From valenzi at iigb.na.cnr.it Mon Jan 8 11:01:39 2001 From: valenzi at iigb.na.cnr.it (Marco Valenzi) Date: Mon, 8 Jan 2001 17:01:39 +0100 Subject: RedHat 7.0 Message-ID: Does anyone know if Emboss is compatible with RedHat release 7.0 ? We must decide wich Red Hat release to install in our server . Thanks Marco Valenzi -- Marco Valenzi Istituto Internazionale di Genetica e Biofisica via Guglielmo Marconi 10 80125 Napoli E-mail valenzi at iigbna.iigb.na.cnr.it tel. 081-7257303 From mlahtela at csc.fi Tue Jan 9 00:06:26 2001 From: mlahtela at csc.fi (Maija Lahtela) Date: Tue, 9 Jan 2001 07:06:26 +0200 Subject: Installing EMBASSY Message-ID: Dear All, I would appreciate your help in my problem dealing with the installation of embassy. I have just installed EMBOSS 1.8.0 and it seems to work well, but as I tried to install phylip in our SGI Origin 2000 I ran it to difficulties. The procedure was following ./configure --prefix=/emboss/EMBOSS-1.8.0/EMBASSY/PHYLIP-3.573c make install During the installation several warning messages appeared ld32: WARNING 84 : /usr/lib32/libsocket.so is not used for resolving any symbol. And testing the program /emboss/EMBOSS-1.8.0/EMBASSY/PHYLIP-3.573c/src> ednaml test ld32: WARNING 84 : /usr/lib32/libsocket.so is not used for resolving any symbol. EMBOSS An error in ajacd.c at line 1143:acdfile '/emboss/EMBOSS-1.8.0/embassy/phylip/emboss_acd/ednaml.acd' not opened Thanks in advance! Yours, Maija Lahtela-Kakkonen ***************************************************** Maija Lahtela-Kakkonen, Researcher CSC-Scientific Computing Tekniikantie 15 a D, P.O.Box 405 FIN-02101 ESPOO FINLAND TEL 358-9-4572079 /050-3819506, FAX 358-9-4572302 E-MAIL mlahtela at csc.fi, Internet:www.csc.fi **************************************************** From mlahtela at csc.fi Tue Jan 9 00:13:17 2001 From: mlahtela at csc.fi (Maija Lahtela) Date: Tue, 9 Jan 2001 07:13:17 +0200 Subject: Installing Embassy package Message-ID: Dear All, I would appreciate your help in my problem dealing with the installation of embassy. I have just installed EMBOSS 1.8.0 and it seems to work well, but as I tried to install Phylip in our SGI Origin 2000 I ran it to difficulties. The procedure was following ./configure --prefix=/emboss/EMBOSS-1.8.0/EMBASSY/PHYLIP-3.573c make install During the installation several warning messages appeared ld32: WARNING 84 : /usr/lib32/libsocket.so is not used for resolving any symbol. And testing the program /emboss/EMBOSS-1.8.0/EMBASSY/PHYLIP-3.573c/src> ednaml test ld32: WARNING 84 : /usr/lib32/libsocket.so is not used for resolving any symbol. EMBOSS An error in ajacd.c at line 1143:acdfile '/emboss/EMBOSS-1.8.0/embassy/phylip/emboss_acd/ednaml.acd' not opened Thanks in advance! Yours, Maija Lahtela-Kakkonen ***************************************************** Maija Lahtela-Kakkonen, Researcher CSC-Scientific Computing Tekniikantie 15 a D, P.O.Box 405 FIN-02101 ESPOO FINLAND TEL 358-9-4572079 /050-3819506, FAX 358-9-4572302 E-MAIL mlahtela at csc.fi, Internet:www.csc.fi **************************************************** From mlahtela at csc.fi Tue Jan 16 00:35:55 2001 From: mlahtela at csc.fi (Maija Lahtela) Date: Tue, 16 Jan 2001 07:35:55 +0200 Subject: Application Entret Message-ID: Dear Emboss Users, While testing EMBOSS-1.8.0 we noticed that entret writes the all documentation but the sequence is missing. For example, entret embl:hsfau the end of hsfau.entret file is following RT combinatorial libraries"; RL J. Mol. Biol. 0:0-0(1993). XX FH Key Location/Qualifiers FH FT source 1. .408 FT /db_xref="taxon:9606" FT /sex="male" FT /organism="Homo sapiens" FT /cell_type="B-cell" FT /dev_stage="adult" FT /tissue_type="bone marrow" FT /tissue_lib="BMHIV" XX SQ Sequence 408 BP; 102 A; 101 C; 117 G; 88 T; 0 other; ~ ~ ~ What should be done to get sequence also in entret file as in example displayed in EMBOSS page ? Yours, Maija Lahtela-Kakkonen ***************************************************** Maija Lahtela-Kakkonen, Researcher