Package: mQTL.NMR

Version: 1.12.0

Command: rm -rf mQTL.NMR.buildbin-libdir mQTL.NMR.Rcheck && mkdir mQTL.NMR.buildbin-libdir mQTL.NMR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mQTL.NMR.buildbin-libdir mQTL.NMR_1.12.0.tar.gz >mQTL.NMR.Rcheck\00install.out 2>&1 && cp mQTL.NMR.Rcheck\00install.out mQTL.NMR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=mQTL.NMR.buildbin-libdir --install="check:mQTL.NMR-install.out" --force-multiarch --no-vignettes --timings mQTL.NMR_1.12.0.tar.gz

StartedAt: 2018-04-12 01:37:32 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:42:40 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 308.3 seconds

RetCode: 0

Status:  OK

CheckDir: mQTL.NMR.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf mQTL.NMR.buildbin-libdir mQTL.NMR.Rcheck && mkdir mQTL.NMR.buildbin-libdir mQTL.NMR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mQTL.NMR.buildbin-libdir mQTL.NMR_1.12.0.tar.gz >mQTL.NMR.Rcheck\00install.out 2>&1 && cp mQTL.NMR.Rcheck\00install.out mQTL.NMR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=mQTL.NMR.buildbin-libdir --install="check:mQTL.NMR-install.out" --force-multiarch --no-vignettes --timings mQTL.NMR_1.12.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/mQTL.NMR.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 'mQTL.NMR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mQTL.NMR' version '1.12.0'
* 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 'mQTL.NMR' 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 ... NOTE
Found the following CITATION file in a non-standard place:
  inst/CITATION.Rd
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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
circle_mQTL: no visible global function definition for 'rainbow'
post_mQTL: no visible global function definition for 'dev.new'
post_mQTL: no visible global function definition for 'png'
post_mQTL: no visible global function definition for 'dev.off'
ppersp: no visible global function definition for 'colorRampPalette'
Undefined global functions or variables:
  colorRampPalette dev.new dev.off png rainbow
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.new", "dev.off",
             "png", "rainbow")
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 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
pre_mQTL         36.00   0.17   36.17
mQTL.NMR-package 34.55   0.16   34.74
align_mQTL       26.95   0.11   27.06
process_mGWA      5.95   0.02    6.14
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mQTL.NMR-package 41.18   0.11   41.55
pre_mQTL         32.53   0.11   32.64
align_mQTL       29.91   0.09   30.00
process_mGWA      7.85   0.00    7.97
* 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/mQTL.NMR.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'mQTL.NMR' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'mQTL.NMR'
    finding HTML links ... done
    SRV                                     html  
    SRV.plot                                html  
    SRV_lod.plot                            html  
    Top_SRV.plot                            html  
    alignSp                                 html  
    align_mQTL                              html  
    attachSegments                          html  
    circle_mQTL                             html  
    configureRSPA                           html  
    format_mGWA                             html  
    format_mQTL                             html  
    load_datafiles                          html  
    load_demo_data                          html  
    mQTL.NMR-package                        html  
    matchSegments                           html  
    normalise                               html  
    normalise_mQTL                          html  
    peakPeaks                               html  
    post_mQTL                               html  
    ppersp                                  html  
    pplot                                   html  
    pre_mQTL                                html  
    process_mGWA                            html  
    process_mQTL                            html  
    segmentateSp                            html  
    selectRefSp                             html  
    setupRSPA                               html  
    sgolay                                  html  
    sgolayDeriv                             html  
    simple.plot                             html  
    summary_mQTL                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'mQTL.NMR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mQTL.NMR' as mQTL.NMR_1.12.0.zip
* DONE (mQTL.NMR)
In R CMD INSTALL
In R CMD INSTALL