More about the basic perl module installation steps check this http://bioinformaticsonline.com/blog/view/710/how-to-install-perl-modules-manually-using-cpan-command-and-other-quick-ways

installing Bio::SCF perl module is daunting task, specieally because of it dependencies. Here is the steps, you need to follow to sucessfully install Bio::SCF module

#sudo apt-get install libbio-scf-perl #trev for visualization of scf file

1. You will need the zlib library which can be found at http://www.zlib.net/.

install zlib library first:

jitendra@jitendra-UNLOCK-INSTALL[zlib-1.2.11] ./configure []
Checking for gcc...
Checking for shared library support...
Building shared library libz.so.1.2.11 with gcc.
Checking for size_t... Yes.
Checking for off64_t... Yes.
Checking for fseeko... Yes.
Checking for strerror... Yes.
Checking for unistd.h... Yes.
Checking for stdarg.h... Yes.
Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf().
Checking for vsnprintf() in stdio.h... Yes.
Checking for return value of vsnprintf()... Yes.
Checking for attribute(visibility) support... Yes.
jitendra@jitendra-UNLOCK-INSTALL[zlib-1.2.11] make []
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -c -o example.o test/example.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o adler32.o adler32.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o crc32.o crc32.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o deflate.o deflate.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o infback.o infback.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o inffast.o inffast.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o inflate.o inflate.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o inftrees.o inftrees.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o trees.o trees.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o zutil.o zutil.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o compress.o compress.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o uncompr.o uncompr.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzclose.o gzclose.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzlib.o gzlib.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzread.o gzread.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzwrite.o gzwrite.c
ar rc libz.a adler32.o crc32.o deflate.o infback.o inffast.o inflate.o inftrees.o trees.o zutil.o compress.o uncompr.o gzclose.o gzlib.o gzread.o gzwrite.o
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o example example.o -L. libz.a
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -c -o minigzip.o test/minigzip.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o minigzip minigzip.o -L. libz.a
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/adler32.o adler32.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/crc32.o crc32.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/deflate.o deflate.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/infback.o infback.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inffast.o inffast.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inflate.o inflate.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inftrees.o inftrees.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/trees.o trees.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/zutil.o zutil.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/compress.o compress.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/uncompr.o uncompr.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzclose.o gzclose.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzlib.o gzlib.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzread.o gzread.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzwrite.o gzwrite.c
gcc -shared -Wl,-soname,libz.so.1,--version-script,zlib.map -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o libz.so.1.2.11 adler32.lo crc32.lo deflate.lo infback.lo inffast.lo inflate.lo inftrees.lo trees.lo zutil.lo compress.lo uncompr.lo gzclose.lo gzlib.lo gzread.lo gzwrite.lo -lc
rm -f libz.so libz.so.1
ln -s libz.so.1.2.11 libz.so
ln -s libz.so.1.2.11 libz.so.1
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o examplesh example.o -L. libz.so.1.2.11
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o minigzipsh minigzip.o -L. libz.so.1.2.11
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o example64.o test/example.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o example64 example64.o -L. libz.a
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o minigzip64.o test/minigzip.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o minigzip64 minigzip64.o -L. libz.a
jitendra@jitendra-UNLOCK-INSTALL[zlib-1.2.11] sudo make install []
[sudo] password for jitendra:
rm -f /usr/local/lib/libz.a
cp libz.a /usr/local/lib
chmod 644 /usr/local/lib/libz.a
cp libz.so.1.2.11 /usr/local/lib
chmod 755 /usr/local/lib/libz.so.1.2.11
rm -f /usr/local/share/man/man3/zlib.3
cp zlib.3 /usr/local/share/man/man3
chmod 644 /usr/local/share/man/man3/zlib.3
rm -f /usr/local/lib/pkgconfig/zlib.pc
cp zlib.pc /usr/local/lib/pkgconfig
chmod 644 /usr/local/lib/pkgconfig/zlib.pc
rm -f /usr/local/include/zlib.h /usr/local/include/zconf.h
cp zlib.h zconf.h /usr/local/include
chmod 644 /usr/local/include/zlib.h /usr/local/include/zconf.h
 

2. Now make io_lib-1.9

In order to install this perl extension you have to install io-lib version 1.9 or higher from the Staden library (staden.sourceforge.net). This can be downloaded from https://sourceforge.net/project/showfiles.php?group_id=100316&package_id=108243&release_id=340318 confirm that the package installed correctly look for a library named "libread".