CSC-Scientific Computing Tekniikantie 15 a D, P.O.Box 405 FIN-02101 ESPOO FINLAND TEL 358-9-4572079 /050-3819506, FAX 358-9-4572302 E-MAIL mlahtela at csc.fi, Internet:www.csc.fi **************************************************** From mlahtela at csc.fi Tue Jan 16 00:35:55 2001 From: mlahtela at csc.fi (Maija Lahtela) Date: Tue, 16 Jan 2001 07:35:55 +0200 Subject: Application Entret Message-ID: Dear Emboss Users, While testing EMBOSS-1.8.0 we noticed that entret writes the all documentation but the sequence is missing. For example, entret embl:hsfau the end of hsfau.entret file is following From bauer at genprofile.com Tue Jan 16 02:00:00 2001 From: bauer at genprofile.com (David Bauer) Date: Tue, 16 Jan 2001 08:00:00 +0100 Subject: Application Entret References: Message-ID: <3A63F170.645AA505@genprofile.com> Hi, I just tried to reproduce your problem, but I always get the whole entry WITH the sequence. So I think your problem is somewhere in your database retrieval configuration. I could get the hsfau entry from genbank and from embl while I have the following configuration entries for EMBL and GenBank in my emboss.default: #EMBL DB embldb [ type: N method: url format: embl url: "http://www.ebi.ac.uk/htbin/emblfetch?%s" comment: "EMBL via EBI WWW Server" ] #NCBI GenBank DB gb [ type: N method: url format: gb url: "http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=s&form=6&dopt=g&html=no&uid=%s" comment: "GenBank via Entrez WWW Server" ] I just don't remember all the emblfetch syntax but I'm nearly sure you can also specify that you want retrieve only the header and not the sequence. Maija Lahtela wrote: > > Dear Emboss Users, > > While testing EMBOSS-1.8.0 we noticed that entret writes > the all documentation but the sequence is missing. > For example, entret embl:hsfau the end of hsfau.entret file is following > RT combinatorial libraries"; > RL J. Mol. Biol. 0:0-0(1993). > XX > FH Key Location/Qualifiers > FH > FT source 1. .408 > FT /db_xref="taxon:9606" > FT /sex="male" > FT /organism="Homo sapiens" > FT /cell_type="B-cell" > FT /dev_stage="adult" > FT /tissue_type="bone marrow" > FT /tissue_lib="BMHIV" > XX > SQ Sequence 408 BP; 102 A; 101 C; 117 G; 88 T; 0 other; > ~ > ~ > ~ > What should be done to get sequence also in entret file as in example > displayed in EMBOSS page ? > > Yours, > Maija Lahtela-Kakkonen > ***************************************************** > Maija Lahtela-Kakkonen, Researcher > CSC-Scientific Computing > Tekniikantie 15 a D, P.O.Box 405 > FIN-02101 ESPOO FINLAND > TEL 358-9-4572079 /050-3819506, FAX 358-9-4572302 > E-MAIL mlahtela at csc.fi, Internet:www.csc.fi > **************************************************** -- Dr. David Bauer GenProfile AG, Max-Delbrueck-Center, Erwin-Negelein-Haus Robert-Roessle-Str. 10, D-13125 Berlin, Germany bauer at genprofile.com, Tel:49-30-94892165, FAX:49-30-94892151 From bauer at genprofile.com Tue Jan 16 02:00:00 2001 From: bauer at genprofile.com (David Bauer) Date: Tue, 16 Jan 2001 08:00:00 +0100 Subject: Application Entret References: Message-ID: <3A63F170.645AA505@genprofile.com> Hi, I just tried to reproduce your problem, but I always get the whole entry WITH the sequence. So I think your problem is somewhere in your database retrieval From ableasby at hgmp.mrc.ac.uk Tue Jan 16 02:46:36 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 16 Jan 2001 07:46:36 GMT Subject: Application Entret Message-ID: <200101160746.HAA25135@tin.hgmp.mrc.ac.uk> I suspect the "problem" is that you're using GCG indexed databases. Entret will currently only reproduce the original entry for databases which hold the whole entry in one file (e.g. the original flatfiles or SRS indexed databases). I originally announced the program mentioning this but it doesn't seem to be in the documentation; the one line description when the program is run does hint at this though. Alan From ableasby at hgmp.mrc.ac.uk Tue Jan 16 02:46:36 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 