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CHECK report for FRGEpistasis on tokay1

This page was generated on 2019-04-13 11:23:44 -0400 (Sat, 13 Apr 2019).

Package 559/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FRGEpistasis 1.18.0
Futao Zhang
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/FRGEpistasis
Branch: RELEASE_3_8
Last Commit: c71d0ad
Last Changed Date: 2018-10-30 11:41:53 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 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: FRGEpistasis
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FRGEpistasis.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings FRGEpistasis_1.18.0.tar.gz
StartedAt: 2019-04-13 02:20:28 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:24:12 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 223.9 seconds
RetCode: 0
Status:  OK  
CheckDir: FRGEpistasis.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FRGEpistasis.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings FRGEpistasis_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/FRGEpistasis.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'FRGEpistasis/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FRGEpistasis' version '1.18.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'FRGEpistasis' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
pCAPiontwiseEpistasis 49.57   0.03   49.61
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
pCAPiontwiseEpistasis 55.6   0.08   55.69
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/FRGEpistasis.Rcheck/00check.log'
for details.



Installation output

FRGEpistasis.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/FRGEpistasis_1.18.0.tar.gz && rm -rf FRGEpistasis.buildbin-libdir && mkdir FRGEpistasis.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FRGEpistasis.buildbin-libdir FRGEpistasis_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL FRGEpistasis_1.18.0.zip && rm FRGEpistasis_1.18.0.tar.gz FRGEpistasis_1.18.0.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  133k  100  133k    0     0  4172k      0 --:--:-- --:--:-- --:--:-- 4609k

install for i386

* installing *source* package 'FRGEpistasis' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'FRGEpistasis'
    finding HTML links ... done
    FRGEpistasis-package                    html  
    fRGEpistasis                            html  
    fRGInteraction                          html  
    fourierExpansion                        html  
    frgEpistasisTest                        html  
    innerEpi                                html  
    innerSnpListInteraction                 html  
    logTransPheno                           html  
    outerEpi                                html  
    outerSnpListInteraction                 html  
    pCAInteraction                          html  
    pCAPiontwiseEpistasis                   html  
    pointwiseInteraction                    html  
    rankTransPheno                          html  
    reduceGeno                              html  
    snpPairInteraction                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'FRGEpistasis' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FRGEpistasis' as FRGEpistasis_1.18.0.zip
* DONE (FRGEpistasis)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'FRGEpistasis' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

FRGEpistasis.Rcheck/examples_i386/FRGEpistasis-Ex.timings

nameusersystemelapsed
fRGEpistasis1.770.032.83
fRGInteraction0.020.000.01
fourierExpansion0.070.010.10
frgEpistasisTest0.750.040.78
innerEpi0.020.000.02
innerSnpListInteraction000
logTransPheno000
outerEpi0.090.000.09
outerSnpListInteraction0.000.010.01
pCAInteraction0.570.000.57
pCAPiontwiseEpistasis49.57 0.0349.61
pointwiseInteraction0.210.020.22
rankTransPheno000
reduceGeno0.370.010.39
snpPairInteraction000

FRGEpistasis.Rcheck/examples_x64/FRGEpistasis-Ex.timings

nameusersystemelapsed
fRGEpistasis1.890.041.92
fRGInteraction000
fourierExpansion0.080.000.08
frgEpistasisTest0.550.000.54
innerEpi0.010.000.02
innerSnpListInteraction000
logTransPheno0.020.000.02
outerEpi0.080.000.07
outerSnpListInteraction0.010.000.02
pCAInteraction0.360.010.37
pCAPiontwiseEpistasis55.60 0.0855.69
pointwiseInteraction0.20.00.2
rankTransPheno000
reduceGeno0.300.030.33
snpPairInteraction000