jitendra@jitendra-UNLOCK-INSTALL[io_lib-1.9.0] export CFLAGS="-fPIC" && ./configure
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
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 ANSI C... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for a BSD-compatible install... /usr/bin/install -c
checking for ranlib... ranlib
checking for main in -lz... yes
checking how to run the C preprocessor... gcc -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... 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 fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for unistd.h... (cached) yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking whether byte ordering is bigendian... no
checking for short... yes
checking size of short... 2
checking for int... yes
checking size of int... 4
checking for long... yes
checking size of long... 8
checking for inline... inline
checking for mode_t... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for cos in -lm... yes
checking for strdup... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating read/Makefile
config.status: creating progs/Makefile
config.status: creating config.h
config.status: executing depfiles commands
jitendra@jitendra-UNLOCK-INSTALL[io_lib-1.9.0] make []
make all-recursive
make[1]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0'
Making all in read
make[2]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0/read'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT Read.o -MD -MP -MF ".deps/Read.Tpo" -c -o Read.o Read.c; \
then mv -f ".deps/Read.Tpo" ".deps/Read.Po"; else rm -f ".deps/Read.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT scf_extras.o -MD -MP -MF ".deps/scf_extras.Tpo" -c -o scf_extras.o scf_extras.c; \
then mv -f ".deps/scf_extras.Tpo" ".deps/scf_extras.Po"; else rm -f ".deps/scf_extras.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT translate.o -MD -MP -MF ".deps/translate.Tpo" -c -o translate.o translate.c; \
then mv -f ".deps/translate.Tpo" ".deps/translate.Po"; else rm -f ".deps/translate.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT compression.o -MD -MP -MF ".deps/compression.Tpo" -c -o compression.o `test -f '../ztr/compression.c' || echo './'`../ztr/compression.c; \
then mv -f ".deps/compression.Tpo" ".deps/compression.Po"; else rm -f ".deps/compression.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT ztr.o -MD -MP -MF ".deps/ztr.Tpo" -c -o ztr.o `test -f '../ztr/ztr.c' || echo './'`../ztr/ztr.c; \
then mv -f ".deps/ztr.Tpo" ".deps/ztr.Po"; else rm -f ".deps/ztr.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT ztr_translate.o -MD -MP -MF ".deps/ztr_translate.Tpo" -c -o ztr_translate.o `test -f '../ztr/ztr_translate.c' || echo './'`../ztr/ztr_translate.c; \
then mv -f ".deps/ztr_translate.Tpo" ".deps/ztr_translate.Po"; else rm -f ".deps/ztr_translate.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT fpoint.o -MD -MP -MF ".deps/fpoint.Tpo" -c -o fpoint.o `test -f '../abi/fpoint.c' || echo './'`../abi/fpoint.c; \
then mv -f ".deps/fpoint.Tpo" ".deps/fpoint.Po"; else rm -f ".deps/fpoint.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT seqIOABI.o -MD -MP -MF ".deps/seqIOABI.Tpo" -c -o seqIOABI.o `test -f '../abi/seqIOABI.c' || echo './'`../abi/seqIOABI.c; \
then mv -f ".deps/seqIOABI.Tpo" ".deps/seqIOABI.Po"; else rm -f ".deps/seqIOABI.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT seqIOALF.o -MD -MP -MF ".deps/seqIOALF.Tpo" -c -o seqIOALF.o `test -f '../alf/seqIOALF.c' || echo './'`../alf/seqIOALF.c; \
then mv -f ".deps/seqIOALF.Tpo" ".deps/seqIOALF.Po"; else rm -f ".deps/seqIOALF.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT ctfCompress.o -MD -MP -MF ".deps/ctfCompress.Tpo" -c -o ctfCompress.o `test -f '../ctf/ctfCompress.c' || echo './'`../ctf/ctfCompress.c; \
then mv -f ".deps/ctfCompress.Tpo" ".deps/ctfCompress.Po"; else rm -f ".deps/ctfCompress.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT seqIOCTF.o -MD -MP -MF ".deps/seqIOCTF.Tpo" -c -o seqIOCTF.o `test -f '../ctf/seqIOCTF.c' || echo './'`../ctf/seqIOCTF.c; \
then mv -f ".deps/seqIOCTF.Tpo" ".deps/seqIOCTF.Po"; else rm -f ".deps/seqIOCTF.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT expFileIO.o -MD -MP -MF ".deps/expFileIO.Tpo" -c -o expFileIO.o `test -f '../exp_file/expFileIO.c' || echo './'`../exp_file/expFileIO.c; \
then mv -f ".deps/expFileIO.Tpo" ".deps/expFileIO.Po"; else rm -f ".deps/expFileIO.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT seqIOPlain.o -MD -MP -MF ".deps/seqIOPlain.Tpo" -c -o seqIOPlain.o `test -f '../plain/seqIOPlain.c' || echo './'`../plain/seqIOPlain.c; \
