* Package: sci-biology/blasr-9999  * Repository: science  * Maintainer: sci-biology@gentoo.org  * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU  * FEATURES: nostrip preserve-libs sandbox splitdebug userpriv usersandbox >>> Unpacking source... * Fetching https://github.com/PacificBiosciences/blasr.git ... git fetch https://github.com/PacificBiosciences/blasr.git +HEAD:refs/git-r3/HEAD git symbolic-ref refs/git-r3/sci-biology/blasr/0/__main__ refs/git-r3/HEAD * Fetching git://github.com/PacificBiosciences/blasr_libcpp.git ... git fetch git://github.com/PacificBiosciences/blasr_libcpp.git --prune +refs/heads/*:refs/heads/* +refs/tags/*:refs/tags/* +refs/notes/*:refs/notes/* +HEAD:refs/git-r3/HEAD git update-ref --no-deref refs/git-r3/sci-biology/blasr/0/libcpp/__main__ 7af74b9bc5ebbb19b6a466dfc43815ed1cf8ac39 * Checking out https://github.com/PacificBiosciences/blasr.git to /scratch/var/tmp/portage/sci-biology/blasr-9999/work/blasr-9999 ... git checkout --quiet refs/git-r3/HEAD GIT update --> repository: https://github.com/PacificBiosciences/blasr.git at the commit: 3194382a781276fb6bc52f71cfad6f69b3a97abb * Checking out git://github.com/PacificBiosciences/blasr_libcpp.git to /scratch/var/tmp/portage/sci-biology/blasr-9999/work/blasr-9999/libcpp ... git checkout --quiet 7af74b9bc5ebbb19b6a466dfc43815ed1cf8ac39 GIT update --> repository: git://github.com/PacificBiosciences/blasr_libcpp.git at the commit: 7af74b9bc5ebbb19b6a466dfc43815ed1cf8ac39 >>> Source unpacked in /scratch/var/tmp/portage/sci-biology/blasr-9999/work >>> Preparing source in /scratch/var/tmp/portage/sci-biology/blasr-9999/work/blasr-9999 ... >>> Source prepared. >>> Configuring source in /scratch/var/tmp/portage/sci-biology/blasr-9999/work/blasr-9999 ... `uname` Linux writing to '/scratch/var/tmp/portage/sci-biology/blasr-9999/work/blasr-9999/defines.mk': """ LIBPBDATA_LIB ?= /scratch/var/tmp/portage/sci-biology/blasr-9999/work/blasr-9999/libcpp/pbdata LIBBLASR_LIBFLAGS ?= -lblasr SHELL ?= bash DL_LIBFLAGS ?= -ldl LIBPBDATA_INC ?= /scratch/var/tmp/portage/sci-biology/blasr-9999/work/blasr-9999/libcpp/pbdata LIBPBIHDF_LIBFLAGS ?= -lpbihdf LIBPBIHDF_INC ?= /scratch/var/tmp/portage/sci-biology/blasr-9999/work/blasr-9999/libcpp/hdf LIBBLASR_LIB ?= /scratch/var/tmp/portage/sci-biology/blasr-9999/work/blasr-9999/libcpp/alignment CXXFLAGS ?= -O2 -pipe -maes -mpclmul -mpopcnt -mavx -march=native RT_LIBFLAGS ?= -lrt HDF5_LIBFLAGS ?= -lhdf5_cpp -lhdf5 LIBPBDATA_LIBFLAGS ?= -lpbdata ZLIB_LIBFLAGS ?= -lz LIBBLASR_INC ?= /scratch/var/tmp/portage/sci-biology/blasr-9999/work/blasr-9999/libcpp/alignment PTHREAD_LIBFLAGS ?= -lpthread NOPBBAM ?= 1 LIBPBIHDF_LIB ?= /scratch/var/tmp/portage/sci-biology/blasr-9999/work/blasr-9999/libcpp/hdf """ ---- >>> Source configured. >>> Compiling source in /scratch/var/tmp/portage/sci-biology/blasr-9999/work/blasr-9999 ... make -j2 g++ -O2 -pipe -maes -mpclmul -mpopcnt -mavx -march=native -O3 -g -DSHA1_7=\"3194382\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -I/scratch/var/tmp/portage/sci-biology/blasr-9999/work/blasr-9999/libcpp/alignment -I/scratch/var/tmp/portage/sci-biology/blasr-9999/work/blasr-9999/libcpp/hdf -I/scratch/var/tmp/portage/sci-biology/blasr-9999/work/blasr-9999/libcpp/pbdata -c -o Blasr.o Blasr.cpp make -C utils make[1]: Entering directory '/scratch/var/tmp/portage/sci-biology/blasr-9999/work/blasr-9999/utils' g++ -O2 -pipe -maes -mpclmul -mpopcnt -mavx -march=native -O3 -g -DSHA1_7=\"3194382\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -I/scratch/var/tmp/portage/sci-biology/blasr-9999/work/blasr-9999/libcpp/alignment -I/scratch/var/tmp/portage/sci-biology/blasr-9999/work/blasr-9999/libcpp/hdf -I/scratch/var/tmp/portage/sci-biology/blasr-9999/work/blasr-9999/libcpp/pbdata -c -o LoadPulses.o LoadPulses.cpp In file included from LoadPulses.cpp:3:0: /scratch/var/tmp/portage/sci-biology/blasr-9999/work/blasr-9999/libcpp/hdf/HDFCmpFile.hpp:9:19: fatal error: H5Cpp.h: No such file or directory compilation terminated. : recipe for target 'LoadPulses.o' failed make[1]: *** [LoadPulses.o] Error 1 make[1]: Leaving directory '/scratch/var/tmp/portage/sci-biology/blasr-9999/work/blasr-9999/utils' makefile:67: recipe for target 'makeutils' failed make: *** [makeutils] Error 2 make: *** Waiting for unfinished jobs.... In file included from /scratch/var/tmp/portage/sci-biology/blasr-9999/work/blasr-9999/libcpp/alignment/files/../../hdf/HDFBasReader.hpp:18:0, from /scratch/var/tmp/portage/sci-biology/blasr-9999/work/blasr-9999/libcpp/alignment/files/ReaderAgglomerate.hpp:14, from iblasr/BlasrHeaders.h:78, from iblasr/BlasrMiscs.hpp:4, from Blasr.cpp:3: /scratch/var/tmp/portage/sci-biology/blasr-9999/work/blasr-9999/libcpp/alignment/files/../../hdf/HDFArray.hpp:7:19: fatal error: H5Cpp.h: No such file or directory compilation terminated. : recipe for target 'Blasr.o' failed make: *** [Blasr.o] Error 1 * ERROR: sci-biology/blasr-9999::science failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/blasr-9999::science'`, * the complete build log and the output of `emerge -pqv '=sci-biology/blasr-9999::science'`. * The complete build log is located at '/scratch/var/tmp/portage/sci-biology/blasr-9999/temp/build.log'. * The ebuild environment file is located at '/scratch/var/tmp/portage/sci-biology/blasr-9999/temp/environment'. * Working directory: '/scratch/var/tmp/portage/sci-biology/blasr-9999/work/blasr-9999' * S: '/scratch/var/tmp/portage/sci-biology/blasr-9999/work/blasr-9999'