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AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for cn.farms on tokay1

This page was generated on 2018-04-12 13:20:45 -0400 (Thu, 12 Apr 2018).

Package 255/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.farms 1.26.0
Andreas Mitterecker
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/cn.farms
Branch: RELEASE_3_6
Last Commit: 30312a1
Last Changed Date: 2017-10-30 12:39:33 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cn.farms
Version: 1.26.0
Command: rm -rf cn.farms.buildbin-libdir cn.farms.Rcheck && mkdir cn.farms.buildbin-libdir cn.farms.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cn.farms.buildbin-libdir cn.farms_1.26.0.tar.gz >cn.farms.Rcheck\00install.out 2>&1 && cp cn.farms.Rcheck\00install.out cn.farms-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=cn.farms.buildbin-libdir --install="check:cn.farms-install.out" --force-multiarch --no-vignettes --timings cn.farms_1.26.0.tar.gz
StartedAt: 2018-04-11 23:01:30 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 23:06:14 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 284.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: cn.farms.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf cn.farms.buildbin-libdir cn.farms.Rcheck && mkdir cn.farms.buildbin-libdir cn.farms.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cn.farms.buildbin-libdir cn.farms_1.26.0.tar.gz >cn.farms.Rcheck\00install.out 2>&1 && cp cn.farms.Rcheck\00install.out cn.farms-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=cn.farms.buildbin-libdir --install="check:cn.farms-install.out" --force-multiarch --no-vignettes --timings cn.farms_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/cn.farms.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 'cn.farms/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cn.farms' version '1.26.0'
* 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 'cn.farms' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/cn.farms.Rd:16: missing file link 'ExpressionSet-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/combineData.Rd:10: missing file link 'ExpressionSet-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/combineData.Rd:13: missing file link 'ExpressionSet-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/combineData.Rd:29: missing file link 'ExpressionSet-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/dnaCopySf.Rd:22: missing file link 'ExpressionSet-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/fragLengCorr.Rd:10: missing file link 'ExpressionSet-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/fragLengCorr.Rd:20: missing file link 'ExpressionSet-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/mlSummarization.Rd:10: missing file link 'ExpressionSet-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/mlSummarization.Rd:36: missing file link 'ExpressionSet-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/normalizeNone.Rd:29: missing file link 'ExpressionSet-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/normalizeNpData.Rd:25: missing file link 'ExpressionSet-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/normalizeSequenceEffect.Rd:11: missing file link 'ExpressionSet-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/normalizeSor.Rd:29: missing file link 'ExpressionSet-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/plotEvalIc.Rd:12: missing file link 'ExpressionSet-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/plotRegions.Rd:10: missing file link 'ExpressionSet-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/plotRegions.Rd:12: missing file link 'ExpressionSet-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/plotSmoothScatter.Rd:9: missing file link 'ExpressionSet-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/plotViolines.Rd:10: missing file link 'ExpressionSet-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/slSummarization.Rd:12: missing file link 'ExpressionSet-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/slSummarization.Rd:35: missing file link 'ExpressionSet-class'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/cn.farms.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
calcDistance: no visible global function definition for 'density'
callSummarizeH01: no visible binding for global variable 'var'
callSummarizeH01: no visible global function definition for 'rnorm'
createAnnotation: no visible global function definition for
  'installed.packages'
determineBaselineArray: no visible binding for global variable 'median'
flcSnp6Std: no visible global function definition for 'lowess'
flcSnp6Std: no visible global function definition for 'approx'
flcSnp6StdH01: no visible global function definition for 'lowess'
flcSnp6StdH01: no visible global function definition for 'approx'
flcStd: no visible global function definition for 'lowess'
flcStd: no visible global function definition for 'approx'
flcStdH01: no visible global function definition for 'lowess'
flcStdH01: no visible global function definition for 'approx'
getProbePositionEffectDesignMatrix: no visible global function
  definition for 'head'
getVar: no visible global function definition for 'getFromNamespace'
initializeBigMatrix: no visible global function definition for
  'isPackageLoaded'
normalizeAverage: no visible binding for global variable 'median'
