##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL DNAcopy
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘DNAcopy’ ...
** using staged installation
** libs
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2  -Wall -c cbsWtstats.f -o cbsWtstats.o
cbsWtstats.f:283:0:

  283 |       iseg(2) = tmaxj
      | 
Warning: ‘tmaxj’ may be used uninitialized in this function [-Wmaybe-uninitialized]
cbsWtstats.f:282:0:

  282 |       iseg(1) = tmaxi
      | 
Warning: ‘tmaxi’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2  -Wall -c cbststats.f -o cbststats.o
cbststats.f:258:0:

  258 |                      tmaxj = sxmxi + i2j
      | 
Warning: ‘sxmxi’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2  -Wall -c changepoints-wtd.f -o changepoints-wtd.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2  -Wall -c changepoints.f -o changepoints.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2  -Wall -c esegment.f -o esegment.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c flchoose.c -o flchoose.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c fphyper.c -o fphyper.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c fpnorm.c -o fpnorm.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2  -Wall -c getbdry.f -o getbdry.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2  -Wall -c prune.f -o prune.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c rshared.c -o rshared.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2  -Wall -c segmentp.f -o segmentp.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2  -Wall -c smoothCNA.f -o smoothCNA.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2  -Wall -c tailprobs.f -o tailprobs.o
gcc -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o DNAcopy.so cbsWtstats.o cbststats.o changepoints-wtd.o changepoints.o esegment.o flchoose.o fphyper.o fpnorm.o getbdry.o prune.o rshared.o segmentp.o smoothCNA.o tailprobs.o -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-DNAcopy/00new/DNAcopy/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** 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 (DNAcopy)