CHECK report for cn.farms on tokay1
This page was generated on 2018-04-12 13:20:45 -0400 (Thu, 12 Apr 2018).
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 | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
Summary
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
###
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* 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
|
cn.farms.Rcheck/examples_x64/cn.farms-Ex.timings
|