Package: ELBOW

Version: 1.14.0

Command: rm -rf ELBOW.buildbin-libdir ELBOW.Rcheck && mkdir ELBOW.buildbin-libdir ELBOW.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ELBOW.buildbin-libdir ELBOW_1.14.0.tar.gz >ELBOW.Rcheck\00install.out 2>&1 && cp ELBOW.Rcheck\00install.out ELBOW-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ELBOW.buildbin-libdir --install="check:ELBOW-install.out" --force-multiarch --no-vignettes --timings ELBOW_1.14.0.tar.gz

StartedAt: 2018-04-11 23:44:25 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 23:45:15 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 49.6 seconds

RetCode: 0

Status:  OK

CheckDir: ELBOW.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf ELBOW.buildbin-libdir ELBOW.Rcheck && mkdir ELBOW.buildbin-libdir ELBOW.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ELBOW.buildbin-libdir ELBOW_1.14.0.tar.gz >ELBOW.Rcheck\00install.out 2>&1 && cp ELBOW.Rcheck\00install.out ELBOW-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ELBOW.buildbin-libdir --install="check:ELBOW-install.out" --force-multiarch --no-vignettes --timings ELBOW_1.14.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ELBOW.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ELBOW/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ELBOW' version '1.14.0'
* 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 'ELBOW' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
do_elbow: no visible global function definition for 'smooth.spline'
do_elbow: no visible global function definition for 'predict'
do_elbow_rnaseq: no visible global function definition for 'na.omit'
get_pvalue: no visible global function definition for 'glm'
get_pvalue: no visible global function definition for 'binomial'
null_variance: no visible binding for global variable 'median'
plot_dataset: no visible global function definition for 'plot'
plot_dataset: no visible global function definition for 'abline'
plot_elbow: no visible global function definition for 'plot'
plot_elbow: no visible global function definition for 'abline'
plot_elbow: no visible global function definition for 'lines'
plot_elbow: no visible global function definition for 'text'
replicates_to_fold: no visible global function definition for 'head'
Undefined global functions or variables:
  abline binomial glm head lines median na.omit plot predict
  smooth.spline text
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "text")
  importFrom("stats", "binomial", "glm", "median", "na.omit", "predict",
             "smooth.spline")
  importFrom("utils", "head")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
do_elbow_rnaseq 4.89   0.14    5.04
* 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-3.6-bioc/meat/ELBOW.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'ELBOW' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'ELBOW'
    finding HTML links ... done
    ELBOW-package                           html  
    EcoliMutMA                              html  
    EcoliWT                                 html  
    GSE20986_design                         html  
    GSE20986_eset_exprs                     html  
    analyze_elbow                           html  
    do_elbow                                html  
    do_elbow_rnaseq                         html  
    elbow_variance                          html  
    extract_working_sets                    html  
    get_elbow_limma                         html  
    get_pvalue                              html  
    null_variance                           html  
    plot_dataset                            html  
    plot_elbow                              html  
    replicates_to_fold                      html  
    yeast_nbinomTest_results                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'ELBOW' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ELBOW' as ELBOW_1.14.0.zip
* DONE (ELBOW)
In R CMD INSTALL
In R CMD INSTALL