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### Running command:
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### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/cn.farms_1.42.0.tar.gz && rm -rf cn.farms.buildbin-libdir && mkdir cn.farms.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cn.farms.buildbin-libdir cn.farms_1.42.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL cn.farms_1.42.0.zip && rm cn.farms_1.42.0.tar.gz cn.farms_1.42.0.zip
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install for i386
* installing *source* package 'cn.farms' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_cnfarms.c -o R_init_cnfarms.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sparse_farms.c -o sparse_farms.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o cn.farms.dll tmp.def R_init_cnfarms.o laplace.o sparse_farms.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/cn.farms.buildbin-libdir/00LOCK-cn.farms/00new/cn.farms/libs/i386
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'cn.farms'
finding HTML links ... done
callSummarize html
cn.farms html
cnLibrary html
combineData html
createAnnotation html
createMatrix html
distributionDistance html
dnaCopySf html
doCnFarmsSingle html
flcSnp6Std html
flcStd html
fragLengCorr html
getFragmentSet html
getSingleProbeSetSize html
mlSummarization html
normAdd html
normalizeAverage html
normalizeCels html
normalizeNone html
normalizeNpData html
normalizeQuantiles html
normalizeSequenceEffect html
normalizeSor html
plotDendrogram html
plotDensity html
plotEvalIc html
plotRegions html
plotSmoothScatter html
plotViolines html
slSummarization html
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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'cn.farms' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_cnfarms.c -o R_init_cnfarms.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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:364:35: warning: 'I1left' may be used uninitialized in this function [-Wmaybe-uninitialized]
double I2left=(-leftMy/leftSigma)*I1left+I0left;
~~~~~~~~~~~~~~~~~~~^~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sparse_farms.c -o sparse_farms.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o cn.farms.dll tmp.def R_init_cnfarms.o laplace.o sparse_farms.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-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_1.42.0.zip
* DONE (cn.farms)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'cn.farms' successfully unpacked and MD5 sums checked
