Bioperl-ext problem: Can't install staden io

bilogical has asked for the wisdom of the Perl Monks concerning the following question:

Hi monks,

Thanks to you all for your time to read this message. Your help will be greatly appreciated.

I desperately need Bioperl module, so I have to install the prerequisite module bioperl-ext, which requires staden io_lib_1.8.12. So I installed MinGW and MSYS in my PC with Windows XP 2002 system, and used MSYS to install io_lib_1.8.12. Prior to that, I installed Staden-windows-1-7-0 in C:\languages\staden. So before installing io_lib_1.8.12 under MSYS shell, I changed the line "ac_default_prefix=/usr/local" in the file "configure" to "ac_default_prefix=/C/languages/staden". Then I ran "./configure", "make", "make install". The first command looks to run through, but the "make" and "make install" returns error messages (the run log is attached below with the commands hightlighted).

I am stucked here. Would somebody please help me out? my email: guohongh@princeton.edu. Thank you in advance.

Log:

guohong@LENOVO-1A8D9427 /c/downloads/io_lib-1.8.12 
$ ./configure 
checking for a BSD-compatible install... /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... a.exe 
checking whether the C compiler works... yes 
checking whether we are cross compiling... no 
checking for suffix of executables... .exe 
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 ranlib... ranlib 
checking for a BSD-compatible install... /bin/install -c 
checking build system type... i686-pc-mingw32 
checking host system type... i686-pc-mingw32 
checking for ld used by GCC... C:/languages/minGW/mingw32/bin/ld.exe 
checking if the linker (C:/languages/minGW/mingw32/bin/ld.exe) is GNU 
+ld... yes 
checking for C:/languages/minGW/mingw32/bin/ld.exe option to reload ob
+ject files... -r 
checking for BSD-compatible nm... /mingw/bin/nm 
checking for a sed that does not truncate output... /bin/sed 
checking whether ln -s works... yes 
checking how to recognise dependent libraries... file_magic file forma
+t pei*-i386(.*architecture: i386)? 
checking command to parse /mingw/bin/nm output... ok 
checking how to run the C preprocessor... gcc -E 
checking for egrep... 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 dlfcn.h usability... no 
checking dlfcn.h presence... no 
checking for dlfcn.h... no 
checking for ranlib... (cached) ranlib 
checking for strip... strip 
checking for objdir... .libs 
checking for gcc option to produce PIC... -DDLL_EXPORT 
checking if gcc PIC flag -DDLL_EXPORT works... yes 
checking if gcc static flag -static works... yes 
checking if gcc supports -c -o file.o... yes 
checking if gcc supports -c -o file.lo... yes 
checking if gcc supports -fno-rtti -fno-exceptions... yes 
checking whether the linker (C:/languages/minGW/mingw32/bin/ld.exe) su
+pports shared libraries... yes 
checking how to hardcode library paths into programs... immediate 
checking whether stripping libraries is possible... yes 
checking dynamic linker characteristics... Win32 ld.exe 
checking if libtool supports shared libraries... yes 
checking whether to build shared libraries... yes 
checking whether to build static libraries... yes 
creating libtool 
./configure: SC_ENABLE_SHARED: command not found 
./configure: SC_CONFIG_SHLIB_FLAGS: command not found 
checking for main in -lz... no 
configure: WARNING: *** zlib not found; hence no ZTR support 
checking for ANSI C header files... (cached) 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... no 
checking zlib.h presence... no 
checking for zlib.h... no 
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... 4 
checking for inline... inline 
checking for mode_t... yes 
checking for main in -lm... yes 
checking for strdup... yes 
configure: creating ./config.status 
config.status: creating Makefile 
config.status: creating utils/Makefile 
config.status: creating abi/Makefile 
config.status: creating alf/Makefile 
config.status: creating ctf/Makefile 
config.status: creating exp_file/Makefile 
config.status: creating plain/Makefile 
config.status: creating scf/Makefile 
config.status: creating ztr/Makefile 
config.status: creating read/Makefile 
config.status: creating progs/Makefile 
config.status: creating config.h 
config.status: config.h is unchanged 
config.status: executing depfiles commands 
 
