############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL snapCGH ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘snapCGH’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c optimizer.c -o optimizer.o optimizer.c: In function ‘fr_two’: optimizer.c:26:30: warning: unused variable ‘temp3’ [-Wunused-variable] 26 | double denom, temp, temp2, temp3; | ^~~~~ optimizer.c:26:23: warning: unused variable ‘temp2’ [-Wunused-variable] 26 | double denom, temp, temp2, temp3; | ^~~~~ optimizer.c:26:10: warning: unused variable ‘denom’ [-Wunused-variable] 26 | double denom, temp, temp2, temp3; | ^~~~~ optimizer.c: In function ‘fr_three’: optimizer.c:195:30: warning: unused variable ‘temp3’ [-Wunused-variable] 195 | double denom, temp, temp2, temp3; | ^~~~~ optimizer.c:195:23: warning: unused variable ‘temp2’ [-Wunused-variable] 195 | double denom, temp, temp2, temp3; | ^~~~~ optimizer.c:195:10: warning: unused variable ‘denom’ [-Wunused-variable] 195 | double denom, temp, temp2, temp3; | ^~~~~ optimizer.c:194:69: warning: unused variable ‘alphahat’ [-Wunused-variable] 194 | 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] 413 | double denom, temp, temp2, temp3; | ^~~~~ optimizer.c:413:23: warning: unused variable ‘temp2’ [-Wunused-variable] 413 | double denom, temp, temp2, temp3; | ^~~~~ optimizer.c:413:10: warning: unused variable ‘denom’ [-Wunused-variable] 413 | double denom, temp, temp2, temp3; | ^~~~~ optimizer.c:412:69: warning: unused variable ‘alphahat’ [-Wunused-variable] 412 | 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] 687 | double denom, temp, temp2, temp3; | ^~~~~ optimizer.c:687:23: warning: unused variable ‘temp2’ [-Wunused-variable] 687 | double denom, temp, temp2, temp3; | ^~~~~ optimizer.c:687:10: warning: unused variable ‘denom’ [-Wunused-variable] 687 | double denom, temp, temp2, temp3; | ^~~~~ optimizer.c:686:69: warning: unused variable ‘alphahat’ [-Wunused-variable] 686 | double gammaA[5][5], gammaB[5][5], gammaC[5][5], alpha[5][nrow1], alphahat[5][nrow1], emis_prob[5][nrow1]; | ^~~~~~~~ gcc -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o snapCGH.so optimizer.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-snapCGH/00new/snapCGH/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (snapCGH)