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CHECK report for CorMut on tokay1

This page was generated on 2020-04-15 12:20:49 -0400 (Wed, 15 Apr 2020).

Package 367/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CorMut 1.28.0
Zhenpeng Li
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/CorMut
Branch: RELEASE_3_10
Last Commit: 97cddf9
Last Changed Date: 2019-10-29 13:08:33 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CorMut
Version: 1.28.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CorMut.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings CorMut_1.28.0.tar.gz
StartedAt: 2020-04-15 02:20:19 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 02:22:24 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 125.1 seconds
RetCode: 0
Status:  OK  
CheckDir: CorMut.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CorMut.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings CorMut_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/CorMut.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.28.0'
* 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
* 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 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
biCompare-methods 15.16   0.03   15.24
miAA              10.73   0.06   10.79
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
biCompare-methods 17.54   0.05   17.59
miAA               8.54   0.00    8.54
* 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


Installation output

CorMut.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/CorMut_1.28.0.tar.gz && rm -rf CorMut.buildbin-libdir && mkdir CorMut.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CorMut.buildbin-libdir CorMut_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL CorMut_1.28.0.zip && rm CorMut_1.28.0.tar.gz CorMut_1.28.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 41480  100 41480    0     0   990k      0 --:--:-- --:--:-- --:--:-- 1094k

install for i386

* installing *source* package 'CorMut' ...
** using staged installation
** 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
  converting help for package 'CorMut'
    finding HTML links ... done
    CorMut-package                          html  
    JI-class                                html  
    MI-class                                html  
    biCkaksCodon-class                      html  
    biCompare-class                         html  
    biCompare-methods                       html  
    ckaks-class                             html  
    ckaksAA                                 html  
    ckaksCodon                              html  
    filterSites-methods                     html  
    jiAA                                    html  
    kaksAA-class                            html  
    kaksAA                                  html  
    kaksCodon-class                         html  
    kaksCodon                               html  
    miAA                                    html  
    miCodon                                 html  
    plot-methods                            html  
    seqFormat-methods                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'CorMut' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CorMut' as CorMut_1.28.0.zip
* DONE (CorMut)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'CorMut' successfully unpacked and MD5 sums checked

Tests output


Example timings

CorMut.Rcheck/examples_i386/CorMut-Ex.timings

nameusersystemelapsed
JI-class000
MI-class000
biCkaksCodon-class000
biCompare-class000
biCompare-methods15.16 0.0315.24
ckaks-class000
ckaksAA2.920.002.92
ckaksCodon2.190.002.22
filterSites-methods1.780.001.78
jiAA3.660.033.69
kaksAA-class000
kaksAA2.310.022.33
kaksCodon-class000
kaksCodon1.610.001.61
miAA10.73 0.0610.79
miCodon2.460.002.46
plot-methods2.120.002.12
seqFormat-methods0.340.000.34

CorMut.Rcheck/examples_x64/CorMut-Ex.timings

nameusersystemelapsed
JI-class000
MI-class000
biCkaksCodon-class000
biCompare-class000
biCompare-methods17.54 0.0517.59
ckaks-class0.000.010.02
ckaksAA3.220.003.22
ckaksCodon2.110.022.12
filterSites-methods1.050.021.06
jiAA2.700.012.72
kaksAA-class000
kaksAA2.380.002.38
kaksCodon-class000
kaksCodon1.220.001.22
miAA8.540.008.54
miCodon3.390.023.42
plot-methods3.870.013.92
seqFormat-methods0.490.000.49