Package: msmsTests

Version: 1.16.0

Command: rm -rf msmsTests.buildbin-libdir msmsTests.Rcheck && mkdir msmsTests.buildbin-libdir msmsTests.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=msmsTests.buildbin-libdir msmsTests_1.16.0.tar.gz >msmsTests.Rcheck\00install.out 2>&1 && cp msmsTests.Rcheck\00install.out msmsTests-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=msmsTests.buildbin-libdir --install="check:msmsTests-install.out" --force-multiarch --no-vignettes --timings msmsTests_1.16.0.tar.gz

StartedAt: 2018-04-12 01:39:29 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:43:10 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 220.9 seconds

RetCode: 0

Status:  OK

CheckDir: msmsTests.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf msmsTests.buildbin-libdir msmsTests.Rcheck && mkdir msmsTests.buildbin-libdir msmsTests.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=msmsTests.buildbin-libdir msmsTests_1.16.0.tar.gz >msmsTests.Rcheck\00install.out 2>&1 && cp msmsTests.Rcheck\00install.out msmsTests-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=msmsTests.buildbin-libdir --install="check:msmsTests-install.out" --force-multiarch --no-vignettes --timings msmsTests_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/msmsTests.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 'msmsTests/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'msmsTests' version '1.16.0'
* 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 'msmsTests' 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
* 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 ... NOTE
Packages in Depends field not imported from:
  'MSnbase' 'msmsEDA'
  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
glm.pois: no visible global function definition for 'glm'
glm.pois: no visible global function definition for 'as.formula'
glm.pois: no visible global function definition for 'poisson'
glm.pois: no visible global function definition for 'coef'
glm.pois: no visible global function definition for 'anova'
msms.edgeR: no visible global function definition for 'exprs'
msms.edgeR: no visible global function definition for 'pData'
msms.edgeR: no visible global function definition for 'model.matrix'
msms.edgeR: no visible global function definition for 'as.formula'
msms.glm.pois: no visible global function definition for 'exprs'
msms.glm.pois: no visible global function definition for 'pData'
msms.glm.qlll: no visible global function definition for 'exprs'
msms.glm.qlll: no visible global function definition for 'pData'
qp.test: no visible global function definition for 'glm'
qp.test: no visible global function definition for 'as.formula'
qp.test: no visible global function definition for 'quasi'
qp.test: no visible binding for global variable 'mu'
qp.test: no visible global function definition for 'coef'
qp.test: no visible global function definition for 'anova'
res.volcanoplot: no visible global function definition for 'plot'
res.volcanoplot: no visible global function definition for 'grid'
res.volcanoplot: no visible global function definition for 'abline'
res.volcanoplot: no visible global function definition for 'points'
res.volcanoplot: no visible global function definition for 'text'
test.results: no visible global function definition for 'exprs'
test.results: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  abline anova as.formula coef exprs glm grid model.matrix mu p.adjust
  pData plot points poisson quasi text
Consider adding
  importFrom("graphics", "abline", "grid", "plot", "points", "text")
  importFrom("stats", "anova", "as.formula", "coef", "glm",
             "model.matrix", "p.adjust", "poisson", "quasi")
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
test.results    8.66   0.01    8.67
res.volcanoplot 7.29   0.00    7.29
msms.glm.pois   6.87   0.00    6.87
pval.by.fc      6.58   0.00    6.58
msms.glm.qlll   6.35   0.03    6.38
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
msms.glm.pois   9.42   0.00    9.42
msms.glm.qlll   8.22   0.00    8.22
test.results    8.02   0.01    8.03
res.volcanoplot 7.72   0.00    7.72
pval.by.fc      6.50   0.02    6.52
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'xtable'
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/msmsTests.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'msmsTests' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'msmsTests'
    finding HTML links ... done
    msms.edgeR                              html  
    finding level-2 HTML links ... done

    msms.glm.pois                           html  
    msms.glm.qlll                           html  
    msms.spk                                html  
    msmsTests-package                       html  
    pval.by.fc                              html  
    res.volcanoplot                         html  
    test.results                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'msmsTests' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'msmsTests' as msmsTests_1.16.0.zip
* DONE (msmsTests)
In R CMD INSTALL
In R CMD INSTALL