then mv -f ".deps/seqIOPlain.Tpo" ".deps/seqIOPlain.Po"; else rm -f ".deps/seqIOPlain.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT misc_scf.o -MD -MP -MF ".deps/misc_scf.Tpo" -c -o misc_scf.o `test -f '../scf/misc_scf.c' || echo './'`../scf/misc_scf.c; \
then mv -f ".deps/misc_scf.Tpo" ".deps/misc_scf.Po"; else rm -f ".deps/misc_scf.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT read_scf.o -MD -MP -MF ".deps/read_scf.Tpo" -c -o read_scf.o `test -f '../scf/read_scf.c' || echo './'`../scf/read_scf.c; \
then mv -f ".deps/read_scf.Tpo" ".deps/read_scf.Po"; else rm -f ".deps/read_scf.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT write_scf.o -MD -MP -MF ".deps/write_scf.Tpo" -c -o write_scf.o `test -f '../scf/write_scf.c' || echo './'`../scf/write_scf.c; \
then mv -f ".deps/write_scf.Tpo" ".deps/write_scf.Po"; else rm -f ".deps/write_scf.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT array.o -MD -MP -MF ".deps/array.Tpo" -c -o array.o `test -f '../utils/array.c' || echo './'`../utils/array.c; \
then mv -f ".deps/array.Tpo" ".deps/array.Po"; else rm -f ".deps/array.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT compress.o -MD -MP -MF ".deps/compress.Tpo" -c -o compress.o `test -f '../utils/compress.c' || echo './'`../utils/compress.c; \
then mv -f ".deps/compress.Tpo" ".deps/compress.Po"; else rm -f ".deps/compress.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT error.o -MD -MP -MF ".deps/error.Tpo" -c -o error.o `test -f '../utils/error.c' || echo './'`../utils/error.c; \
then mv -f ".deps/error.Tpo" ".deps/error.Po"; else rm -f ".deps/error.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT files.o -MD -MP -MF ".deps/files.Tpo" -c -o files.o `test -f '../utils/files.c' || echo './'`../utils/files.c; \
then mv -f ".deps/files.Tpo" ".deps/files.Po"; else rm -f ".deps/files.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT find.o -MD -MP -MF ".deps/find.Tpo" -c -o find.o `test -f '../utils/find.c' || echo './'`../utils/find.c; \
then mv -f ".deps/find.Tpo" ".deps/find.Po"; else rm -f ".deps/find.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT mach-io.o -MD -MP -MF ".deps/mach-io.Tpo" -c -o mach-io.o `test -f '../utils/mach-io.c' || echo './'`../utils/mach-io.c; \
then mv -f ".deps/mach-io.Tpo" ".deps/mach-io.Po"; else rm -f ".deps/mach-io.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT open_trace_file.o -MD -MP -MF ".deps/open_trace_file.Tpo" -c -o open_trace_file.o `test -f '../utils/open_trace_file.c' || echo './'`../utils/open_trace_file.c; \
then mv -f ".deps/open_trace_file.Tpo" ".deps/open_trace_file.Po"; else rm -f ".deps/open_trace_file.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT read_alloc.o -MD -MP -MF ".deps/read_alloc.Tpo" -c -o read_alloc.o `test -f '../utils/read_alloc.c' || echo './'`../utils/read_alloc.c; \
then mv -f ".deps/read_alloc.Tpo" ".deps/read_alloc.Po"; else rm -f ".deps/read_alloc.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT strings.o -MD -MP -MF ".deps/strings.Tpo" -c -o strings.o `test -f '../utils/strings.c' || echo './'`../utils/strings.c; \
then mv -f ".deps/strings.Tpo" ".deps/strings.Po"; else rm -f ".deps/strings.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT traceType.o -MD -MP -MF ".deps/traceType.Tpo" -c -o traceType.o `test -f '../utils/traceType.c' || echo './'`../utils/traceType.c; \
then mv -f ".deps/traceType.Tpo" ".deps/traceType.Po"; else rm -f ".deps/traceType.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT xalloc.o -MD -MP -MF ".deps/xalloc.Tpo" -c -o xalloc.o `test -f '../utils/xalloc.c' || echo './'`../utils/xalloc.c; \
then mv -f ".deps/xalloc.Tpo" ".deps/xalloc.Po"; else rm -f ".deps/xalloc.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT vlen.o -MD -MP -MF ".deps/vlen.Tpo" -c -o vlen.o `test -f '../utils/vlen.c' || echo './'`../utils/vlen.c; \
then mv -f ".deps/vlen.Tpo" ".deps/vlen.Po"; else rm -f ".deps/vlen.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT hash_table.o -MD -MP -MF ".deps/hash_table.Tpo" -c -o hash_table.o `test -f '../utils/hash_table.c' || echo './'`../utils/hash_table.c; \
then mv -f ".deps/hash_table.Tpo" ".deps/hash_table.Po"; else rm -f ".deps/hash_table.Tpo"; exit 1; fi
../utils/hash_table.c: In function ‘HashFileOpen’:
../utils/hash_table.c:920:21: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=]
sprintf(aname, "%.*s%s", cp-fname+1, fname, hf->archive);
^
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT mFILE.o -MD -MP -MF ".deps/mFILE.Tpo" -c -o mFILE.o `test -f '../utils/mFILE.c' || echo './'`../utils/mFILE.c; \
then mv -f ".deps/mFILE.Tpo" ".deps/mFILE.Po"; else rm -f ".deps/mFILE.Tpo"; exit 1; fi
rm -f libread.a
