Package: CODEX

Version: 1.10.0

Command: rm -rf CODEX.buildbin-libdir CODEX.Rcheck && mkdir CODEX.buildbin-libdir CODEX.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CODEX.buildbin-libdir CODEX_1.10.0.tar.gz >CODEX.Rcheck\00install.out 2>&1 && cp CODEX.Rcheck\00install.out CODEX-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CODEX.buildbin-libdir --install="check:CODEX-install.out" --force-multiarch --no-vignettes --timings CODEX_1.10.0.tar.gz

StartedAt: 2018-04-11 23:05:45 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 23:13:14 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 448.5 seconds

RetCode: 0

Status:  OK

CheckDir: CODEX.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf CODEX.buildbin-libdir CODEX.Rcheck && mkdir CODEX.buildbin-libdir CODEX.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CODEX.buildbin-libdir CODEX_1.10.0.tar.gz >CODEX.Rcheck\00install.out 2>&1 && cp CODEX.Rcheck\00install.out CODEX-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CODEX.buildbin-libdir --install="check:CODEX-install.out" --force-multiarch --no-vignettes --timings CODEX_1.10.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/CODEX.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 'CODEX/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CODEX' version '1.10.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'Rsamtools' 'GenomeInfoDb' 'BSgenome.Hsapiens.UCSC.hg19' 'IRanges'
  'Biostrings' 'S4Vectors'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'CODEX' 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
choiceofK: no visible global function definition for 'pdf'
choiceofK: no visible global function definition for 'par'
choiceofK: no visible global function definition for 'plot'
choiceofK: no visible global function definition for 'dev.off'
getbambed: no visible global function definition for 'read.table'
normalize : <anonymous>: no visible global function definition for
  'smooth.spline'
normalize : <anonymous>: no visible global function definition for
  'predict'
normalize: no visible global function definition for 'glm'
normalize: no visible binding for global variable 'poisson'
normalize: no visible global function definition for 'lm'
normalize2 : <anonymous>: no visible global function definition for
  'smooth.spline'
normalize2 : <anonymous>: no visible global function definition for
  'predict'
normalize2: no visible global function definition for 'glm'
normalize2: no visible binding for global variable 'poisson'
normalize2: no visible global function definition for 'lm'
Undefined global functions or variables:
  dev.off glm lm par pdf plot poisson predict read.table smooth.spline
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "glm", "lm", "poisson", "predict", "smooth.spline")
  importFrom("utils", "read.table")
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
Examples with CPU or elapsed time > 5s
             user system elapsed
normalize   33.87   0.28   34.17
normalize2  22.94   0.00   22.94
getcoverage 10.13   0.50   35.92
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
normalize   39.09   0.02   39.11
normalize2  27.72   0.03   27.75
getcoverage  9.47   0.53   10.01
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/CODEX.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'CODEX' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'CODEX'
    finding HTML links ... done
    CODEX-package                           html  
    bambedObjDemo                           html  
    choiceofK                               html  
    coverageObjDemo                         html  
    gcDemo                                  html  
    getbambed                               html  
    getcoverage                             html  
    getgc                                   html  
    getmapp                                 html  
    mappDemo                                html  
    mapp_ref                                html  
    mappability                             html  
    normObjDemo                             html  
    normalize                               html  
    normalize2                              html  
    qc                                      html  
    qcObjDemo                               html  
    segment                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'CODEX' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CODEX' as CODEX_1.10.0.zip
* DONE (CODEX)
In R CMD INSTALL
In R CMD INSTALL