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BioC 3.2: CHECK report for CorMut on windows1.bioconductor.org

This page was generated on 2015-10-27 17:30:02 -0400 (Tue, 27 Oct 2015).

Package 227/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CorMut 1.12.0
Zhenpeng Li
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/CorMut
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  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 && C:\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 && C:\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: 2015-10-27 00:58:13 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 01:00:16 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 122.7 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 && C:\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  && C:\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 'C:/biocbld/bbs-3.2-bioc/meat/CorMut.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* 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' ... [46s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
biCompare-methods 14.72      0   14.72
miAA               8.80      0    8.80
** running examples for arch 'x64' ... [51s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
biCompare-methods 16.48   0.02   16.50
miAA               8.75   0.00    8.75
* 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
  'C:/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-methods14.72 0.0014.72
ckaks-class000
ckaksAA3.330.003.33
ckaksCodon2.320.002.33
filterSites-methods1.660.011.67
jiAA2.800.022.81
kaksAA-class000
kaksAA2.170.002.18
kaksCodon-class000
kaksCodon1.800.001.79
miAA8.80.08.8
miCodon3.120.003.12
plot-methods3.640.013.66
seqFormat-methods0.730.000.74

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

nameusersystemelapsed
JI-class000
MI-class000
biCkaksCodon-class000
biCompare-class000
biCompare-methods16.48 0.0216.50
ckaks-class000
ckaksAA4.180.004.17
ckaksCodon2.930.022.95
filterSites-methods1.940.001.94
jiAA3.520.003.51
kaksAA-class000
kaksAA2.650.022.67
kaksCodon-class000
kaksCodon2.050.002.05
miAA8.750.008.75
miCodon3.000.013.01
plot-methods4.200.004.21
seqFormat-methods1.050.001.04