kmc (homebrew/science/kmc) on "Red Hat Enterprise Linux Server release 7.2 (Maipo)" - Homebrew build logs

# kmc - 2016-05-14_09-07-12.txt

Homebrew build logs for homebrew/science/kmc on "Red Hat Enterprise Linux Server release 7.2 (Maipo)"
Build date: 2016-05-14 09:07:12

00.config.out

HOMEBREW_VERSION: 0.9.9
ORIGIN: https://github.com/Linuxbrew/brew.git
HEAD: b570bf7ea17ad9cebb5adc9296f4f77aaaed50d8
Last commit: 3 days ago
Core tap ORIGIN: https://github.com/Linuxbrew/homebrew-core
Core tap HEAD: c22d002f6d0b8921e6a4f2dcf861312f6568768e
Core tap last commit: 4 days ago
HOMEBREW_PREFIX: /bio/linuxbrew
HOMEBREW_REPOSITORY: /bio/linuxbrew
HOMEBREW_CELLAR: /bio/linuxbrew/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://linuxbrew.bintray.com
CPU: 72-core 64-bit haswell
Kernel: Linux 3.10.0-327.13.1.el7.x86_64 x86_64 GNU/Linux
OS: Red Hat Enterprise Linux Server release 7.2 (Maipo)
Codename: Maipo
OS glibc: 2.17
OS gcc: 4.8.5
Linuxbrew glibc: N/A
Linuxbrew gcc: 5.3.0
Clang: N/A
X11: 2.7.8 => /usr
System Ruby: 2.3.0 => /bio/linuxbrew/Cellar/ruby/2.3.0/bin/ruby
Perl: /usr/bin/perl
Python: /bio/linuxbrew/bin/python => /bio/linuxbrew/Cellar/python/2.7.11/bin/python2.7
Ruby: /bio/linuxbrew/bin/ruby => /bio/linuxbrew/Cellar/ruby/2.3.0/bin/ruby
Java: openjdk version "1.8.0_77"

00.doctor.out

Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry and just ignore them. Thanks!

Warning: You have unlinked kegs in your Cellar
Leaving kegs unlinked can lead to build-trouble and cause brews that depend on
those kegs to fail to run properly once built. Run `brew link` on these:
    minia
    viennarna
    barrnap
    libdivsufsort
    pillow
    snippy
    prokka
    abricate
    nullarbor
    tmux

Warning: Broken symlinks were found. Remove them with `brew prune`:
    /bio/linuxbrew/lib/R/library/survival/NEWS.Rd.orig

00.tap.out

Formula: kmc
Tap: homebrew/science
Path: /bio/linuxbrew/Library/Taps/homebrew/homebrew-science/kmc.rb

01.make

2016-05-14 09:07:12 +1000

make
CC=/bio/linuxbrew/bin/g++-5
-fmakefile

makefile:73: target 'kmc_api/mmer.o' given more than once in the same rule
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11  -c kmer_counter/kmer_counter.cpp -o kmer_counter/kmer_counter.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11  -c kmer_counter/mmer.cpp -o kmer_counter/mmer.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11  -c kmer_counter/mem_disk_file.cpp -o kmer_counter/mem_disk_file.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11  -c kmer_counter/rev_byte.cpp -o kmer_counter/rev_byte.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11  -c kmer_counter/bkb_writer.cpp -o kmer_counter/bkb_writer.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11  -c kmer_counter/bkb_reader.cpp -o kmer_counter/bkb_reader.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11  -c kmer_counter/fastq_reader.cpp -o kmer_counter/fastq_reader.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11  -c kmer_counter/timer.cpp -o kmer_counter/timer.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11  -c kmer_counter/radix.cpp -o kmer_counter/radix.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11  -c kmer_counter/kb_completer.cpp -o kmer_counter/kb_completer.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11  -c kmer_counter/kb_storer.cpp -o kmer_counter/kb_storer.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11  -c kmer_counter/kmer.cpp -o kmer_counter/kmer.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11  -c kmer_counter/prob_qual.cpp -o kmer_counter/prob_qual.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11  -c kmc_dump/nc_utils.cpp -o kmc_dump/nc_utils.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11  -c kmc_api/mmer.cpp -o kmc_api/mmer.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11  -c kmc_dump/kmc_dump.cpp -o kmc_dump/kmc_dump.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11  -c kmc_api/kmc_file.cpp -o kmc_api/kmc_file.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11  -c kmc_api/kmer_api.cpp -o kmc_api/kmer_api.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14 -c kmc_tools/kmc_header.cpp -o kmc_tools/kmc_header.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14 -c kmc_tools/kmc_tools.cpp -o kmc_tools/kmc_tools.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14 -c kmc_tools/nc_utils.cpp -o kmc_tools/nc_utils.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14 -c kmc_tools/parameters_parser.cpp -o kmc_tools/parameters_parser.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14 -c kmc_tools/parser.cpp -o kmc_tools/parser.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14 -c kmc_tools/tokenizer.cpp -o kmc_tools/tokenizer.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14 -c kmc_tools/fastq_filter.cpp -o kmc_tools/fastq_filter.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14 -c kmc_tools/fastq_reader.cpp -o kmc_tools/fastq_reader.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14 -c kmc_tools/fastq_writer.cpp -o kmc_tools/fastq_writer.o
/bio/linuxbrew/bin/g++-5 -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14 -c kmc_tools/percent_progress.cpp -o kmc_tools/percent_progress.o
kmc_api/kmc_file.cpp: In member function 'bool CKMCFile::BinarySearch(int64, int64, const CKmerAPI&, uint64&, uint32)':
kmc_api/kmc_file.cpp:1360:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if (index_start >= total_kmers)
                  ^
mkdir -p bin
/bio/linuxbrew/bin/g++-5 -lm -static -fopenmp -O3 -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11  -o bin/kmc_dump kmc_dump/nc_utils.o kmc_api/mmer.o kmc_dump/kmc_dump.o kmc_api/kmc_file.o kmc_api/kmer_api.o
/bio/linuxbrew/bin/ld: cannot find -lpthread
/bio/linuxbrew/bin/ld: cannot find -lm
/bio/linuxbrew/bin/ld: cannot find -ldl
/bio/linuxbrew/bin/ld: cannot find -lpthread
/bio/linuxbrew/bin/ld: cannot find -lc
collect2: error: ld returned 1 exit status
makefile:84: recipe for target 'kmc_dump' failed
make: *** [kmc_dump] Error 1
make: *** Waiting for unfinished jobs....

