Bug #18178 for Tree-Suffix: Installation Problem in Local Directory

Tue Mar 14 22:48:20 2006 Guest - Ticket created

Subject:

Installation Problem in Local Directory

Dear Gray, I tried to install your module with CPAN shell in my local directory of my office server. The location of my libstree library is shown here: [ewijaya@voyager ~]$ ll -Shst MyBioTool/libstree-0.4.2 total 1.6M 4.0K drwxrwxr-x 3 ewijaya ewijaya 4.0K Mar 15 11:08 include 4.0K drwxrwxr-x 2 ewijaya ewijaya 4.0K Mar 15 11:08 lib 4.0K drwxrwxr-x 3 ewijaya ewijaya 4.0K Mar 15 11:08 share 28K -rw-rw-r-- 1 ewijaya ewijaya 28K Mar 15 11:07 config.log 40K -rwxrwxr-x 1 ewijaya ewijaya 37K Mar 15 11:07 config.status 4.0K drwxrwxr-x 5 ewijaya ewijaya 4.0K Mar 15 11:07 docs 216K -rwxrwxr-x 1 ewijaya ewijaya 209K Mar 15 11:07 libtool 20K -rw-rw-r-- 1 ewijaya ewijaya 19K Mar 15 11:07 Makefile 4.0K drwxrwxr-x 4 ewijaya ewijaya 4.0K Mar 15 11:07 src 4.0K -rw-rw-r-- 1 ewijaya ewijaya 23 Mar 15 11:07 stamp-h1 4.0K drwxrwxr-x 4 ewijaya ewijaya 4.0K Mar 15 11:07 test 4.0K -rw-rw-r-- 1 ewijaya ewijaya 1.6K Mar 15 10:45 config.h 4.0K -rw-r--r-- 1 ewijaya ewijaya 1.5K Mar 1 22:10 config.h.in 656K -rwxrwxr-x 1 ewijaya ewijaya 652K Mar 1 22:07 configure 20K -rw-rw-r-- 1 ewijaya ewijaya 19K Mar 1 22:07 Makefile.in 248K -rw-rw-r-- 1 ewijaya ewijaya 243K Mar 1 22:05 aclocal.m4 44K -rwxr-xr-x 1 ewijaya ewijaya 42K Mar 1 22:04 config.guess 32K -rwxr-xr-x 1 ewijaya ewijaya 30K Mar 1 22:04 config.sub 184K -rw-r--r-- 1 ewijaya ewijaya 180K Mar 1 22:04 ltmain.sh 4.0K -rw-r--r-- 1 ewijaya ewijaya 2.2K Mar 1 22:04 ChangeLog 4.0K -rw-r--r-- 1 ewijaya ewijaya 2.5K Mar 1 22:04 configure.in 4.0K -rw-r--r-- 1 ewijaya ewijaya 1.2K Mar 1 22:04 COPYING 4.0K -rw-r--r-- 1 ewijaya ewijaya 2.8K Feb 23 07:23 README 16K -rwxr-xr-x 1 ewijaya ewijaya 15K Jan 16 19:22 depcomp 12K -rwxr-xr-x 1 ewijaya ewijaya 9.0K Jan 16 19:22 install-sh 12K -rwxr-xr-x 1 ewijaya ewijaya 11K Jan 16 19:22 missing 4.0K -rwxr-xr-x 1 ewijaya ewijaya 2.9K Jan 16 19:21 autogen.sh 4.0K -rw-r--r-- 1 ewijaya ewijaya 91 Jan 13 2004 AUTHORS 4.0K -rw-rw-r-- 1 ewijaya ewijaya 181 Sep 10 2003 Makefile.am 12K -rw-rw-r-- 1 ewijaya ewijaya 9.1K Sep 10 2003 INSTALL 4.0K -rw-rw-r-- 1 ewijaya ewijaya 15 Sep 10 2003 NEWS 24K -rwxrwxr-x 1 ewijaya ewijaya 24K Sep 10 2003 shtool I have already set the path into the that particular library location: PATH=$PATH:$HOME/bin:$HOME/MyBioTool/libstree-0.4.2:$HOME/MyBioTool/ libstree-0.4.2/test: However when I tried to install the module, I found the following error message, that cause the installation failure: __BEGIN__ Show quoted text

