2: CHECK report for CorMut on moscato1

This page was generated on 2016-04-23 10:18:38 -0700 (Sat, 23 Apr 2016).

Package 227/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CorMut 1.12.0
Zhenpeng Li
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/CorMut
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CorMut
Version: 1.12.0
Command: rm -rf CorMut.buildbin-libdir CorMut.Rcheck && mkdir CorMut.buildbin-libdir CorMut.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CorMut.buildbin-libdir CorMut_1.12.0.tar.gz >CorMut.Rcheck\00install.out 2>&1 && cp CorMut.Rcheck\00install.out CorMut-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=CorMut.buildbin-libdir --install="check:CorMut-install.out" --force-multiarch --no-vignettes --timings CorMut_1.12.0.tar.gz
StartedAt: 2016-04-23 01:10:40 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 01:14:01 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 202.0 seconds
RetCode: 0
Status:  OK  
CheckDir: CorMut.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CorMut.buildbin-libdir CorMut.Rcheck && mkdir CorMut.buildbin-libdir CorMut.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CorMut.buildbin-libdir CorMut_1.12.0.tar.gz >CorMut.Rcheck\00install.out 2>&1 && cp CorMut.Rcheck\00install.out CorMut-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=CorMut.buildbin-libdir --install="check:CorMut-install.out" --force-multiarch --no-vignettes --timings CorMut_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/CorMut.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CorMut/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CorMut' version '1.12.0'
* 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 '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
* 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
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'
biCompare,biCkaksAA : .local : <anonymous>: no visible global function
  definition for 'c2s'
biCompare,biCkaksAA : .local : <anonymous>: no visible global function
  definition for 's2c'
plot,JI : .local: no visible global function definition for
  'graph.edgelist'
plot,JI : .local: no visible global function definition for 'E'
plot,JI : .local: no visible global function definition for 'E<-'
plot,JI : .local: no visible global function definition for 'V'
plot,JI : .local: no visible binding for global variable
  'layout.fruchterman.reingold'
plot,MI : .local: no visible global function definition for
  'graph.edgelist'
plot,MI : .local: no visible global function definition for 'E'
plot,MI : .local: no visible global function definition for 'E<-'
plot,MI : .local: no visible global function definition for 'V'
plot,MI : .local: no visible binding for global variable
  'layout.fruchterman.reingold'
plot,biCompare : .local: no visible global function definition for
  'graph.adjacency'
plot,biCompare : .local: no visible global function definition for
  'layout.fruchterman.reingold'
plot,biCompare : .local: no visible global function definition for
  'vcount'
plot,biCompare : .local: no visible global function definition for 'V'
plot,biCompare : .local: no visible global function definition for 'E'
plot,ckaks : .local: no visible global function definition for
  'graph.edgelist'
plot,ckaks : .local: no visible global function definition for 'E'
plot,ckaks : .local: no visible global function definition for 'E<-'
plot,ckaks : .local: no visible global function definition for 'V'
plot,ckaks : .local: no visible binding for global variable
  'layout.fruchterman.reingold'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [78s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
biCompare-methods 23.10      0   23.10
miAA              14.39      0   14.40
plot-methods       7.10      0    7.10
ckaksAA            6.05      0    6.05
jiAA               5.35      0    5.36
** running examples for arch 'x64' ... [77s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
biCompare-methods 28.06   0.00   28.06
miAA              12.02   0.00   12.03
ckaksAA            6.30   0.02    6.35
plot-methods       5.60   0.02    5.62
* 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
  'D:/biocbld/bbs-3.2-bioc/meat/CorMut.Rcheck/00check.log'
for details.


CorMut.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'CorMut' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CorMut' as CorMut_1.12.0.zip
* DONE (CorMut)

CorMut.Rcheck/examples_i386/CorMut-Ex.timings:

nameusersystemelapsed
JI-class000
MI-class000
biCkaksCodon-class000
biCompare-class000
biCompare-methods23.1 0.023.1
ckaks-class000
ckaksAA6.050.006.05
ckaksCodon4.240.004.24
filterSites-methods2.340.002.34
jiAA5.350.005.36
kaksAA-class0.020.000.01
kaksAA4.150.004.15
kaksCodon-class000
kaksCodon4.150.024.17
miAA14.39 0.0014.40
miCodon4.390.004.38
plot-methods7.10.07.1
seqFormat-methods1.630.001.64

CorMut.Rcheck/examples_x64/CorMut-Ex.timings:

nameusersystemelapsed
JI-class000
MI-class000
biCkaksCodon-class000
biCompare-class000
biCompare-methods28.06 0.0028.06
ckaks-class000
ckaksAA6.300.026.35
ckaksCodon3.950.013.96
filterSites-methods2.540.002.55
jiAA4.920.004.91
kaksAA-class000
kaksAA4.210.004.21
kaksCodon-class000
kaksCodon2.950.002.95
miAA12.02 0.0012.03
miCodon3.940.003.93
plot-methods5.600.025.62
seqFormat-methods1.150.001.15