Package: SimBindProfiles

Version: 1.16.0

Command: rm -rf SimBindProfiles.buildbin-libdir SimBindProfiles.Rcheck && mkdir SimBindProfiles.buildbin-libdir SimBindProfiles.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SimBindProfiles.buildbin-libdir SimBindProfiles_1.16.0.tar.gz >SimBindProfiles.Rcheck\00install.out 2>&1 && cp SimBindProfiles.Rcheck\00install.out SimBindProfiles-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SimBindProfiles.buildbin-libdir --install="check:SimBindProfiles-install.out" --force-multiarch --no-vignettes --timings SimBindProfiles_1.16.0.tar.gz

StartedAt: 2018-04-12 03:13:39 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:17:15 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 216.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: SimBindProfiles.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf SimBindProfiles.buildbin-libdir SimBindProfiles.Rcheck && mkdir SimBindProfiles.buildbin-libdir SimBindProfiles.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SimBindProfiles.buildbin-libdir SimBindProfiles_1.16.0.tar.gz >SimBindProfiles.Rcheck\00install.out 2>&1 && cp SimBindProfiles.Rcheck\00install.out SimBindProfiles-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SimBindProfiles.buildbin-libdir --install="check:SimBindProfiles-install.out" --force-multiarch --no-vignettes --timings SimBindProfiles_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/SimBindProfiles.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 'SimBindProfiles/DESCRIPTION' ... OK
* this is package 'SimBindProfiles' 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 'SimBindProfiles' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaYEZ1I/R.INSTALL344c41f54815/SimBindProfiles/man/probeAnnoFromESet.Rd:33: missing file link 'probeAnno-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaYEZ1I/R.INSTALL344c41f54815/SimBindProfiles/man/readSgrFiles.Rd:29: missing file link 'ExpressionSet'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/SimBindProfiles.Rcheck/00install.out' for details.
* 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
compensationRegions: no visible global function definition for
  'write.table'
eSetScatterPlot : upPan: no visible global function definition for
  'par'
eSetScatterPlot : upPan: no visible global function definition for
  'smoothScatter'
eSetScatterPlot : lowPan: no visible global function definition for
  'text'
eSetScatterPlot : lowPan: no visible global function definition for
  'par'
eSetScatterPlot : lowPan: no visible global function definition for
  'cor'
eSetScatterPlot: no visible global function definition for 'pairs'
filterRegionsPairwise: no visible global function definition for 'tail'
filterRegionsThreeway: no visible global function definition for 'tail'
findBoundCutoff: no visible global function definition for 'hist'
findBoundCutoff: no visible global function definition for 'p.adjust'
increasedBindingRegions: no visible global function definition for
  'write.table'
normalNull: no visible global function definition for 'na.omit'
normalNull: no visible global function definition for 'density'
normalNull: no visible global function definition for 'sd'
normalNull: no visible global function definition for 'pnorm'
pairwiseRegions: no visible global function definition for
  'write.table'
plotBoundProbes: no visible global function definition for 'points'
probeLengthPlot: no visible global function definition for 'tail'
readSgrFiles: no visible global function definition for 'read.delim'
threewayRegions: no visible global function definition for
  'write.table'
twoGaussiansNull.BF: no visible global function definition for
  'na.omit'
twoGaussiansNull.BF: no visible global function definition for 'dnorm'
twoGaussiansNull.BF: no visible global function definition for 'lines'
twoGaussiansNull.BF: no visible global function definition for 'legend'
twoGaussiansNull.BF: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  cor density dnorm hist legend lines na.omit p.adjust pairs par pnorm
  points read.delim sd smoothScatter tail text write.table
Consider adding
  importFrom("graphics", "hist", "legend", "lines", "pairs", "par",
             "points", "smoothScatter", "text")
  importFrom("stats", "cor", "density", "dnorm", "na.omit", "p.adjust",
             "pnorm", "sd")
  importFrom("utils", "read.delim", "tail", "write.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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/SimBindProfiles.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'SimBindProfiles' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'SimBindProfiles'
    finding HTML links ... done
    SGR                                     html  
    SimBindProfiles-package                 html  
    compensationRegions                     html  
    eSetScatterPlot                         html  
    findBoundCutoff                         html  
    increasedBindingRegions                 html  
    pairwiseRegions                         html  
    plotBoundProbes                         html  
    probeAnnoFromESet                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaYEZ1I/R.INSTALL344c41f54815/SimBindProfiles/man/probeAnnoFromESet.Rd:33: missing file link 'probeAnno-class'
    probeLengthPlot                         html  
    readSgrFiles                            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpaYEZ1I/R.INSTALL344c41f54815/SimBindProfiles/man/readSgrFiles.Rd:29: missing file link 'ExpressionSet'
    threewayRegions                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'SimBindProfiles' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SimBindProfiles' as SimBindProfiles_1.16.0.zip
* DONE (SimBindProfiles)
In R CMD INSTALL
In R CMD INSTALL