guohong@LENOVO-1A8D9427 /c/downloads/io_lib-1.8.12 
$ make 
make all-recursive 
make[1]: Entering directory `/c/downloads/io_lib-1.8.12' 
Making all in utils 
make[2]: Entering directory `/c/downloads/io_lib-1.8.12/utils' 
source='open_trace_file.c' object='open_trace_file.lo' libtool=yes \ 
depfile='.deps/open_trace_file.Plo' tmpdepfile='.deps/open_trace_file.
+TPlo' \ 
depmode=gcc3 /bin/sh ../depcomp \ 
/bin/sh ../libtool --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.
+. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../pla
+in -I../scf -I../exp_file -I../utils -I/usr/local/include -g -O2 -c -
+o open_trace_file.lo `test -f 'open_trace_file.c' || echo './'`open_t
+race_file.c 
rm -f .libs/open_trace_file.lo 
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../uti
+ls -I/usr/local/include -g -O2 -c open_trace_file.c -MT open_trace_fi
+le.lo -MD -MP -MF .deps/open_trace_file.TPlo -DDLL_EXPORT -DPIC -o .l
+ibs/open_trace_file.lo 
open_trace_file.c:11:26: sys/socket.h: No such file or directory 
open_trace_file.c:12:26: netinet/in.h: No such file or directory 
open_trace_file.c:13:21: netdb.h: No such file or directory 
open_trace_file.c:18:24: sys/wait.h: No such file or directory 
open_trace_file.c: In function `find_file_archive': 
open_trace_file.c:227: error: storage size of 'saddr' isn't known 
open_trace_file.c:244: warning: assignment makes pointer from integer 
+without a cast 
open_trace_file.c:249: error: dereferencing pointer to incomplete type
+ 
open_trace_file.c:250: error: dereferencing pointer to incomplete type
+ 
open_trace_file.c:250: error: dereferencing pointer to incomplete type
+ 
open_trace_file.c:251: error: `AF_INET' undeclared (first use in this 
+function) 
open_trace_file.c:251: error: (Each undeclared identifier is reported 
+only once 
open_trace_file.c:251: error: for each function it appears in.) 
open_trace_file.c:251: error: `SOCK_STREAM' undeclared (first use in t
+his function) 
open_trace_file.c:251: error: `IPPROTO_TCP' undeclared (first use in t
+his function) 
open_trace_file.c:295: error: `SOL_SOCKET' undeclared (first use in th
+is function) 
open_trace_file.c:295: error: `SO_RCVTIMEO' undeclared (first use in t
+his function) 
open_trace_file.c:300: error: `EWOULDBLOCK' undeclared (first use in t
+his function) 
make[2]: *** [open_trace_file.lo] Error 1 
make[2]: Leaving directory `/c/downloads/io_lib-1.8.12/utils' 
make[1]: *** [all-recursive] Error 1 
make[1]: Leaving directory `/c/downloads/io_lib-1.8.12' 
make: *** [all] Error 2 
 
guohong@LENOVO-1A8D9427 /c/downloads/io_lib-1.8.12 
$ make install 
Making install in utils 
make[1]: Entering directory `/c/downloads/io_lib-1.8.12/utils' 
source='open_trace_file.c' object='open_trace_file.lo' libtool=yes \ 
depfile='.deps/open_trace_file.Plo' tmpdepfile='.deps/open_trace_file.
+TPlo' \ 
depmode=gcc3 /bin/sh ../depcomp \ 
/bin/sh ../libtool --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.
+. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../pla
+in -I../scf -I../exp_file -I../utils -I/usr/local/include -g -O2 -c -
+o open_trace_file.lo `test -f 'open_trace_file.c' || echo './'`open_t
+race_file.c 
rm -f .libs/open_trace_file.lo 
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../uti
+ls -I/usr/local/include -g -O2 -c open_trace_file.c -MT open_trace_fi
+le.lo -MD -MP -MF .deps/open_trace_file.TPlo -DDLL_EXPORT -DPIC -o .l
+ibs/open_trace_file.lo 
open_trace_file.c:11:26: sys/socket.h: No such file or directory 
open_trace_file.c:12:26: netinet/in.h: No such file or directory 
open_trace_file.c:13:21: netdb.h: No such file or directory 
open_trace_file.c:18:24: sys/wait.h: No such file or directory 
open_trace_file.c: In function `find_file_archive': 
open_trace_file.c:227: error: storage size of 'saddr' isn't known 
open_trace_file.c:244: warning: assignment makes pointer from integer 
+without a cast 
open_trace_file.c:249: error: dereferencing pointer to incomplete type
+ 
open_trace_file.c:250: error: dereferencing pointer to incomplete type
+ 
open_trace_file.c:250: error: dereferencing pointer to incomplete type
+ 
open_trace_file.c:251: error: `AF_INET' undeclared (first use in this 
+function) 
open_trace_file.c:251: error: (Each undeclared identifier is reported 
+only once 
open_trace_file.c:251: error: for each function it appears in.) 
open_trace_file.c:251: error: `SOCK_STREAM' undeclared (first use in t
+his function) 
open_trace_file.c:251: error: `IPPROTO_TCP' undeclared (first use in t
+his function) 
open_trace_file.c:295: error: `SOL_SOCKET' undeclared (first use in th
+is function) 
open_trace_file.c:295: error: `SO_RCVTIMEO' undeclared (first use in t
+his function) 
open_trace_file.c:300: error: `EWOULDBLOCK' undeclared (first use in t
+his function) 
make[1]: *** [open_trace_file.lo] Error 1 
make[1]: Leaving directory `/c/downloads/io_lib-1.8.12/utils' 
make: *** [install-recursive] Error 1
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Comment on Bioperl-ext problem: Can't install staden io_lib on windows XP Download Code

