Package: EBSeqHMM

Version: 1.18.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EBSeqHMM.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings EBSeqHMM_1.18.0.tar.gz

StartedAt: 2019-10-16 03:26:29 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:27:51 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 82.1 seconds

RetCode: 0

Status:  OK

CheckDir: EBSeqHMM.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EBSeqHMM.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings EBSeqHMM_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/EBSeqHMM.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'EBSeqHMM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'EBSeqHMM' version '1.18.0'
* 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 'EBSeqHMM' 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 ... NOTE
EBHMMNBfun: no visible binding for global variable 'median'
EBHMMNBfun : : no visible global function definition for
  'quantile'
EBHMMNBfun: no visible global function definition for 'optim'
EBHMMNBfunForMulti: no visible binding for global variable 'median'
EBHMMNBfunForMulti : : no visible global function definition
  for 'quantile'
EBHMMNBfunForMulti: no visible global function definition for 'optim'
EBSeqHMMTest : : no visible global function definition for
  'quantile'
EBTest_ext: no visible global function definition for 'quantile'
EBTest_ext: no visible binding for global variable 'var'
PlotExp: no visible global function definition for 'plot'
PlotExp: no visible global function definition for 'axis'
PlotExp : : no visible global function definition for
  'median'
PlotExp: no visible global function definition for 'lines'
beta.mom: no visible global function definition for 'var'
Undefined global functions or variables:
  axis lines median optim plot quantile var
Consider adding
  importFrom("graphics", "axis", "lines", "plot")
  importFrom("stats", "median", "optim", "quantile", "var")
to your NAMESPACE file.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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-3.9-bioc/meat/EBSeqHMM.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/EBSeqHMM_1.18.0.tar.gz && rm -rf EBSeqHMM.buildbin-libdir && mkdir EBSeqHMM.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=EBSeqHMM.buildbin-libdir EBSeqHMM_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL EBSeqHMM_1.18.0.zip && rm EBSeqHMM_1.18.0.tar.gz EBSeqHMM_1.18.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100  550k  100  550k    0     0  8129k      0 --:--:-- --:--:-- --:--:-- 9020k

install for i386

* installing *source* package 'EBSeqHMM' ...
** using staged installation
** R
** data
** demo
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'EBSeqHMM'
    finding HTML links ... done
    EBHMMNBMultiEM_2chain                   html  
    EBHMMNBfun                              html  
    EBHMMNBfunForMulti                      html  
    EBSeqHMM-package                        html  
    EBSeqHMMTest                            html  
    EBTest_ext                              html  
    finding level-2 HTML links ... done

    GeneExampleData                         html  
    GetAllPaths                             html  
    GetConfidentCalls                       html  
    GetDECalls                              html  
    IsoExampleList                          html  
    LikefunNBHMM                            html  
    PlotExp                                 html  
    beta.mom                                html  
    f0                                      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 'EBSeqHMM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'EBSeqHMM' as EBSeqHMM_1.18.0.zip
* DONE (EBSeqHMM)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'EBSeqHMM' successfully unpacked and MD5 sums checked