cpan> install Tree::Suffix

CPAN: Storable loaded ok Going to read /home/ewijaya/.cpan/Metadata Database was generated on Tue, 14 Mar 2006 16:19:09 GMT Running install for module Tree::Suffix Running make for G/GR/GRAY/Tree-Suffix-0.12.tar.gz CPAN: Digest::MD5 loaded ok CPAN: Compress::Zlib loaded ok Checksum for /home/ewijaya/.cpan/sources/authors/id/G/GR/GRAY/Tree- Suffix-0.12.tar.gz ok Scanning cache /home/ewijaya/.cpan/build for sizes Deleting from cache: /home/ewijaya/.cpan/build/Module-Build-0.27_05 (10. Show quoted text

7>10.0 MB)

Tree-Suffix-0.12/ Tree-Suffix-0.12/Changes Tree-Suffix-0.12/MANIFEST Tree-Suffix-0.12/META.yml Tree-Suffix-0.12/Makefile.PL Tree-Suffix-0.12/README Tree-Suffix-0.12/Suffix.xs Tree-Suffix-0.12/lib/ Tree-Suffix-0.12/lib/Tree/ Tree-Suffix-0.12/lib/Tree/Suffix.pm Tree-Suffix-0.12/ppport.h Tree-Suffix-0.12/t/ Tree-Suffix-0.12/t/00_load.t Tree-Suffix-0.12/t/01_new.t Tree-Suffix-0.12/t/02_insert.t Tree-Suffix-0.12/t/03_lcs.t Tree-Suffix-0.12/t/04_lrs.t Tree-Suffix-0.12/t/05_clear.t Tree-Suffix-0.12/t/06_remove.t Tree-Suffix-0.12/t/07_memleak.t Tree-Suffix-0.12/t/08_find.t Tree-Suffix-0.12/t/09_duplicates.t Tree-Suffix-0.12/t/10_pod.t Tree-Suffix-0.12/t/11_pod_coverage.t Tree-Suffix-0.12/t/12_string.t Removing previously used /home/ewijaya/.cpan/build/Tree-Suffix-0.12 CPAN.pm: Going to build G/GR/GRAY/Tree-Suffix-0.12.tar.gz Checking if your kit is complete... Looks good Note (probably harmless): No library found for -lstree Writing Makefile for Tree::Suffix /usr/bin/perl /usr/lib/perl5/5.8.5/ExtUtils/xsubpp -typemap /usr/lib/ perl5/5.8.5/ExtUtils/typemap Suffix.xs > Suffix.xsc && mv Suffix.xsc Suffix.c cp lib/Tree/Suffix.pm blib/lib/Tree/Suffix.pm Running Mkbootstrap for Tree::Suffix () gcc -c -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing - pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/ usr/include/gdbm -O2 -g -pipe -m32 -march=i386 -mtune=pentium4 - DVERSION=\"0.12\" -DXS_VERSION=\"0.12\" -fPIC "-I/usr/lib/perl5/5.8.5/ i386-linux-thread-multi/CORE" Suffix.c chmod 644 Suffix.bs cp Suffix.bs blib/arch/auto/Tree/Suffix/Suffix.bs chmod 644 blib/arch/auto/Tree/Suffix/Suffix.bs Suffix.xs:6:22: libstree.h: No such file or directory Suffix.xs:19: error: syntax error before '*' token Suffix.xs:20: error: syntax error before '*' token Suffix.xs: In function `follow_string': Suffix.xs:21: error: `LST_Node' undeclared (first use in this function) Suffix.xs:21: error: (Each undeclared identifier is reported only once Suffix.xs:21: error: for each function it appears in.) Suffix.xs:21: error: `node' undeclared (first use in this function) Suffix.xs:21: error: `tree' undeclared (first use in this function) Suffix.xs:22: error: `LST_Edge' undeclared (first use in this function) Suffix.xs:22: error: `edge' undeclared (first use in this function) Suffix.xs:24: error: `string' undeclared (first use in this function) Suffix.xs: In function `XS_Tree__Suffix_new': Suffix.xs:54: error: `LST_STree' undeclared (first use in this function) Suffix.xs:54: error: `tree' undeclared (first use in this function) Suffix.xs: In function `XS_Tree__Suffix_DESTROY': Suffix.xs:78: error: `LST_STree' undeclared (first use in this function) Suffix.xs:78: error: `tree' undeclared (first use in this function) Suffix.xs:80: error: syntax error before ')' token Suffix.xs: In function `XS_Tree__Suffix_allow_duplicates': Suffix.xs:90: error: `LST_STree' undeclared (first use in this function) Suffix.xs:90: error: `tree' undeclared (first use in this function) Suffix.xs:92: error: syntax error before ')' token Suffix.xs: In function `XS_Tree__Suffix_insert': Suffix.xs:105: error: `LST_STree' undeclared (first use in this function) Suffix.xs:105: error: `tree' undeclared (first use in this function) Suffix.xs:112: error: syntax error before ')' token Suffix.xs: In function `XS_Tree__Suffix_strings': Suffix.xs:128: error: `LST_STree' undeclared (first use in this function) Suffix.xs:128: error: `tree' undeclared (first use in this function) Suffix.xs:129: error: `LST_StringHash' undeclared (first use in this function) Suffix.xs:129: error: `hash' undeclared (first use in this function) Suffix.xs:130: error: `LST_StringHashItem' undeclared (first use in this function) Suffix.xs:130: error: `hi' undeclared (first use in this function) Suffix.xs:133: error: syntax error before ')' token Suffix.xs:137: error: `LST_STRING_HASH_SIZE' undeclared (first use in this function) Suffix.xs: In function `XS_Tree__Suffix_nodes': Suffix.xs:149: error: `LST_STree' undeclared (first use in this function) Suffix.xs:149: error: `tree' undeclared (first use in this function) Suffix.xs:151: error: syntax error before ')' token Suffix.xs: In function `XS_Tree__Suffix_clear': Suffix.xs:160: error: `LST_STree' undeclared (first use in this function) Suffix.xs:160: error: `tree' undeclared (first use in this function) Suffix.xs:162: error: syntax error before ')' token Suffix.xs: In function `XS_Tree__Suffix_dump': Suffix.xs:172: error: `LST_STree' undeclared (first use in this function) Suffix.xs:172: error: `tree' undeclared (first use in this function) Suffix.xs:175: error: syntax error before ')' token Suffix.xs: In function `XS_Tree__Suffix_remove': Suffix.xs:187: error: `LST_STree' undeclared (first use in this function) Suffix.xs:187: error: `tree' undeclared (first use in this function) Suffix.xs:188: error: `LST_StringHash' undeclared (first use in this function) Suffix.xs:188: error: `hash' undeclared (first use in this function) Suffix.xs:189: error: `LST_StringHashItem' undeclared (first use in this function) Suffix.xs:189: error: `hi' undeclared (first use in this function) Suffix.xs:190: error: `LST_String' undeclared (first use in this function) Suffix.xs:190: error: `str' undeclared (first use in this function) Suffix.xs:195: error: syntax error before ')' token Suffix.xs:204: error: `LST_STRING_HASH_SIZE' undeclared (first use in this function) Suffix.xs: In function `XS_Tree__Suffix__algorithm_longest_substrings': Suffix.xs:236: error: `LST_STree' undeclared (first use in this function) Suffix.xs:236: error: `tree' undeclared (first use in this function) Suffix.xs:237: error: `LST_StringSet' undeclared (first use in this function) Suffix.xs:237: error: `res' undeclared (first use in this function) Suffix.xs:238: error: `LST_String' undeclared (first use in this function) Suffix.xs:238: error: `str' undeclared (first use in this function) Suffix.xs:240: error: syntax error before ')' token Suffix.xs: In function `XS_Tree__Suffix_find': Suffix.xs:262: error: `LST_STree' undeclared (first use in this function) Suffix.xs:262: error: `tree' undeclared (first use in this function) Suffix.xs:263: error: `LST_String' undeclared (first use in this function) Suffix.xs:263: error: `str' undeclared (first use in this function) Suffix.xs:264: error: `LST_Edge' undeclared (first use in this function) Suffix.xs:264: error: `edge' undeclared (first use in this function) Suffix.xs:265: error: `LST_Node' undeclared (first use in this function) Suffix.xs:265: error: `node' undeclared (first use in this function) Suffix.xs:266: error: `shead' undeclared (first use in this function) Suffix.xs:266: error: `lst_node' undeclared (first use in this function) Suffix.xs:266: error: syntax error before "stack" Suffix.xs:270: error: syntax error before ')' token Suffix.xs:281: error: `stack' undeclared (first use in this function) Suffix.xs:282: error: `iteration' undeclared (first use in this function) Suffix.xs: In function `XS_Tree__Suffix_string': Suffix.xs:308: error: `LST_STree' undeclared (first use in this function) Suffix.xs:308: error: `tree' undeclared (first use in this function) Suffix.xs:309: error: `LST_StringHash' undeclared (first use in this function) Suffix.xs:309: error: `hash' undeclared (first use in this function) Suffix.xs:310: error: `LST_StringHashItem' undeclared (first use in this function) Suffix.xs:310: error: `hi' undeclared (first use in this function) Suffix.xs:311: error: `LST_StringIndex' undeclared (first use in this function) Suffix.xs:311: error: syntax error before "range" Suffix.xs:314: error: syntax error before ')' token Suffix.xs:315: error: `LST_STRING_HASH_SIZE' undeclared (first use in this function) Suffix.xs:320: error: `range' undeclared (first use in this function) make: *** [Suffix.o] Error 1 /usr/bin/make -j3 -- NOT OK Running make test Can't test without successful make Running make install make had returned bad status, install seems impossible __END__ Is there any way I can fix the problem? Really hope to hear from you again. I'm using: Tree::Suffix version 0.12 perl, v5.8.5 built for i386-linux-thread-multi Linux hostname.org.sg 2.6.9-22.0.2.ELsmp #1 SMP Thu Jan 5 17:13:01 EST 2006 i686 i686 i386 GNU/Linux -- Regards, Edward WIJAYA