HOMEBREW_VERSION: 0.9.9
ORIGIN: https://github.com/Linuxbrew/brew.git
HEAD: b570bf7ea17ad9cebb5adc9296f4f77aaaed50d8
Last commit: 3 days ago
Core tap ORIGIN: https://github.com/Linuxbrew/homebrew-core
Core tap HEAD: c22d002f6d0b8921e6a4f2dcf861312f6568768e
Core tap last commit: 4 days ago
HOMEBREW_PREFIX: /bio/linuxbrew
HOMEBREW_REPOSITORY: /bio/linuxbrew
HOMEBREW_CELLAR: /bio/linuxbrew/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://linuxbrew.bintray.com
CPU: 72-core 64-bit haswell
Kernel: Linux 3.10.0-327.13.1.el7.x86_64 x86_64 GNU/Linux
OS: Red Hat Enterprise Linux Server release 7.2 (Maipo)
Codename: Maipo
OS glibc: 2.17
OS gcc: 4.8.5
Linuxbrew glibc: N/A
Linuxbrew gcc: 5.3.0
Clang: N/A
X11: 2.7.8 => /usr
System Ruby: 2.3.0 => /bio/linuxbrew/Cellar/ruby/2.3.0/bin/ruby
Perl: /usr/bin/perl
Python: /bio/linuxbrew/bin/python => /bio/linuxbrew/Cellar/python/2.7.11/bin/python2.7
Ruby: /bio/linuxbrew/bin/ruby => /bio/linuxbrew/Cellar/ruby/2.3.0/bin/ruby
Java: openjdk version "1.8.0_77"

CC: /bio/linuxbrew/bin/gcc-5 => /bio/linuxbrew/Cellar/gcc/5.3.0/bin/gcc-5
CXX: /bio/linuxbrew/bin/g++-5 => /bio/linuxbrew/Cellar/gcc/5.3.0/bin/g++-5
OBJC: /bio/linuxbrew/bin/gcc-5
OBJCXX: /bio/linuxbrew/bin/g++-5
CFLAGS: -Os -w -pipe -march=native
CXXFLAGS: -Os -w -pipe -march=native
CPPFLAGS: -isystem/bio/linuxbrew/include
LDFLAGS: -L/bio/linuxbrew/lib -Wl,--dynamic-linker=/bio/linuxbrew/lib/ld.so -Wl,-rpath,/bio/linuxbrew/lib
MAKEFLAGS: -j72
CMAKE_PREFIX_PATH: /bio/linuxbrew
PKG_CONFIG_LIBDIR: /bio/linuxbrew/lib/pkgconfig:/bio/linuxbrew/share/pkgconfig
HOMEBREW_BUILD_FROM_SOURCE: 1
PATH: /home/tseemann/perl5/bin:/bio/perl5/bin:/bio/linuxbrew/bin:/bio/linuxbrew/sbin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/bio/sw/hierBAPS:/bio/sw/brat:/bio/sw/mauve:/bio/sw/splitstree4:/bio/sw/vbc/fqa-tools:/bio/sw/vbc/misc:/bio/sw/tablet:/home/tseemann/git/wombac/bin:/home/tseemann/git/snippy/bin:/home/tseemann/git/barrnap/bin:/home/tseemann/git/nullarbor/bin:/home/tseemann/git/prokka/bin:/home/tseemann/git/mlst/bin:/home/tseemann/git/abricate/bin:/home/tseemann/git/mdu-tools/bin:/usr/local/sbin:/usr/sbin:/home/tseemann/.local/bin:/home/tseemann/bin:/bio/linuxbrew/Library/ENV/scm
CPATH: /bio/linuxbrew/include
LD_LIBRARY_PATH: /bio/linuxbrew/Cellar/kmc/2.3/lib:/bio/linuxbrew/Cellar/kmc/2.3
LD_RUN_PATH: /bio/linuxbrew/lib
LIBRARY_PATH: /bio/linuxbrew/lib