Package: TDARACNE

Version: 1.28.0

Command: rm -rf TDARACNE.buildbin-libdir TDARACNE.Rcheck && mkdir TDARACNE.buildbin-libdir TDARACNE.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TDARACNE.buildbin-libdir TDARACNE_1.28.0.tar.gz >TDARACNE.Rcheck\00install.out 2>&1 && cp TDARACNE.Rcheck\00install.out TDARACNE-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=TDARACNE.buildbin-libdir --install="check:TDARACNE-install.out" --force-multiarch --no-vignettes --timings TDARACNE_1.28.0.tar.gz

StartedAt: 2018-04-12 03:33:50 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:35:04 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 73.7 seconds

RetCode: 0

Status:  OK

CheckDir: TDARACNE.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf TDARACNE.buildbin-libdir TDARACNE.Rcheck && mkdir TDARACNE.buildbin-libdir TDARACNE.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TDARACNE.buildbin-libdir TDARACNE_1.28.0.tar.gz >TDARACNE.Rcheck\00install.out 2>&1 && cp TDARACNE.Rcheck\00install.out TDARACNE-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=TDARACNE.buildbin-libdir --install="check:TDARACNE-install.out" --force-multiarch --no-vignettes --timings TDARACNE_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/TDARACNE.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 'TDARACNE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TDARACNE' 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 'TDARACNE' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Found the following CITATION file in a non-standard place:
  inst/CITATION.txt
Most likely 'inst/CITATION' should be used instead.
* 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
'library' or 'require' calls to packages already attached by Depends:
  'Biobase' 'GenKern' 'Rgraphviz'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Biobase' 'GenKern' 'Rgraphviz'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CalcMI_time2: no visible global function definition for 'dpik'
CalcMI_time2: no visible global function definition for 'KernSec'
CalcMI_time2: no visible global function definition for 'KernSur'
MItimeThreshperm2: no visible global function definition for 'sd'
PercentileC: no visible global function definition for 'quantile'
TDARACNE: no visible global function definition for 'exprs'
TDARACNE: no visible global function definition for 'as'
TDARACNEdataPublished: no visible global function definition for 'data'
TDARACNEdataPublished: no visible binding for global variable
  'dataYeast'
TDARACNEdataPublished: no visible binding for global variable
  'dataSOSmean'
TDARACNEdataPublished: no visible binding for global variable
  'dataIRMAon'
TDARACNEdataPublished: no visible binding for global variable
  'threshIRMAon'
TDARACNEdataPublished: no visible binding for global variable
  'threshSOSmean'
TDARACNEdataPublished: no visible binding for global variable
  'threshYeast'
bootstrap: no visible global function definition for 'runif'
bootstrap: no visible global function definition for 'rgeom'
plotRgraphviz: no visible global function definition for 'new'
plotRgraphviz: no visible global function definition for 'plot'
Undefined global functions or variables:
  KernSec KernSur as data dataIRMAon dataSOSmean dataYeast dpik exprs
  new plot quantile rgeom runif sd threshIRMAon threshSOSmean
  threshYeast
Consider adding
  importFrom("graphics", "plot")
  importFrom("methods", "as", "new")
  importFrom("stats", "quantile", "rgeom", "runif", "sd")
  importFrom("utils", "data")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
Examples with CPU or elapsed time > 5s
                      user system elapsed
TDARACNEdataPublished  9.8   0.11     9.9
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
TDARACNEdataPublished 10.51   0.09   10.61
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/TDARACNE.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'TDARACNE' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'TDARACNE'
    finding HTML links ... done
    CalcMI_time2                            html  
    DPI2_TDAracne                           html  
    DPI_TDAracne                            html  
    IcEfx                                   html  
    MItimeIcE2                              html  
    MItimeThreshperm2                       html  
    PercentileC                             html  
    RangeRank2                              html  
    TDARACNE                                html  
    TDARACNEdataPublished                   html  
    ToTheGraph_timeShiftmax2                html  
    bootstrap                               html  
    dataIRMAoff                             html  
    dataIRMAon                              html  
    dataSOSmean                             html  
    dataYeast                               html  
    plotRgraphviz                           html  
    saveTime                                html  
    threshIRMAon                            html  
    threshSOSmean                           html  
    threshYeast                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'TDARACNE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TDARACNE' as TDARACNE_1.28.0.zip
* DONE (TDARACNE)
In R CMD INSTALL
In R CMD INSTALL