ar cru libread.a Read.o scf_extras.o translate.o compression.o ztr.o ztr_translate.o fpoint.o seqIOABI.o seqIOALF.o ctfCompress.o seqIOCTF.o expFileIO.o seqIOPlain.o misc_scf.o read_scf.o write_scf.o array.o compress.o error.o files.o find.o mach-io.o open_trace_file.o read_alloc.o strings.o traceType.o xalloc.o vlen.o hash_table.o mFILE.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libread.a
make[2]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0/read'
Making all in progs
make[2]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0/progs'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT convert_trace.o -MD -MP -MF ".deps/convert_trace.Tpo" -c -o convert_trace.o convert_trace.c; \
then mv -f ".deps/convert_trace.Tpo" ".deps/convert_trace.Po"; else rm -f ".deps/convert_trace.Tpo"; exit 1; fi
gcc -fPIC -o convert_trace convert_trace.o ../read/libread.a -lz -lm
../read/libread.a(open_trace_file.o): In function `find_file_url':
open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT makeSCF.o -MD -MP -MF ".deps/makeSCF.Tpo" -c -o makeSCF.o makeSCF.c; \
then mv -f ".deps/makeSCF.Tpo" ".deps/makeSCF.Po"; else rm -f ".deps/makeSCF.Tpo"; exit 1; fi
gcc -fPIC -o makeSCF makeSCF.o ../read/libread.a -lz -lm
../read/libread.a(open_trace_file.o): In function `find_file_url':
open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT extract_seq.o -MD -MP -MF ".deps/extract_seq.Tpo" -c -o extract_seq.o extract_seq.c; \
then mv -f ".deps/extract_seq.Tpo" ".deps/extract_seq.Po"; else rm -f ".deps/extract_seq.Tpo"; exit 1; fi
gcc -fPIC -o extract_seq extract_seq.o ../read/libread.a -lz -lm
../read/libread.a(open_trace_file.o): In function `find_file_url':
open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT index_tar.o -MD -MP -MF ".deps/index_tar.Tpo" -c -o index_tar.o index_tar.c; \
then mv -f ".deps/index_tar.Tpo" ".deps/index_tar.Po"; else rm -f ".deps/index_tar.Tpo"; exit 1; fi
gcc -fPIC -o index_tar index_tar.o
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT scf_dump.o -MD -MP -MF ".deps/scf_dump.Tpo" -c -o scf_dump.o scf_dump.c; \
then mv -f ".deps/scf_dump.Tpo" ".deps/scf_dump.Po"; else rm -f ".deps/scf_dump.Tpo"; exit 1; fi
gcc -fPIC -o scf_dump scf_dump.o ../read/libread.a -lz -lm
../read/libread.a(open_trace_file.o): In function `find_file_url':
open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT scf_info.o -MD -MP -MF ".deps/scf_info.Tpo" -c -o scf_info.o scf_info.c; \
then mv -f ".deps/scf_info.Tpo" ".deps/scf_info.Po"; else rm -f ".deps/scf_info.Tpo"; exit 1; fi
gcc -fPIC -o scf_info scf_info.o ../read/libread.a -lz -lm
../read/libread.a(open_trace_file.o): In function `find_file_url':
open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT scf_update.o -MD -MP -MF ".deps/scf_update.Tpo" -c -o scf_update.o scf_update.c; \
then mv -f ".deps/scf_update.Tpo" ".deps/scf_update.Po"; else rm -f ".deps/scf_update.Tpo"; exit 1; fi
gcc -fPIC -o scf_update scf_update.o ../read/libread.a -lz -lm
../read/libread.a(open_trace_file.o): In function `find_file_url':
open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT get_comment.o -MD -MP -MF ".deps/get_comment.Tpo" -c -o get_comment.o get_comment.c; \
then mv -f ".deps/get_comment.Tpo" ".deps/get_comment.Po"; else rm -f ".deps/get_comment.Tpo"; exit 1; fi
gcc -fPIC -o get_comment get_comment.o ../read/libread.a -lz -lm
../read/libread.a(open_trace_file.o): In function `find_file_url':
open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT hash_tar.o -MD -MP -MF ".deps/hash_tar.Tpo" -c -o hash_tar.o hash_tar.c; \
then mv -f ".deps/hash_tar.Tpo" ".deps/hash_tar.Po"; else rm -f ".deps/hash_tar.Tpo"; exit 1; fi
gcc -fPIC -o hash_tar hash_tar.o ../read/libread.a -lz -lm
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT hash_extract.o -MD -MP -MF ".deps/hash_extract.Tpo" -c -o hash_extract.o hash_extract.c; \
then mv -f ".deps/hash_extract.Tpo" ".deps/hash_extract.Po"; else rm -f ".deps/hash_extract.Tpo"; exit 1; fi
gcc -fPIC -o hash_extract hash_extract.o ../read/libread.a -lz -lm
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT trace_dump.o -MD -MP -MF ".deps/trace_dump.Tpo" -c -o trace_dump.o trace_dump.c; \
then mv -f ".deps/trace_dump.Tpo" ".deps/trace_dump.Po"; else rm -f ".deps/trace_dump.Tpo"; exit 1; fi
gcc -fPIC -o trace_dump trace_dump.o ../read/libread.a -lz -lm
../read/libread.a(open_trace_file.o): In function `find_file_url':
open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
make[2]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0/progs'
make[2]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0'
make[2]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0'
make[1]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0'