Tue Mar 14 23:07:27 2006 gray [...] cpan.org - Correspondence added

Message body is not shown because it is too large.

Tue Mar 14 23:07:28 2006 The RT System itself - Status changed from 'new' to 'open'

Tue Mar 14 23:11:28 2006 gray [...] cpan.org - Correspondence added

that should be: setenv CFLAGS "$CFLAGS -I$HOME/MyBioTool/libstree-0.4.2/include" setenv LDFLAGS "$LDFLAGS -L$HOME/MyBioTool/libstree-0.4.2/lib" On Tue Mar 14 23:07:27 2006, GRAY wrote: Show quoted text

> that's not a problem with the module. the libstree library and headers > have to be in a standard location for any program to find them. if > they're not, you have to explicitly tell it where they are located. > setting the CFLAGS and LDFLAGS environment variables may work for you: > # for tcsh > setenv CFLAGS $HOME/MyBioTool/libstree-0.4.2/include > setenv LDFLAGS $HOME/MyBioTool/libstree-0.4.2/lib > > # for bash > export CFLAGS=$HOME/MyBioTool/libstree-0.4.2/include > export LDFLAGS=$HOME/MyBioTool/libstree-0.4.2/lib >

Tue Mar 14 23:11:57 2006 gray [...] cpan.org - Status changed from 'open' to 'resolved'

Wed Mar 15 00:05:32 2006 ewijaya [...] i2r.a-star.edu.sg - Correspondence added

CC:	gray [...] cpan.org
Subject:	Re: [rt.cpan.org #18178] Installation Problem in Local Directory
Date:	Wed, 15 Mar 2006 13:05:07 +0800
To:	bug-Tree-Suffix [...] rt.cpan.org
From:	Wijaya Edward <ewijaya [...] i2r.a-star.edu.sg>

Hi Gray, Thanks a lot for the reply. I'm using bash. You mean putting these lines in the .bash_profile file right? export CFLAGS = $HOME/MyBioTool/libstree-0.4.2/include export LDFLAGS = $HOME/MyBioTool/libstree-0.4.2/lib This doesn't seem to work. It says that it is not a valid identifier. Is there anything I miss here? -- Regards, Edward WIJAYA Show quoted text

