Package: DEqMS

Version: 1.0.1

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEqMS.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DEqMS_1.0.1.tar.gz

StartedAt: 2019-04-13 01:43:41 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 01:50:48 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 427.0 seconds

RetCode: 0

Status:  OK

CheckDir: DEqMS.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEqMS.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DEqMS_1.0.1.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/DEqMS.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DEqMS/DESCRIPTION' ... OK
* this is package 'DEqMS' version '1.0.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'DEqMS' 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 ... 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
peptideProfilePlot: no visible binding for global variable 'variable'
peptideProfilePlot: no visible binding for global variable 'value'
peptideProfilePlot: no visible binding for global variable 'PSM_id'
peptideProfilePlot: no visible binding for global variable 'Peptide'
Undefined global functions or variables:
  PSM_id Peptide value variable
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
medpolishSummary         71.05   0.07   71.21
farmsSummary             33.02   0.86   34.05
equalMedianNormalization 12.83   0.91   14.02
medianSummary             6.98   0.18    7.26
outputResult              6.39   0.24    6.73
plotFitCurve              6.07   0.23    6.35
spectraCounteBayes        6.12   0.10    6.29
medianSweeping            5.39   0.18    5.64
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
medpolishSummary         85.45   0.16   85.72
farmsSummary             35.54   0.68   36.42
equalMedianNormalization 11.91   0.91   13.05
plotFitCurve              6.69   0.12    6.87
outputResult              6.30   0.09    6.52
spectraCounteBayes        6.14   0.16    6.38
medianSummary             6.04   0.16    6.30
medianSweeping            5.66   0.14    5.86
* 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-3.8-bioc/meat/DEqMS.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/DEqMS_1.0.1.tar.gz && rm -rf DEqMS.buildbin-libdir && mkdir DEqMS.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DEqMS.buildbin-libdir DEqMS_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL DEqMS_1.0.1.zip && rm DEqMS_1.0.1.tar.gz DEqMS_1.0.1.zip
###
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install for i386

* installing *source* package 'DEqMS' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DEqMS'
    finding HTML links ... done
    equalMedianNormalization                html  
    farmsSummary                            html  
    medianSummary                           html  
    medianSweeping                          html  
    medpolishSummary                        html  
    outputResult                            html  
    peptideProfilePlot                      html  
    plotFitCurve                            html  
    spectraCounteBayes                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'DEqMS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DEqMS' as DEqMS_1.0.1.zip
* DONE (DEqMS)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'DEqMS' successfully unpacked and MD5 sums checked
In R CMD INSTALL