jitendra@jitendra-UNLOCK-INSTALL[io_lib-1.9.0] sudo make install []
[sudo] password for jitendra:
Making install in read
make[1]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0/read'
make[2]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0/read'
test -z "/usr/local/lib" || mkdir -p -- "/usr/local/lib"
/usr/bin/install -c -m 644 'libread.a' '/usr/local/lib/libread.a'
ranlib '/usr/local/lib/libread.a'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0/read'
make[1]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0/read'
Making install in progs
make[1]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0/progs'
make[2]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0/progs'
test -z "/usr/local/bin" || mkdir -p -- "/usr/local/bin"
/usr/bin/install -c 'convert_trace' '/usr/local/bin/convert_trace'
/usr/bin/install -c 'makeSCF' '/usr/local/bin/makeSCF'
/usr/bin/install -c 'extract_seq' '/usr/local/bin/extract_seq'
/usr/bin/install -c 'index_tar' '/usr/local/bin/index_tar'
/usr/bin/install -c 'scf_dump' '/usr/local/bin/scf_dump'
/usr/bin/install -c 'scf_info' '/usr/local/bin/scf_info'
/usr/bin/install -c 'scf_update' '/usr/local/bin/scf_update'
/usr/bin/install -c 'get_comment' '/usr/local/bin/get_comment'
/usr/bin/install -c 'hash_tar' '/usr/local/bin/hash_tar'
/usr/bin/install -c 'hash_extract' '/usr/local/bin/hash_extract'
/usr/bin/install -c 'trace_dump' '/usr/local/bin/trace_dump'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0/progs'
make[1]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0/progs'
make[1]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0'
make[2]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0'
make[2]: Nothing to be done for 'install-exec-am'.
test -z "/usr/local/man/man3" || mkdir -p -- "/usr/local/man/man3"
/usr/bin/install -c -m 644 './man/man3/exp2read.3' '/usr/local/man/man3/exp2read.3'
/usr/bin/install -c -m 644 './man/man3/ExperimentFile.3' '/usr/local/man/man3/ExperimentFile.3'
/usr/bin/install -c -m 644 './man/man3/fread_reading.3' '/usr/local/man/man3/fread_reading.3'
/usr/bin/install -c -m 644 './man/man3/fread_scf.3' '/usr/local/man/man3/fread_scf.3'
/usr/bin/install -c -m 644 './man/man3/fwrite_reading.3' '/usr/local/man/man3/fwrite_reading.3'
/usr/bin/install -c -m 644 './man/man3/fwrite_scf.3' '/usr/local/man/man3/fwrite_scf.3'
/usr/bin/install -c -m 644 './man/man3/read2exp.3' '/usr/local/man/man3/read2exp.3'
/usr/bin/install -c -m 644 './man/man3/read2scf.3' '/usr/local/man/man3/read2scf.3'
/usr/bin/install -c -m 644 './man/man3/read_allocate.3' '/usr/local/man/man3/read_allocate.3'
/usr/bin/install -c -m 644 './man/man3/read_deallocate.3' '/usr/local/man/man3/read_deallocate.3'
/usr/bin/install -c -m 644 './man/man3/read_reading.3' '/usr/local/man/man3/read_reading.3'
/usr/bin/install -c -m 644 './man/man3/read_scf.3' '/usr/local/man/man3/read_scf.3'
/usr/bin/install -c -m 644 './man/man3/read_scf_header.3' '/usr/local/man/man3/read_scf_header.3'