normalizeAverage: no visible global function definition for 'median'
normalizeSorH01: no visible binding for global variable 'pairs'
normalizeSorH01: no visible global function definition for 'median'
plotDendrogram : colLab: no visible global function definition for
  'is.leaf'
plotDendrogram: no visible global function definition for
  'as.dendrogram'
plotDendrogram: no visible global function definition for 'hclust'
plotDendrogram: no visible global function definition for
  'order.dendrogram'
plotDendrogram: no visible global function definition for 'dendrapply'
plotDendrogram: no visible global function definition for 'plot'
plotDensity: no visible global function definition for 'density'
plotDensity: no visible global function definition for 'plot'
plotDensity: no visible global function definition for 'lines'
plotEvalIc: no visible global function definition for 'rgb'
plotEvalIc: no visible global function definition for 'plot'
plotEvalIc: no visible global function definition for 'rect'
plotEvalIc: no visible global function definition for 'points'
plotEvalIc: no visible global function definition for 'densCols'
plotEvalIc: no visible global function definition for 'mtext'
plotRegions: no visible global function definition for 'pdf'
plotRegions: no visible global function definition for 'plot'
plotRegions: no visible global function definition for 'text'
plotRegions: no visible global function definition for 'par'
plotRegions: no visible global function definition for 'matplot'
plotRegions: no visible global function definition for 'abline'
plotRegions: no visible global function definition for 'matlines'
plotRegions: no visible global function definition for 'legend'
plotRegions: no visible global function definition for 'axis'
plotRegions: no visible global function definition for 'nclass.Sturges'
plotRegions: no visible global function definition for 'dev.off'
plotSmoothScatter: no visible global function definition for 'pdf'
plotSmoothScatter: no visible global function definition for
  'smoothScatter'
plotSmoothScatter: no visible global function definition for 'abline'
plotSmoothScatter: no visible global function definition for 'loess'
plotSmoothScatter: no visible global function definition for 'points'
plotSmoothScatter: no visible global function definition for 'dev.off'
setVar: no visible global function definition for 'assignInNamespace'
sfClusterSetupSPRNG: no visible global function definition for 'runif'
sfExport: no visible global function definition for 'getFromNamespace'
sfExportAll: no visible global function definition for 'na.omit'
sfInit: no visible global function definition for 'packageDescription'
sfTest : testCalc1: no visible global function definition for 'runif'
sfTest : testCalc2: no visible global function definition for 'runif'
summarizeFarmsExact: no visible global function definition for 'median'
summarizeFarmsExact: no visible binding for global variable 'median'
summarizeFarmsExact: no visible global function definition for 'pchisq'
summarizeFarmsExact2: no visible global function definition for
  'median'
summarizeFarmsExact2: no visible binding for global variable 'median'
summarizeFarmsExact2: no visible global function definition for
  'pchisq'
summarizeFarmsExact3: no visible global function definition for
  'median'
summarizeFarmsExact3: no visible binding for global variable 'median'
summarizeFarmsExact3: no visible global function definition for
  'pchisq'
summarizeFarmsGaussian: no visible global function definition for
  'median'
summarizeFarmsGaussian: no visible binding for global variable 'median'
summarizeFarmsGaussian: no visible global function definition for 'var'
summarizeFarmsStatistics: no visible binding for global variable
  'median'
summarizeFarmsStatistics: no visible global function definition for
  'median'
summarizeFarmsVariational: no visible binding for global variable
  'median'
summarizeFarmsVariational: no visible global function definition for
  'sd'
summarizeFarmsVariational: no visible global function definition for
  'median'
summarizeFarmsVariational: no visible global function definition for
  'var'
Undefined global functions or variables:
  abline approx as.dendrogram assignInNamespace axis dendrapply
  densCols density dev.off getFromNamespace hclust head
  installed.packages is.leaf isPackageLoaded legend lines loess lowess
  matlines matplot median mtext na.omit nclass.Sturges order.dendrogram
  packageDescription pairs par pchisq pdf plot points rect rgb rnorm
  runif sd smoothScatter text var
Consider adding
  importFrom("grDevices", "densCols", "dev.off", "nclass.Sturges", "pdf",
             "rgb")
  importFrom("graphics", "abline", "axis", "legend", "lines", "matlines",
             "matplot", "mtext", "pairs", "par", "plot", "points",
             "rect", "smoothScatter", "text")
  importFrom("stats", "approx", "as.dendrogram", "dendrapply", "density",
             "hclust", "is.leaf", "loess", "lowess", "median", "na.omit",
             "order.dendrogram", "pchisq", "rnorm", "runif", "sd", "var")
  importFrom("utils", "assignInNamespace", "getFromNamespace", "head",
             "installed.packages", "packageDescription")
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 R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/cn.farms.buildbin-libdir/cn.farms/libs/i386/cn.farms.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/cn.farms.Rcheck/00check.log'
for details.



