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BioC 3.3: INSTALL report for snapCGH on moscato2

This page was generated on 2016-10-13 12:47:44 -0700 (Thu, 13 Oct 2016).

Package 1089/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
snapCGH 1.42.0
John Marioni
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/snapCGH
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: snapCGH
Version: 1.42.0
Command: rm -rf snapCGH.buildbin-libdir && mkdir snapCGH.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.3/bioc/src/contrib/snapCGH_1.42.0.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --library=snapCGH.buildbin-libdir --merge-multiarch snapCGH_1.42.0.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL snapCGH_1.42.0.zip && rm snapCGH_1.42.0.tar.gz snapCGH_1.42.0.zip
StartedAt: 2016-10-12 19:02:28 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 19:03:55 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 86.7 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf snapCGH.buildbin-libdir && mkdir snapCGH.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.3/bioc/src/contrib/snapCGH_1.42.0.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --library=snapCGH.buildbin-libdir --merge-multiarch snapCGH_1.42.0.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL snapCGH_1.42.0.zip  && rm snapCGH_1.42.0.tar.gz snapCGH_1.42.0.zip
###
##############################################################################
##############################################################################




install for i386

* installing *source* package 'snapCGH' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/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]
   double denom, temp, temp2, temp3;
                              ^
optimizer.c:26:23: warning: unused variable 'temp2' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                       ^
optimizer.c:26:10: warning: unused variable 'denom' [-Wunused-variable]
   double denom, temp, temp2, temp3;
          ^
optimizer.c: In function 'fr_three':
optimizer.c:195:30: warning: unused variable 'temp3' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                              ^
optimizer.c:195:23: warning: unused variable 'temp2' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                       ^
optimizer.c:195:10: warning: unused variable 'denom' [-Wunused-variable]
   double denom, temp, temp2, temp3;
          ^
optimizer.c:194:69: warning: unused variable 'alphahat' [-Wunused-variable]
   double gammaA[3][3], gammaB[3][3], gammaC[3][3], alpha[3][nrow1], alphahat[3][nrow1], emis_prob[3][nrow1];
                                                                     ^
optimizer.c: In function 'fr_four':
optimizer.c:413:30: warning: unused variable 'temp3' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                              ^
optimizer.c:413:23: warning: unused variable 'temp2' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                       ^
optimizer.c:413:10: warning: unused variable 'denom' [-Wunused-variable]
   double denom, temp, temp2, temp3;
          ^
optimizer.c:412:69: warning: unused variable 'alphahat' [-Wunused-variable]
   double gammaA[4][4], gammaB[4][4], gammaC[4][4], alpha[4][nrow1], alphahat[4][nrow1], emis_prob[4][nrow1];
                                                                     ^
optimizer.c: In function 'fr_five':
optimizer.c:687:30: warning: unused variable 'temp3' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                              ^
optimizer.c:687:23: warning: unused variable 'temp2' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                       ^
optimizer.c:687:10: warning: unused variable 'denom' [-Wunused-variable]
   double denom, temp, temp2, temp3;
          ^
optimizer.c:686:69: warning: unused variable 'alphahat' [-Wunused-variable]
   double gammaA[5][5], gammaB[5][5], gammaC[5][5], alpha[5][nrow1], alphahat[5][nrow1], emis_prob[5][nrow1];
                                                                     ^
optimizer.c: In function 'fr_two':
optimizer.c:150:58: warning: 'gammaC[1][1]' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 alpha[k][t] = alpha[k][t] + alpha[d][t-1]*gammaC[d][k];
                                                          ^
optimizer.c:150:58: warning: 'gammaC[1][0]' may be used uninitialized in this function [-Wmaybe-uninitialized]
optimizer.c:150:58: warning: 'gammaC[0][1]' may be used uninitialized in this function [-Wmaybe-uninitialized]
optimizer.c:150:58: warning: 'gammaC[0][0]' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o snapCGH.dll tmp.def optimizer.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/snapCGH.buildbin-libdir/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 *source* package 'snapCGH' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/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]
   double denom, temp, temp2, temp3;
                              ^
optimizer.c:26:23: warning: unused variable 'temp2' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                       ^
optimizer.c:26:10: warning: unused variable 'denom' [-Wunused-variable]
   double denom, temp, temp2, temp3;
          ^
optimizer.c: In function 'fr_three':
optimizer.c:195:30: warning: unused variable 'temp3' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                              ^
optimizer.c:195:23: warning: unused variable 'temp2' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                       ^
optimizer.c:195:10: warning: unused variable 'denom' [-Wunused-variable]
   double denom, temp, temp2, temp3;
          ^
optimizer.c:194:69: warning: unused variable 'alphahat' [-Wunused-variable]
   double gammaA[3][3], gammaB[3][3], gammaC[3][3], alpha[3][nrow1], alphahat[3][nrow1], emis_prob[3][nrow1];
                                                                     ^
optimizer.c: In function 'fr_four':
optimizer.c:413:30: warning: unused variable 'temp3' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                              ^
optimizer.c:413:23: warning: unused variable 'temp2' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                       ^
optimizer.c:413:10: warning: unused variable 'denom' [-Wunused-variable]
   double denom, temp, temp2, temp3;
          ^
optimizer.c:412:69: warning: unused variable 'alphahat' [-Wunused-variable]
   double gammaA[4][4], gammaB[4][4], gammaC[4][4], alpha[4][nrow1], alphahat[4][nrow1], emis_prob[4][nrow1];
                                                                     ^
optimizer.c: In function 'fr_five':
optimizer.c:687:30: warning: unused variable 'temp3' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                              ^
optimizer.c:687:23: warning: unused variable 'temp2' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                       ^
optimizer.c:687:10: warning: unused variable 'denom' [-Wunused-variable]
   double denom, temp, temp2, temp3;
          ^
optimizer.c:686:69: warning: unused variable 'alphahat' [-Wunused-variable]
   double gammaA[5][5], gammaB[5][5], gammaC[5][5], alpha[5][nrow1], alphahat[5][nrow1], emis_prob[5][nrow1];
                                                                     ^
optimizer.c:943:4: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
    for(t = 1; t < nrow1; t++){
    ^
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]
 for(t = 1; t < nrow1; t++){  
 ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o snapCGH.dll tmp.def optimizer.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/snapCGH.buildbin-libdir/snapCGH/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'snapCGH' as snapCGH_1.42.0.zip
* DONE (snapCGH)
* installing to library 'E:/biocbld/bbs-3.3-bioc/R/library'
package 'snapCGH' successfully unpacked and MD5 sums checked