/usr/bin/install -c -m 644 './man/man3/scf2read.3' '/usr/local/man/man3/scf2read.3'
/usr/bin/install -c -m 644 './man/man3/write_reading.3' '/usr/local/man/man3/write_reading.3'
/usr/bin/install -c -m 644 './man/man3/write_scf.3' '/usr/local/man/man3/write_scf.3'
/usr/bin/install -c -m 644 './man/man3/write_scf_header.3' '/usr/local/man/man3/write_scf_header.3'
test -z "/usr/local/man/man4" || mkdir -p -- "/usr/local/man/man4"
/usr/bin/install -c -m 644 './man/man4/Read.4' '/usr/local/man/man4/Read.4'
test -z "/usr/local/include/io_lib" || mkdir -p -- "/usr/local/include/io_lib"
/usr/bin/install -c -m 644 'read/Read.h' '/usr/local/include/io_lib/Read.h'
/usr/bin/install -c -m 644 'read/scf_extras.h' '/usr/local/include/io_lib/scf_extras.h'
/usr/bin/install -c -m 644 'read/translate.h' '/usr/local/include/io_lib/translate.h'
/usr/bin/install -c -m 644 'abi/abi.h' '/usr/local/include/io_lib/abi.h'
/usr/bin/install -c -m 644 'abi/fpoint.h' '/usr/local/include/io_lib/fpoint.h'
/usr/bin/install -c -m 644 'abi/seqIOABI.h' '/usr/local/include/io_lib/seqIOABI.h'
/usr/bin/install -c -m 644 'alf/alf.h' '/usr/local/include/io_lib/alf.h'
/usr/bin/install -c -m 644 'ctf/seqIOCTF.h' '/usr/local/include/io_lib/seqIOCTF.h'
/usr/bin/install -c -m 644 'exp_file/expFileIO.h' '/usr/local/include/io_lib/expFileIO.h'
/usr/bin/install -c -m 644 'plain/plain.h' '/usr/local/include/io_lib/plain.h'
/usr/bin/install -c -m 644 'scf/scf.h' '/usr/local/include/io_lib/scf.h'
/usr/bin/install -c -m 644 'utils/array.h' '/usr/local/include/io_lib/array.h'
/usr/bin/install -c -m 644 'utils/compress.h' '/usr/local/include/io_lib/compress.h'
/usr/bin/install -c -m 644 'utils/error.h' '/usr/local/include/io_lib/error.h'
/usr/bin/install -c -m 644 'utils/mach-io.h' '/usr/local/include/io_lib/mach-io.h'
/usr/bin/install -c -m 644 'utils/misc.h' '/usr/local/include/io_lib/misc.h'
/usr/bin/install -c -m 644 'utils/open_trace_file.h' '/usr/local/include/io_lib/open_trace_file.h'
/usr/bin/install -c -m 644 'utils/tar_format.h' '/usr/local/include/io_lib/tar_format.h'
/usr/bin/install -c -m 644 'utils/traceType.h' '/usr/local/include/io_lib/traceType.h'
/usr/bin/install -c -m 644 'utils/xalloc.h' '/usr/local/include/io_lib/xalloc.h'
/usr/bin/install -c -m 644 'utils/mFILE.h' '/usr/local/include/io_lib/mFILE.h'
/usr/bin/install -c -m 644 'utils/stdio_hack.h' '/usr/local/include/io_lib/stdio_hack.h'
/usr/bin/install -c -m 644 'utils/vlen.h' '/usr/local/include/io_lib/vlen.h'
/usr/bin/install -c -m 644 'utils/hash_table.h' '/usr/local/include/io_lib/hash_table.h'
/usr/bin/install -c -m 644 'utils/os.h' '/usr/local/include/io_lib/os.h'
/usr/bin/install -c -m 644 'ztr/compression.h' '/usr/local/include/io_lib/compression.h'
/usr/bin/install -c -m 644 'ztr/ztr.h' '/usr/local/include/io_lib/ztr.h'
make[2]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0'
make[1]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0'

