Hello,
I wonder whether someone could help me with the installation error I get when I
execute 'make' when installing samtools-1.6. I do apologise if this is
something obvious, however I am new to unix and samtools.
I am installing samtools locally in my user login bin
When I run './configure -without-curses' all is fine
Then when I do 'make' I get:
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking location of HTSlib source tree... htslib-1.6
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing regcomp... none required
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
config.status: config.h is unchanged
=== configuring in htslib-1.6 (/data/lasecka/bin/samtools-1.6/htslib-1.6)
configure: running /bin/sh ./configure --disable-option-checking
'--prefix=/usr/local' '--without-curses' --cache-file=/dev/null --srcdir=.
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking shared library type for unknown-Linux... plain .so
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... yes
checking for fdatasync... yes
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
checking for curl_easy_pause in -lcurl... yes
checking for CCHmac... no
checking for library containing HMAC... -lcrypto
checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
config.status: config.h is unchanged
lasecka@mallorn1:~/bin/samtools-1.6$ make
cd htslib-1.6 && make htslib_static.mk
make[1]: Entering directory `/data/lasecka/bin/samtools-1.6/htslib-1.6'
sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS =
/p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp >
htslib_static.mk
make[1]: Leaving directory `/data/lasecka/bin/samtools-1.6/htslib-1.6'
gcc -g -O2 -DMAQ_LONGREADS -I. -Ihtslib-1.6 -c -o misc/maq2sam-long.o
misc/maq2sam.c
misc/maq2sam.c: In function âmainâ:
misc/maq2sam.c:190:42: error: âSAMTOOLS_VERSIONâ undeclared (first use in this
function)
fprintf(stderr, "Version: %s\n", SAMTOOLS_VERSION);
^
misc/maq2sam.c:190:42: note: each undeclared identifier is reported only once
for each function it appears in
make: *** [misc/maq2sam-long.o] Error 1
---- since there is an error it will not allow me to do 'make install'
Since I am installing it on w work cluster I have a limited permissions.
I tried looking up the error on previous posts on different portals however
without any luck.
Any help will be greatly appreciated.
Many thanks,
Lidia
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