BioC 3.2: CHECK report for CorMut on moscato1
This page was generated on 2015-08-20 13:20:57 -0700 (Thu, 20 Aug 2015).
CorMut 1.11.0
Zhenpeng Li
| Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CorMut | | Last Changed Rev: 102594 / Revision: 107602 | | Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015) |
| zin1 | Linux (Ubuntu 14.04.2 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: 1.11.0
|
| 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_1.11.0.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_1.11.0.tar.gz
|
| StartedAt: 2015-08-20 03:13:50 -0700 (Thu, 20 Aug 2015)
|
| EndedAt: 2015-08-20 03:17:21 -0700 (Thu, 20 Aug 2015)
|
| EllapsedTime: 210.9 seconds
|
| RetCode: 0
|
| Status: OK
|
| CheckDir: CorMut.Rcheck
|
| Warnings: 0
|
Command output
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### 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_1.11.0.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_1.11.0.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/CorMut.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.11.0'
* 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' ... [75s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
biCompare-methods 23.57 0 23.59
miAA 14.10 0 14.10
ckaksAA 6.18 0 6.17
plot-methods 5.87 0 5.86
jiAA 5.28 0 5.29
** running examples for arch 'x64' ... [87s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
biCompare-methods 27.14 0 27.18
miAA 15.01 0 15.00
ckaksAA 7.10 0 7.09
plot-methods 6.87 0 6.89
jiAA 5.47 0 5.49
miCodon 5.12 0 5.39
ckaksCodon 5.11 0 5.10
* 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_1.11.0.zip
* DONE (CorMut)
CorMut.Rcheck/examples_i386/CorMut-Ex.timings:
| name | user | system | elapsed
|
| JI-class | 0 | 0 | 0 |
|
| MI-class | 0 | 0 | 0 |
|
| biCkaksCodon-class | 0 | 0 | 0 |
|
| biCompare-class | 0 | 0 | 0 |
|
| biCompare-methods | 23.57 | 0.00 | 23.59 |
|
| ckaks-class | 0 | 0 | 0 |
|
| ckaksAA | 6.18 | 0.00 | 6.17 |
|
| ckaksCodon | 4.21 | 0.00 | 4.22 |
|
| filterSites-methods | 2.61 | 0.00 | 2.60 |
|
| jiAA | 5.28 | 0.00 | 5.29 |
|
| kaksAA-class | 0 | 0 | 0 |
|
| kaksAA | 3.93 | 0.00 | 3.93 |
|
| kaksCodon-class | 0 | 0 | 0 |
|
| kaksCodon | 2.73 | 0.00 | 2.73 |
|
| miAA | 14.1 | 0.0 | 14.1 |
|
| miCodon | 4.23 | 0.00 | 4.23 |
|
| plot-methods | 5.87 | 0.00 | 5.86 |
|
| seqFormat-methods | 1.31 | 0.00 | 1.31 |
|
CorMut.Rcheck/examples_x64/CorMut-Ex.timings:
| name | user | system | elapsed
|
| JI-class | 0 | 0 | 0 |
|
| MI-class | 0 | 0 | 0 |
|
| biCkaksCodon-class | 0 | 0 | 0 |
|
| biCompare-class | 0 | 0 | 0 |
|
| biCompare-methods | 27.14 | 0.00 | 27.18 |
|
| ckaks-class | 0 | 0 | 0 |
|
| ckaksAA | 7.10 | 0.00 | 7.09 |
|
| ckaksCodon | 5.11 | 0.00 | 5.10 |
|
| filterSites-methods | 3.71 | 0.02 | 3.73 |
|
| jiAA | 5.47 | 0.00 | 5.49 |
|
| kaksAA-class | 0 | 0 | 0 |
|
| kaksAA | 4.93 | 0.00 | 4.93 |
|
| kaksCodon-class | 0 | 0 | 0 |
|
| kaksCodon | 3.56 | 0.00 | 3.56 |
|
| miAA | 15.01 | 0.00 | 15.00 |
|
| miCodon | 5.12 | 0.00 | 5.39 |
|
| plot-methods | 6.87 | 0.00 | 6.89 |
|
| seqFormat-methods | 1.53 | 0.00 | 1.53 |
|