Installation output

cn.farms.Rcheck/00install.out


install for i386

* installing *source* package 'cn.farms' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_cnfarms.c -o R_init_cnfarms.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c laplace.cpp -o laplace.o
laplace.cpp: In function 'SEXPREC* momentsGauss(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
laplace.cpp:442:6: warning: unused variable 'method' [-Wunused-variable]
  int method=0;
      ^
laplace.cpp: In function 'void computeParameters(double, double, double, double, double, double, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&)':
laplace.cpp:368:56: warning: 'I1right' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double rightMoment1=1.0*rightMy*I0right+1.0*rightSigma*I1right;
                                                        ^
laplace.cpp:393:86: warning: 'I1left' may be used uninitialized in this function [-Wmaybe-uninitialized]
  moment2 = (-0.5*a+0.25*(b-1/sigmaZ)*(b-1/sigmaZ)+(b*leftWeight)/(sigmaZ)+(leftWeight*I1left*sqrtMa)/(sqrt(2.0)*sigmaZ))/(a*a);
                                                                                      ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c sparse_farms.c -o sparse_farms.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o cn.farms.dll tmp.def R_init_cnfarms.o laplace.o sparse_farms.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/cn.farms.buildbin-libdir/cn.farms/libs/i386
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'cn.farms'
    finding HTML links ... done
    callSummarize                           html  
    cn.farms                                html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/cn.farms.Rd:16: missing file link 'ExpressionSet-class'
    cnLibrary                               html  
    combineData                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/combineData.Rd:10: missing file link 'ExpressionSet-class'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/combineData.Rd:13: missing file link 'ExpressionSet-class'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/combineData.Rd:29: missing file link 'ExpressionSet-class'
    createAnnotation                        html  
    createMatrix                            html  
    distributionDistance                    html  
    dnaCopySf                               html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/dnaCopySf.Rd:22: missing file link 'ExpressionSet-class'
    doCnFarmsSingle                         html  
    flcSnp6Std                              html  
    flcStd                                  html  
    fragLengCorr                            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/fragLengCorr.Rd:10: missing file link 'ExpressionSet-class'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/fragLengCorr.Rd:20: missing file link 'ExpressionSet-class'
    getFragmentSet                          html  
    getSingleProbeSetSize                   html  
    mlSummarization                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/mlSummarization.Rd:10: missing file link 'ExpressionSet-class'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/mlSummarization.Rd:36: missing file link 'ExpressionSet-class'
    normAdd                                 html  
    normalizeAverage                        html  
    normalizeCels                           html  
    normalizeNone                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/normalizeNone.Rd:29: missing file link 'ExpressionSet-class'
    normalizeNpData                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/normalizeNpData.Rd:25: missing file link 'ExpressionSet-class'
    normalizeQuantiles                      html  
    normalizeSequenceEffect                 html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/normalizeSequenceEffect.Rd:11: missing file link 'ExpressionSet-class'
    normalizeSor                            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/normalizeSor.Rd:29: missing file link 'ExpressionSet-class'
    plotDendrogram                          html  
    plotDensity                             html  
    plotEvalIc                              html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/plotEvalIc.Rd:12: missing file link 'ExpressionSet-class'
    plotRegions                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/plotRegions.Rd:10: missing file link 'ExpressionSet-class'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/plotRegions.Rd:12: missing file link 'ExpressionSet-class'
    plotSmoothScatter                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/plotSmoothScatter.Rd:9: missing file link 'ExpressionSet-class'
    plotViolines                            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/plotViolines.Rd:10: missing file link 'ExpressionSet-class'
    slSummarization                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/slSummarization.Rd:12: missing file link 'ExpressionSet-class'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpisI8jF/R.INSTALL1dbc4e7971e1/cn.farms/man/slSummarization.Rd:35: missing file link 'ExpressionSet-class'
    sparseFarmsC                            html  
    summarizeFarmsExact                     html  
    summarizeFarmsExact2                    html  
    summarizeFarmsExact3                    html  
    summarizeFarmsGaussian                  html  
    summarizeFarmsMethods                   html  
    summarizeFarmsStatistics                html  
    summarizeFarmsVariational               html  
    summarizeWindowBps                      html  
    summarizeWindowMethods                  html  
    summarizeWindowStd                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'cn.farms' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_cnfarms.c -o R_init_cnfarms.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c laplace.cpp -o laplace.o
laplace.cpp: In function 'SEXPREC* momentsGauss(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
laplace.cpp:442:6: warning: unused variable 'method' [-Wunused-variable]
  int method=0;
      ^
laplace.cpp: In function 'void computeParameters(double, double, double, double, double, double, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&)':
laplace.cpp:368:56: warning: 'I1right' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double rightMoment1=1.0*rightMy*I0right+1.0*rightSigma*I1right;
                                                        ^
laplace.cpp:367:52: warning: 'I1left' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double leftMoment1=1.0*leftMy*I0left+1.0*leftSigma*I1left;
                                                    ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c sparse_farms.c -o sparse_farms.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o cn.farms.dll tmp.def R_init_cnfarms.o laplace.o sparse_farms.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/cn.farms.buildbin-libdir/cn.farms/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cn.farms' as cn.farms_1.26.0.zip
* DONE (cn.farms)
In R CMD INSTALL
In R CMD INSTALL

