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### Running command:
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### C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.1/bioc/src/contrib/snapCGH_1.38.0.tar.gz && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch snapCGH_1.38.0.tar.gz && rm snapCGH_1.38.0.tar.gz
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install for i386
* installing to library 'E:/biocbld/bbs-3.1-bioc/R/library'
* installing *source* package 'snapCGH' ...
** libs
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c optimizer.c -o optimizer.o
optimizer.c: In function 'fr_two':
optimizer.c:26:30: warning: unused variable 'temp3' [-Wunused-variable]
optimizer.c:26:23: warning: unused variable 'temp2' [-Wunused-variable]
optimizer.c:26:10: warning: unused variable 'denom' [-Wunused-variable]
optimizer.c: In function 'fr_three':
optimizer.c:195:30: warning: unused variable 'temp3' [-Wunused-variable]
optimizer.c:195:23: warning: unused variable 'temp2' [-Wunused-variable]
optimizer.c:195:10: warning: unused variable 'denom' [-Wunused-variable]
optimizer.c:194:69: warning: unused variable 'alphahat' [-Wunused-variable]
optimizer.c: In function 'fr_four':
optimizer.c:413:30: warning: unused variable 'temp3' [-Wunused-variable]
optimizer.c:413:23: warning: unused variable 'temp2' [-Wunused-variable]
optimizer.c:413:10: warning: unused variable 'denom' [-Wunused-variable]
optimizer.c:412:69: warning: unused variable 'alphahat' [-Wunused-variable]
optimizer.c: In function 'fr_five':
optimizer.c:687:30: warning: unused variable 'temp3' [-Wunused-variable]
optimizer.c:687:23: warning: unused variable 'temp2' [-Wunused-variable]
optimizer.c:687:10: warning: unused variable 'denom' [-Wunused-variable]
optimizer.c:686:69: warning: unused variable 'alphahat' [-Wunused-variable]
optimizer.c:997:58: warning: 'gammaC[4][4]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[4][3]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[4][2]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[4][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[4][0]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[3][4]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[3][3]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[3][2]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[3][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[3][0]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[2][4]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[2][3]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[2][2]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[2][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[2][0]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[1][4]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[1][3]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[1][2]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[1][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[1][0]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[0][4]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[0][3]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[0][2]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[0][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:997:58: warning: 'gammaC[0][0]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:943:4: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
optimizer.c: In function 'fr_four':
optimizer.c:641:58: warning: 'gammaC[3][3]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[3][2]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[3][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[3][0]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[2][3]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[2][2]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[2][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[2][0]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[1][3]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[1][2]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[1][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[1][0]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[0][3]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[0][2]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[0][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:641:58: warning: 'gammaC[0][0]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:585:1: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
optimizer.c: In function 'fr_three':
optimizer.c:366:58: warning: 'gammaC[2][2]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:366:58: warning: 'gammaC[2][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:366:58: warning: 'gammaC[2][0]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:366:58: warning: 'gammaC[1][2]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:366:58: warning: 'gammaC[1][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:366:58: warning: 'gammaC[1][0]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:366:58: warning: 'gammaC[0][2]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:366:58: warning: 'gammaC[0][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:366:58: warning: 'gammaC[0][0]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c: In function 'fr_two':
optimizer.c:150:58: warning: 'gammaC[1][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:150:58: warning: 'gammaC[1][0]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:150:58: warning: 'gammaC[0][1]' may be used uninitialized in this function [-Wuninitialized]
optimizer.c:150:58: warning: 'gammaC[0][0]' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -shared -s -static-libgcc -o snapCGH.dll tmp.def optimizer.o -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.1-bioc/R/library/snapCGH/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc, :
No generic function found corresponding to requested imported methods for "as.list" from package "multtest" (malformed exports?)
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc, :
No generic function found corresponding to requested imported methods for "as.list" from package "multtest" (malformed exports?)
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
install for x64
* installing to library 'E:/biocbld/bbs-3.1-bioc/R/library'
* installing *source* package 'snapCGH' ...
** libs
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c optimizer.c -o optimizer.o
optimizer.c: In function 'fr_two':
optimizer.c:26:30: warning: unused variable 'temp3' [-Wunused-variable]
optimizer.c:26:23: warning: unused variable 'temp2' [-Wunused-variable]
optimizer.c:26:10: warning: unused variable 'denom' [-Wunused-variable]
optimizer.c: In function 'fr_three':
optimizer.c:195:30: warning: unused variable 'temp3' [-Wunused-variable]
optimizer.c:195:23: warning: unused variable 'temp2' [-Wunused-variable]
optimizer.c:195:10: warning: unused variable 'denom' [-Wunused-variable]
optimizer.c:194:69: warning: unused variable 'alphahat' [-Wunused-variable]
optimizer.c: In function 'fr_four':
optimizer.c:413:30: warning: unused variable 'temp3' [-Wunused-variable]
optimizer.c:413:23: warning: unused variable 'temp2' [-Wunused-variable]
optimizer.c:413:10: warning: unused variable 'denom' [-Wunused-variable]
optimizer.c:412:69: warning: unused variable 'alphahat' [-Wunused-variable]
optimizer.c: In function 'fr_five':
optimizer.c:687:30: warning: unused variable 'temp3' [-Wunused-variable]
optimizer.c:687:23: warning: unused variable 'temp2' [-Wunused-variable]
optimizer.c:687:10: warning: unused variable 'denom' [-Wunused-variable]
optimizer.c:686:69: warning: unused variable 'alphahat' [-Wunused-variable]
optimizer.c:943:4: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
optimizer.c: In function 'fr_four':
optimizer.c:585:1: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
gcc -m64 -shared -s -static-libgcc -o snapCGH.dll tmp.def optimizer.o -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.1-bioc/R/library/snapCGH/libs/x64
** testing if installed package can be loaded
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc, :
No generic function found corresponding to requested imported methods for "as.list" from package "multtest" (malformed exports?)
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* DONE (snapCGH)