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BioC 2.12: CHECK report for CorMut on moscato2

This page was generated on 2013-10-09 09:39:10 -0700 (Wed, 09 Oct 2013).

Package 152/671HostnameOS / ArchBUILDCHECKBUILD BIN
CorMut 1.2.0
Zhenpeng Li
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/CorMut
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ WARNINGS ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: CorMut
Version: 1.2.0
Command: rm -rf CorMut.buildbin-libdir && mkdir CorMut.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CorMut.buildbin-libdir CorMut_1.2.0.tar.gz >CorMut-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=CorMut.buildbin-libdir --install="check:CorMut-install.out" --force-multiarch --no-vignettes --timings CorMut_1.2.0.tar.gz && mv CorMut.buildbin-libdir/* CorMut.Rcheck/ && rmdir CorMut.buildbin-libdir
StartedAt: 2013-10-09 01:43:14 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 01:48:23 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 308.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: CorMut.Rcheck
Warnings: 1

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/CorMut.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-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 '1.2.0'
* 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 ... WARNING
Found the following significant warnings:
  Warning: package 'igraph' was built under R version 3.0.2
  Warning: package 'igraph' was built under R version 3.0.2
  Warning: package 'igraph' was built under R version 3.0.2
See 'E:/biocbld/bbs-2.12-bioc/meat/CorMut.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package 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
* 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 for unstated 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 installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... [91s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
biCompare-methods 25.26   0.02   25.28
miAA              18.63   0.00   18.63
ckaksAA            7.92   0.00    7.93
plot-methods       7.63   0.00    7.63
ckaksCodon         5.40   0.00    5.39
kaksAA             5.38   0.00    5.38
miCodon            5.37   0.00    5.37
** running examples for arch 'x64' ... [102s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
biCompare-methods   27.05   0.00   27.05
miAA                20.34   0.02   20.36
plot-methods         9.97   0.00   10.01
ckaksAA              8.58   0.00    8.58
miCodon              7.05   0.00    7.05
kaksAA               6.52   0.00    6.52
filterSites-methods  5.37   0.00    5.36
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
See
  'E:/biocbld/bbs-2.12-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
Warning: package 'igraph' was built under R version 3.0.2
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' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for 'kaks' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for 'lod' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for 'q' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Creating a new generic function for 'q' in package 'CorMut'
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for 'ka' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for 'ks' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for 'mi' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for 'p.value' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for 'ckaks' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for 'method' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for 'positiveSite01' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for 'positiveSite02' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for 'state_1' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for 'statistic_1' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for 'state_2' calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for 'statistic_2' 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
Warning: package 'igraph' was built under R version 3.0.2

install for x64

* installing *source* package 'CorMut' ...
** testing if installed package can be loaded
Warning: package 'igraph' was built under R version 3.0.2
* MD5 sums
packaged installation of 'CorMut' as CorMut_1.2.0.zip
* DONE (CorMut)