BioC 3.3: INSTALL report for snapCGH on windows2.bioconductor.org

Package: snapCGH

Version: 1.41.0

Command: C:\cygwin64\bin\curl.exe -O http://linux2.bioconductor.org/BBS/3.3/bioc/src/contrib/snapCGH_1.41.0.tar.gz && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch snapCGH_1.41.0.tar.gz && rm snapCGH_1.41.0.tar.gz

StartedAt: 2015-10-26 21:07:31 -0400 (Mon, 26 Oct 2015)

EndedAt: 2015-10-26 21:07:47 -0400 (Mon, 26 Oct 2015)

EllapsedTime: 16.3 seconds

RetCode: 0

Status:  OK

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### Running command:
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###   C:\cygwin64\bin\curl.exe -O http://linux2.bioconductor.org/BBS/3.3/bioc/src/contrib/snapCGH_1.41.0.tar.gz && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch snapCGH_1.41.0.tar.gz && rm snapCGH_1.41.0.tar.gz
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  619k  100  619k    0     0  52.8M      0 --:--:-- --:--:-- --:--:-- 86.4M

install for i386

* installing to library 'c:/biocbld/bbs-3.3-bioc/R/library'
* installing *source* package 'snapCGH' ...
** libs
gcc -m32 -I"c:/biocbld/BBS-3˜1.3-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 -Lc:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to c:/biocbld/bbs-3.3-bioc/R/library/snapCGH/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing to library 'c:/biocbld/bbs-3.3-bioc/R/library'
* installing *source* package 'snapCGH' ...
** libs
gcc -m64 -I"c:/biocbld/BBS-3˜1.3-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 -Lc:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to c:/biocbld/bbs-3.3-bioc/R/library/snapCGH/libs/x64
** testing if installed package can be loaded
* DONE (snapCGH)