Tests output


Example timings

cn.farms.Rcheck/examples_i386/cn.farms-Ex.timings

nameusersystemelapsed
cn.farms0.020.000.01
combineData1.810.041.97
createAnnotation000
distributionDistance0.170.000.17
dnaCopySf0.530.020.55
fragLengCorr1.800.001.79
mlSummarization3.500.333.83
normalizeAverage000
normalizeCels000
normalizeNpData000
plotDendrogram0.170.000.17
plotDensity0.530.000.53
plotEvalIc0.330.040.38
plotRegions0.210.000.20
plotSmoothScatter0.450.020.47
plotViolines0.120.000.12
slSummarization2.990.173.16
sparseFarmsC000
summarizeFarmsExact000
summarizeFarmsExact2000
summarizeFarmsExact30.020.000.02
summarizeFarmsGaussian000
summarizeFarmsMethods000
summarizeFarmsVariational000
summarizeWindowBps0.030.000.03
summarizeWindowMethods000
summarizeWindowStd000

cn.farms.Rcheck/examples_x64/cn.farms-Ex.timings

nameusersystemelapsed
cn.farms000
combineData2.230.052.36
createAnnotation000
distributionDistance0.190.000.19
dnaCopySf1.390.071.45
fragLengCorr2.670.012.69
mlSummarization3.700.083.78
normalizeAverage000
normalizeCels000
normalizeNpData000
plotDendrogram0.170.020.19
plotDensity0.50.00.5
plotEvalIc0.380.000.37
plotRegions0.560.010.58
plotSmoothScatter0.380.020.39
plotViolines0.120.000.13
slSummarization3.600.003.59
sparseFarmsC000
summarizeFarmsExact0.010.000.02
summarizeFarmsExact2000
summarizeFarmsExact3000
summarizeFarmsGaussian0.020.000.01
summarizeFarmsMethods000
summarizeFarmsVariational000
summarizeWindowBps0.010.000.02
summarizeWindowMethods000
summarizeWindowStd000