16 Jan 2001 07:46:36 GMT Subject: Application Entret Message-ID: <200101160746.HAA25135@tin.hgmp.mrc.ac.uk> I suspect the "problem" is that you're using GCG indexed databases. Entret will currently only reproduce the original entry for databases which hold the whole entry in one file (e.g. the original flatfiles or SRS indexed databases). From bauer at genprofile.com Tue Jan 16 02:52:56 2001 From: bauer at genprofile.com (David Bauer) Date: Tue, 16 Jan 2001 08:52:56 +0100 Subject: List Problem Message-ID: <3A63FDD8.5332008F@genprofile.com> Hi, the list manager software seems to have a problem. >From one email it creates a second copy which contains the first 5 lines of the complete message. David. From bauer at genprofile.com Tue Jan 16 02:52:56 2001 From: bauer at genprofile.com (David Bauer) Date: Tue, 16 Jan 2001 08:52:56 +0100 Subject: List Problem Message-ID: <3A63FDD8.5332008F@genprofile.com> Hi, the list manager software seems to have a problem. >From one email it creates a second copy which contains the first 5 lines of the complete message. From ableasby at hgmp.mrc.ac.uk Tue Jan 16 03:30:46 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 16 Jan 2001 08:30:46 GMT Subject: Test of EMBOSS after bounce fixes(?) Message-ID: <200101160830.IAA09113@bromine.hgmp.mrc.ac.uk> Apologies for the multiple messages. Hopefully this is now fixed. At least the list is free from bad addresses now. Alan From ableasby at hgmp.mrc.ac.uk Tue Jan 16 03:30:46 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 16 Jan 2001 08:30:46 GMT Subject: Test of EMBOSS after bounce fixes(?) Message-ID: <200101160830.IAA09113@bromine.hgmp.mrc.ac.uk> Apologies for the multiple messages. Hopefully this is now fixed. At least the list is free from bad addresses now. Alan From david.martin at biotek.uio.no Tue Jan 16 08:12:06 2001 From: david.martin at biotek.uio.no (David Martin) Date: Tue, 16 Jan 2001 13:12:06 +0000 Subject: Application Entret In-Reply-To: Message-ID: On Tue, 16 Jan 2001, Maija Lahtela wrote: > Hi, > > Our embl database is in gcg format. EMBL database is so hugh that we are > not able to habe both original and gcg format. So are there any > possibilities to change the code in entret program or should we use > embl and genabank databases through www ? I thought that was the case. Why not set up a second embl as a url method to extract the full sequence from a friendly SRS server which wil then work? ..d > > Yours, > Maija L.-K. > > > > > > > In what format is your database. I don't think it is supposed to work > > unless everything is in strict EMBL format (GCG EMBL doesn't work) > > > > ..d > > > > > * Dr. David Martin Biotechnology Centre of Oslo * > > * Node Manager Gaustadalleen 21 * > > * The Norwegian EMBNet Node P.O. box 1125 Blindern * > > * tel +47 22 84 05 35 N-0317 Oslo * > > * fax +47 22 84 05 01 Norway * > > --------------------------------------------------------------------- > > > > ***************************************************** > Maija Lahtela-Kakkonen, Researcher > CSC-Scientific Computing > Tekniikantie 15 a D, P.O.Box 405 > FIN-02101 ESPOO FINLAND > TEL 358-9-4572079 /050-3819506, FAX 358-9-4572302 > E-MAIL mlahtela at csc.fi, Internet:www.csc.fi > **************************************************** > > > --------------------------------------------------------------------- * Dr. David Martin Biotechnology Centre of Oslo * * Node Manager Gaustadalleen 21 * * The Norwegian EMBNet Node P.O. box 1125 Blindern * * tel +47 22 84 05 35 N-0317 Oslo * * fax +47 22 84 05 01 Norway * --------------------------------------------------------------------- From gwilliam at hgmp.mrc.ac.uk Fri Jan 19 06:25:56 2001 From: gwilliam at hgmp.mrc.ac.uk (gwilliam at hgmp.mrc.ac.uk) Date: Fri, 19 Jan 2001 11:25:56 GMT Subject: EMNU v1.0.0 Message-ID: <200101191125.LAA05913@tellurium.hgmp.mrc.ac.uk> The simple character-based menu 'emnu' is now available from the EMBASSY FTP site: ftp://ftp.uk.embnet.org/pub/EMBOSS/EMNU-1.0.0.tar.gz