Replies are listed 'Best First'.
Re: Bioperl-ext problem: Can't install staden io_lib on windows XP by svenXY (Deacon) on Dec 15, 2008 at 15:21 UTC
Hi, first of all - welcome to the monastery! Please do us a favour and remove the pre-tags from the fisrst few lines of your posting as pre-tags prevent wrapping of lines and this makes the node so wiiiide. Thanks. Regarding your actual problem: I'm not so sure what exactly you downloaded and istalled, but the best way to install modules in Windooze is usually ppm and there's a nice tutorial for that exact topic: A guide to installing modules for Win32 Regards, svenXY	[reply]
Re^2: Bioperl-ext problem: Can't install staden io_lib on windows XP by Anonymous Monk on Mar 22, 2009 at 02:06 UTC
Hi svenXY, I have the save problem with Bioperl-ext and io_lib. Did you solve the problem? If yes, tell me what to do. Danke Sch�n! Best regards ahabnar	[reply]
Re^3: Bioperl-ext problem: Can't install staden io_lib on windows XP by syphilis (Archbishop) on Mar 22, 2009 at 04:32 UTC
bilogical's post was mainly about problems building the io_lib library in the MSYS shell using the MinGW port of the gcc compiler. My post in the same thread provides a solution to that problem. Once you've got io_lib installed, it should be plain sailing to install Bioperl. If that's not the case, then please supply details. Details on how to install via ppm were also given by rminner. That might be the easiest route to take. Cheers, Rob	[reply]
Re: Bioperl-ext problem: Can't install staden io_lib on windows XP by rminner (Chaplain) on Dec 15, 2008 at 16:46 UTC
hello bilogical, The easy way to install bioperl is: install Active Perl follow the instructions on the bioperl homepage (just add their repository to ppm, select bioperl, and press install). It is well documented, and it works (installed bioperl on a machine two weeks ago using those instructions).	[reply]
Re: Bioperl-ext problem: Can't install staden io_lib on windows XP by syphilis (Archbishop) on Dec 15, 2008 at 23:00 UTC
So I installed MinGW and MSYS in my PC with Windows XP 2002 system, and used MSYS to install io_lib_1.8.12. I've just built io_lib-1.11.6.1 in the MSYS shell using MinGW. It was straightforward, and all tests passed. I ran: ./configure CPPFLAGS=-I/usr/local/include LDFLAGS=-L/usr/local/lib The inclusion of the CPPFLAGS and LDFLAGS arguments enables libz to be found and used (since I had previously installed libz). Then I ran 'make', followed by 'make check', followed by 'make install'. I didn't make any alterations to the io_lib source at all. Seems they must have fixed the problem with the configure script for 1.8.12. I suggest you give 1.11.6.1 a try if you want to build it yourself. Cheers, Rob	[reply]
Re^2: Bioperl-ext problem: Can't install staden io_lib on windows XP by bilogical (Novice) on Jan 19, 2010 at 05:10 UTC
Hi Syphilis, Sorry I was traveling last year and didn't see your reply. I didn't figure out the problem yet. Would you give more detail on your installation? such as, which version and where did you get the libz? Did you install staden-windows prior to staden-io-lib? Thanks a lot.	[reply]
Re^3: Bioperl-ext problem: Can't install staden io_lib on windows XP by syphilis (Archbishop) on Jan 19, 2010 at 05:48 UTC
I got zlib-1.2.3 source from the zlib Home Site, and built it (also in the MSYS shell) by running: ./configure make make check make install It should then be straightforward to build and install io_lib-1.11.6.1 as per the instructions in my earlier post. Cheers, Rob	[reply]