3. Now install Bio::SCF

Now follows these steps:

tar zxf Bio::SCF.tar
cd Bio::SCF
perl Makefile.PL
make
make test
make install

jitendra@jitendra-UNLOCK-INSTALL[Bio-SCF-1.01] perl Makefile.PL []
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::SCF
Writing MYMETA.yml and MYMETA.json
jitendra@jitendra-UNLOCK-INSTALL[Bio-SCF-1.01] make []
cp SCF.pm blib/lib/Bio/SCF.pm
cp SCF/Arrays.pm blib/lib/Bio/SCF/Arrays.pm
Running Mkbootstrap for Bio::SCF ()
chmod 644 "SCF.bs"
"/usr/bin/perl" "/usr/share/perl/5.22/ExtUtils/xsubpp" -typemap "/usr/share/perl/5.22/ExtUtils/typemap" SCF.xs > SCF.xsc && mv SCF.xsc SCF.c
Please specify prototyping behavior for SCF.xs (see perlxs manual)
x86_64-linux-gnu-gcc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.01\" -DXS_VERSION=\"1.01\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.22/CORE" -DLITTLE_ENDIAN SCF.c
In file included from /usr/lib/x86_64-linux-gnu/perl/5.22/CORE/perl.h:5546:0,
from SCF.xs:5:
SCF.xs: In function ‘XS_Bio__SCF_get_scf_pointer’:
SCF.xs:57:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
ret_val = newSViv((int)scf_data);
^
/usr/lib/x86_64-linux-gnu/perl/5.22/CORE/embed.h:402:40: note: in definition of macro ‘newSViv’
#define newSViv(a) Perl_newSViv(aTHX_ a)
^
SCF.xs: In function ‘XS_Bio__SCF_get_scf_fpointer’:
SCF.xs:80:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
ret_val = newSViv((int)scf_data);
^
/usr/lib/x86_64-linux-gnu/perl/5.22/CORE/embed.h:402:40: note: in definition of macro ‘newSViv’
#define newSViv(a) Perl_newSViv(aTHX_ a)
^
SCF.xs: In function ‘XS_Bio__SCF_scf_free’:
SCF.xs:89:17: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
scf_deallocate((Scf *)scf_pointer);
^
SCF.xs: In function ‘XS_Bio__SCF_get_comments’:
SCF.xs:95:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
Scf *scf_data = (Scf *)scf_pointer;
^
SCF.xs: In function ‘XS_Bio__SCF_set_comments’:
SCF.xs:108:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
Scf *scf_data = (Scf *)scf_pointer;
^
SCF.xs: In function ‘XS_Bio__SCF_scf_write’:
SCF.xs:121:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
Scf *scf_data = (Scf *)scf_pointer;
^
SCF.xs: In function ‘XS_Bio__SCF_scf_fwrite’:
SCF.xs:137:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
Scf *scf_data = (Scf *)scf_pointer;
^
SCF.xs: In function ‘XS_Bio__SCF_get_from_header’:
SCF.xs:159:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
Scf *scf_data = (Scf *)scf_pointer;
^
SCF.xs: In function ‘XS_Bio__SCF_get_at’:
SCF.xs:186:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
Scf *scf_data = (Scf *)scf_pointer;
^
SCF.xs: In function ‘XS_Bio__SCF_set_base_at’:
SCF.xs:242:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
Scf *scf_data = (Scf *)scf_pointer;
^
SCF.xs: In function ‘XS_Bio__SCF_set_at’:
SCF.xs:255:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
Scf *scf_data = (Scf *)scf_pointer;
^
rm -f blib/arch/auto/Bio/SCF/SCF.so
x86_64-linux-gnu-gcc -shared -L/usr/local/lib -fstack-protector-strong SCF.o -o blib/arch/auto/Bio/SCF/SCF.so \
-lread -lz \

/usr/local/lib/libread.a(open_trace_file.o): In function `find_file_url':
open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
chmod 755 blib/arch/auto/Bio/SCF/SCF.so
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- SCF.bs blib/arch/auto/Bio/SCF/SCF.bs 644
Manifying 1 pod document

More at http://www.cmdn.org.np/main/index.php

This is the simple way to use the module

Example1:

use Benchmark;

$first_time = Benchmark->new;

our code……

$second_time = Benchmark->new;

$final_difference = timediff($first_time,$second_time);

print “the code took, timestr($final_difference),”\n”;

that was a very simple way to know the time diff , we can use it to know the time taken by some part of the code in the program.