For documentation see: http://www.hgmp.mrc.ac.uk/Software/EMBOSS/EMBASSY/EMNU/emnu.html This has been classed as an EMBASSY program, not an EMBOSS program, because it is interactive. emnu may be useful for users who dislike the UNIX command line and who are stuck on a telnet (or similar character-based) interface. Please comment on it freely. I hope there are not too many bugs left. I am sure there will be many features that people dislike intensely. :-) Please note that there are more GUIs in the pipeline, so emnu will be only one of several interfaces available. If you don't like emnu, use another interface. Bug reports to 'emboss-bug at embnet.org', please. Thanks, Gary Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From ableasby at hgmp.mrc.ac.uk Mon Jan 22 12:25:21 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Mon, 22 Jan 2001 17:25:21 GMT Subject: EMBOSS 1.9.0 Message-ID: <200101221725.RAA21469@bromine.hgmp.mrc.ac.uk> EMBOSS 1.9.0 is now available. New applications appear below (I may have missed some out but my colleagues will no doubt post if I have). Installation amendment: some sites were experiencing difficulties with autoconf. This was usually manifested by problems installing the ACD files. The installation files have been adjusted to solve this. List file reading: programs will now just give a warning for bad '@'file entries and carry on reading the list. This previously caused program termination Programming libraries: linked lists are now doubly linked. List iteration and string iteration functions have been rewritten. recode ------ This application scans a given nucleotide sequence for restriction sites. It reports single base positions in the restriction pattern which when mutated remove the restriction site whilst maintaining the same translation. Several restriction enzymes can be specified or alternatively all the enzymes in the REBASE database can be investigated. To find out whether the single point mutations found by 'recode', introduce new restriction sites, 'silent' should be run on the original sequence. ('Silent' searches for silent point mutation sites which maintain the same translation, see 'silent' documentation). The output for 'recode' is similar to the format used by 'silent'. abiview ------- This program graphically displays the results in an ABI file. The data for each nucleotide is plotted and the assigned nucleotide (G, A, T, C or N) in the ABI file is overlayed on the graphs. Alan From bauer at genprofile.com Tue Jan 23 02:14:05 2001 From: bauer at genprofile.com (David Bauer) Date: Tue, 23 Jan 2001 08:14:05 +0100 Subject: EMBOSS 1.9.0 References: <200101221725.RAA21469@bromine.hgmp.mrc.ac.uk> Message-ID: <3A6D2F3D.6EBBFD56@genprofile.com> Hi, I had a minor build problem with this version. My gd,z and png libs are in /usr/local/lib. For some strange reason EMBOSS could not find the -lpng while compiling the ajax subdir. As workaround I just added -L/usr/local/lib to the CFLAGS in the ajax/Makefile and EMBOSS is happy now. David. -- Dr. David Bauer GenProfile AG, Max-Delbrueck-Center, Erwin-Negelein-Haus Robert-Roessle-Str. 10, D-13125 Berlin, Germany bauer at genprofile.com, Tel:49-30-94892165, FAX:49-30-94892151 From ableasby at hgmp.mrc.ac.uk Tue Jan 23 02:49:47 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 23 Jan 2001 07:49:47 GMT Subject: EMBOSS 1.9.0 Message-ID: <200101230749.HAA11962@tin.hgmp.mrc.ac.uk> David writes: >For some strange reason EMBOSS could not find the -lpng while compiling >the ajax subdir. Very odd as I haven't (knowingly) changed the configure. >As workaround I just added -L/usr/local/lib to the CFLAGS in the >ajax/Makefile and EMBOSS is happy now. Whatever works I suppose but Makefile hacking is a little dicey as the makefile can be rewritten by auto configuration. Perhaps adding --with-pngdriver=/usr/local to the configure would have worked or, in your case make "CFLAGS= -L/usr/local/lib" might have been OK. I'd be interested to know whether