----- Original Message ----- From: gray via RT <bug-Tree-Suffix@rt.cpan.org> Date: Wednesday, March 15, 2006 12:11 pm Subject: [rt.cpan.org #18178] Installation Problem in Local Directory

> > <URL: http://rt.cpan.org/Ticket/Display.html?id=18178 > > > that should be: > setenv CFLAGS "$CFLAGS -I$HOME/MyBioTool/libstree-0.4.2/include" > setenv LDFLAGS "$LDFLAGS -L$HOME/MyBioTool/libstree-0.4.2/lib" > > > On Tue Mar 14 23:07:27 2006, GRAY wrote:

> > that's not a problem with the module. the libstree library and

> headers> have to be in a standard location for any program to find

> them. if

> > they're not, you have to explicitly tell it where they are located. > > setting the CFLAGS and LDFLAGS environment variables may work for

> you:> # for tcsh

> > setenv CFLAGS $HOME/MyBioTool/libstree-0.4.2/include > > setenv LDFLAGS $HOME/MyBioTool/libstree-0.4.2/lib > > > > # for bash > > export CFLAGS=$HOME/MyBioTool/libstree-0.4.2/include > > export LDFLAGS=$HOME/MyBioTool/libstree-0.4.2/lib > >

> >

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Wed Mar 15 00:05:34 2006 The RT System itself - Status changed from 'resolved' to 'open'

Wed Mar 15 00:21:05 2006 gray [...] cpan.org - Correspondence added

first, i followed up with a correction in tcsh format. in bash it's: export CFLAGS="$CFLAGS -I$HOME/MyBioTool/libstree-0.4.2/include" export LDFLAGS="$LDFLAGS -L$HOME/MyBioTool/libstree-0.4.2/lib" secondly, you are not using proper bash syntax. there can be no spaces next to '='. if you install by hand instead of through cpan, you can pass those settings through the command line: perl CFLAGS=... LDFlAGS=... Makefile.PL if this doesn't work for you, there's always google and the perl newgroups. since this isn't a problem with the module, there's probably others who have encountered and solved the same problem. On Wed Mar 15 00:05:32 2006, ewijaya@i2r.a-star.edu.sg wrote: Show quoted text

> Hi Gray, > > Thanks a lot for the reply. > I'm using bash. > > You mean putting these lines in the > .bash_profile file right? > > export CFLAGS = $HOME/MyBioTool/libstree-0.4.2/include > export LDFLAGS = $HOME/MyBioTool/libstree-0.4.2/lib > > This doesn't seem to work. > It says that it is not a valid identifier. > > Is there anything I miss here? > > -- > Regards, > Edward WIJAYA > > > ----- Original Message ----- > From: gray via RT <bug-Tree-Suffix@rt.cpan.org> > Date: Wednesday, March 15, 2006 12:11 pm > Subject: [rt.cpan.org #18178] Installation Problem in Local Directory >

> > > > <URL: http://rt.cpan.org/Ticket/Display.html?id=18178 > > > > > that should be: > > setenv CFLAGS "$CFLAGS -I$HOME/MyBioTool/libstree-0.4.2/include" > > setenv LDFLAGS "$LDFLAGS -L$HOME/MyBioTool/libstree-0.4.2/lib" > > > > > > On Tue Mar 14 23:07:27 2006, GRAY wrote:

> > > that's not a problem with the module. the libstree library and

> >

> headers> have to be in a standard location for any program to find

> > them. if

> > > they're not, you have to explicitly tell it where they are

> located.

> > > setting the CFLAGS and LDFLAGS environment variables may work for

> > you:> # for tcsh

> > > setenv CFLAGS $HOME/MyBioTool/libstree-0.4.2/include > > > setenv LDFLAGS $HOME/MyBioTool/libstree-0.4.2/lib > > > > > > # for bash > > > export CFLAGS=$HOME/MyBioTool/libstree-0.4.2/include > > > export LDFLAGS=$HOME/MyBioTool/libstree-0.4.2/lib

Wed Mar 15 00:21:07 2006 gray [...] cpan.org - Status changed from 'open' to 'resolved'