I
have just installed cygwin64 on a Windows10 machine and have run into
problems with installing as below. Any assiance appreciated.
Bob
Robert@DESKTOP-14EL82S /usr/local/bin/htslib-1.3
$ ./configure
checking for gcc... gcc
checking whether the C compiler works... no
configure: error: in `/usr/local/bin/htslib-1.3':
configure: error: C compiler cannot create executables
See `config.log' for more details
Robert@DESKTOP-14EL82S /usr/local/bin/htslib-1.3
$ make
gcc -g -Wall -O2 -I. -c -o kfunc.o kfunc.c
gcc: error: spawn: No such file or directory
Makefile:134: recipe for target 'kfunc.o' failed
make: *** [kfunc.o] Error 1
Robert@DESKTOP-14EL82S /usr/local/bin/htslib-1.3
$ make install
gcc -g -Wall -O2 -I. -c -o kfunc.o kfunc.c
gcc: error: spawn: No such file or directory
Makefile:134: recipe for target 'kfunc.o' failed
make: *** [kfunc.o] Error 1
Robert@DESKTOP-14EL82S /usr/local/bin/htslib-1.3
and
Robert@DESKTOP-14EL82S /usr/local/bin/bcftools-1.3
$ make
cd htslib-1.3 && make lib-static
make[1]: Entering directory '/usr/local/bin/bcftools-1.3/htslib-1.3'
gcc -g -Wall -O2 -I. -c -o kfunc.o kfunc.c
gcc: error: spawn: No such file or directory
Makefile:134: recipe for target 'kfunc.o' failed
make[1]: *** [kfunc.o] Error 1
make[1]: Leaving directory '/usr/local/bin/bcftools-1.3/htslib-1.3'
htslib-1.3/htslib.mk:141: recipe for target 'htslib-1.3/libhts.a' failed
make: *** [htslib-1.3/libhts.a] Error 2
Robert@DESKTOP-14EL82S /usr/local/bin/bcftools-1.3
$ make install
cd htslib-1.3 && make lib-static
make[1]: Entering directory '/usr/local/bin/bcftools-1.3/htslib-1.3'
gcc -g -Wall -O2 -I. -c -o kfunc.o kfunc.c
gcc: error: spawn: No such file or directory
Makefile:134: recipe for target 'kfunc.o' failed
make[1]: *** [kfunc.o] Error 1
make[1]: Leaving directory '/usr/local/bin/bcftools-1.3/htslib-1.3'
htslib-1.3/htslib.mk:141: recipe for target 'htslib-1.3/libhts.a' failed
make: *** [htslib-1.3/libhts.a] Error 2
Robert@DESKTOP-14EL82S /usr/local/bin/bcftools-1.3
and
Robert@DESKTOP-14EL82S /usr/local/bin/samtools-1.3
$ ./configure
checking for gcc... gcc
checking whether the C compiler works... no
configure: error: in `/usr/local/bin/samtools-1.3':
configure: error: C compiler cannot create executables
See `config.log' for more details
Robert@DESKTOP-14EL82S /usr/local/bin/samtools-1.3
$ make
gcc
-g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
--D-CURSES_LIB=0 -Dexpl=exp -Dlog1=log -I. -Ihtslib-1.3 -c -o
bam_index.o bam_index.c
gcc: error: unrecognized command line option ‘--D-CURSES_LIB=0’
Makefile:130: recipe for target 'bam_index.o' failed
make: *** [bam_index.o] Error 1
Robert@DESKTOP-14EL82S /usr/local/bin/samtools-1.3
$ make install
gcc
-g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
--D-CURSES_LIB=0 -Dexpl=exp -Dlog1=log -I. -Ihtslib-1.3 -c -o
bam_index.o bam_index.c
gcc: error: unrecognized command line option ‘--D-CURSES_LIB=0’
Makefile:130: recipe for target 'bam_index.o' failed
make: *** [bam_index.o] Error 1
Robert@DESKTOP-14EL82S /usr/local/bin/samtools-1.3
and
Robert@DESKTOP-14EL82S /usr/local/bin/samtools-1.3
$ samtools
-bash: samtools: command not found
Robert@DESKTOP-14EL82S /usr/local/bin/samtools-1.3
and
Robert@DESKTOP-14EL82S /usr/local/bin
$ dir
bcftools-1.3 htslib-1.3 numpy numpy-1.10.2.data numpy-1.10.2.dist-info
samtools-1.3 shore-0.9.3
Bob May
DNA Projects I2b L415, I2c L596 HG, Spriggs of Cleve SA Family & Tyler Surname
and ISOGG YTree
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