More sophisticated way:

use Benchmark;
sub first {

my(arguments) = @_;

}

timethese(100, { first => ‘first_sub(arguments)’});

The first argument to timethese is 100 (evaluate 100 times).

Hope this very small tutorial with Benchmark will help people get started.

If you're interested in refreshing your memory or just new to the series, please check previous entries over here: 1 2 3

https://metacpan.org/pod/AI::MXNet

Address of the bookmark: http://blogs.perl.org/users/sergey_kolychev/2018/07/machine-learning-in-perl-kyuubi-goes-to-a-modelzoo-during-the-starry-night.html

CSIR-IICT is conducting Walk in Interview for the following position on a purely temporary basis for the sponsored project "GENESIS (BSC-0121) at 10.00 AM on 19th August 2014 at IICT, Hyderabad

Position : Research Associate
No of Post : One
Desired Profile : PhD in computation biology or M.Tech in Computational Biology with three years experience in relevant subject and atleast one research paper in SCI journal

Experience : Knowledge in vector and vector borne disease, disease modeling, GIS mapping and modeling.
Age : 35 years
Stipend : Rs 22000/- + HRA

Eligible candidate may download the application form from our website http://www.iictindia.org and appear for interview along with the duly filled in application form supported by bio-data and one set of attested photo copies of certificates of educational qualification, age, experience, caste, latest photograph and the cadndidates are required to bring all the original certificates for verification

Walk in Interview : 19.08.14

Alternatively, use one liner perl script:

perl -ne 'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if @ARGV' GIs.txt >sequence.fasta

where GIs.txt contains a list of GIs or accession IDs.

(from :http://edwards.sdsu.edu/labsite/index.php/robert?start=5)

Address of the bookmark: http://edwards.sdsu.edu/labsite/index.php/robert/380-ncbi-sequence-or-fasta-batch-download-using-entrez

Applications are invited for the post of Junior Research Fellow (JRF) in a DBT funded IYBA project entitled “Generatingaprotein-ncRNA interactome for Dorsal mediated gene regulation and dorso-ventral patterning genes in Drosophila” in the Lab. Of Molecular Biology at the Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi. The project requires extensive use of molecular, genetic and genomic approaches.

POST: Junior Research Fellow (JRF)

NO. OF VACANCIE(S) - (01)

FELLOWSHIP: Rs. 16,000/- plus HRA

PROJECT DURATION: 2014-2016 (Two years)

LAST DATE FOR APPLICATION: Aug 18, 2014.

Eligibility criteria:

M.Sc./M.Tech./ in Biological Sciences/Biotechnology/Bio-Informatics. Candidates with research experience in the field of Drosophila/Yeast genetics will be preferred.

Application Procedure:

A covering letter along with your CV, copy of prior publications (if any) and proof of experience should be e-mailed to lmb_sau@aol.com. Hardcopy of the application should be brought on the day of interview along with other testimonials and marks statements for verification purpose.

IMPORTANT NOTE:

-No TA/DA will be paid for attending the interview.

-SAU may select candidates against the post depending upon qualification and experience of candidates and reserves the right to relax any of the qualifications in case the candidate is found otherwise well qualified by the Selection Committee

-The abovementioned post is temporary and will be initially offered for a period of one year and can be extended, on satisfactory performance.

More at http://www.sau.ac.in/recruitment/vacancy.html

Eligibility : MSc, M Phil / Phd, BE/B.Tech
Location : Himachal Pradesh-other
Job Category : Govt Jobs, Research, Walkin
Last Date : 20 Aug 2014

Advertisement No.6/2014

Post : Project Fellow
Research Associate/ Project Fellow Jobs opportunity in CSIR-Institute of Himalayan Bioresource Technology
M.Sc. in Bioinformatics/Computer Science with 55% marks and (ii) M.Sc. Bioinformatics/ Computational biology/ P.G. Diploma in Bioinformatics/B.Tech. or higher Degree in Bioinformatics with 55% marks

Date of Interview: 29.08.2014.

More at http://www.ihbt.res.in/recruit/AdvtNo6_2014.pdf