anyone else has seen this /usr/local/lib problem. Cheers Alan From bauer at genprofile.com Tue Jan 23 02:50:33 2001 From: bauer at genprofile.com (David Bauer) Date: Tue, 23 Jan 2001 08:50:33 +0100 Subject: abiview References: <200101221725.RAA21469@bromine.hgmp.mrc.ac.uk> Message-ID: <3A6D37C9.3033C911@genprofile.com> Hi, abiview is nice but it suffers from a problem of plplots automatic character scaling. With larger windows (which still show a good readable plot) the sequence characters are too large to fit. Is there a way to change the size of the ploted sequence letters ? David. From johann at egenetics.com Tue Jan 23 07:55:20 2001 From: johann at egenetics.com (Johann Visagie) Date: Tue, 23 Jan 2001 14:55:20 +0200 Subject: EMNU v1.0.0 In-Reply-To: <200101191125.LAA05913@tellurium.hgmp.mrc.ac.uk>; from gwilliam@hgmp.mrc.ac.uk on Fri, Jan 19, 2001 at 11:25:56AM +0000 References: <200101191125.LAA05913@tellurium.hgmp.mrc.ac.uk> Message-ID: <20010123145520.G52192@fling.sanbi.ac.za> gwilliam at hgmp.mrc.ac.uk on 2001-01-19 (Fri) at 11:25:56 +0000: > > The simple character-based menu 'emnu' is now available from the EMBASSY > FTP site: I'm having a bad day. :-) Compilation of EMNU fails for me in such a basic way that I'm sure the answer to the problem is right in front of me, but for the life of me I can't figure it out right now. I'm trying to compile on FreeBSD 5-CURRENT, which ships with ncurses 5.1. Attached is the output of running gmake in EMNU-1.0.0/source. As you can see, emnu.o is compiled but upon trying to link it a whole bunch of undefined references appear. Examination with nm(1) indicates that these symbols are indeed undefined. The problem persists no matter how explicitly I enforce linking in the Makefile (post-configure). It's as linking against libncurses just fails silently. Very worrying. Any ideas or pointers? (The undefined references in libplplot is also worrying... but one problem at a time...) -- Johann -------------- next part -------------- Script started on Tue Jan 23 14:46:26 2001 cc -DPACKAGE=\"EMNU\" -DVERSION=\"1.0.0\" -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBM=1 -I. -I. -I../../../plplot -I../../../nucleus -I../../../ajax -I/usr/local/include/gd -O -c emnu.c /bin/sh ../libtool --mode=link cc -O -o emnu emnu.o ../../../plplot/libplplot.la ../../../ajax/libajax.la ../../../nucleus/libnucleus.la -lm -L/usr/local/lib -lncurses mkdir .libs cc -O -o .libs/emnu emnu.o ../../../plplot/.libs/libplplot.so -L/usr/lib -lm -L/usr/local/lib -lz -lgd -lpng ../../../ajax/.libs/libajax.so -lm -lz -lgd -lpng ../../../nucleus/.libs/libnucleus.so -lm -lz -lgd -lpng -lm -L/usr/local/lib -lncurses -Wl,--rpath -Wl,/usr/local/lib emnu.o: In function `prompt': emnu.o(.text+0x681): undefined reference to `new_field' emnu.o(.text+0x69a): undefined reference to `new_form' emnu.o(.text+0x6a9): undefined reference to `set_form_win' emnu.o(.text+0x6d0): undefined reference to `set_form_sub' emnu.o(.text+0x6ec): undefined reference to `form_opts_off' emnu.o(.text+0x6f8): undefined reference to `post_form' emnu.o(.text+0x71a): undefined reference to `form_win' emnu.o(.text+0x756): undefined reference to `form_driver' emnu.o(.text+0x78d): undefined reference to `form_driver' emnu.o(.text+0x79d): undefined reference to `field_buffer' emnu.o(.text+0x7c9): undefined reference to `field_buffer' emnu.o(.text+0x814): undefined reference to `unpost_form' emnu.o: In function `populate_file_menu': emnu.o(.text+0xe4e): undefined reference to `new_item' emnu.o(.text+0xe62): undefined reference to `new_item' emnu.o(.text+0xe7a): undefined reference to `new_item' emnu.o(.text+0xe8f): undefined reference to `new_item' emnu.o(.text+0xf49): undefined reference to `new_item' emnu.o(.text+0xf5d): more undefined references to `new_item' follow emnu.o: In function `make_label': emnu.o(.text+0x1049): undefined reference to `new_field' emnu.o(.text+0x105e): undefined reference to `set_field_buffer' emnu.o(.text+0x1069): undefined reference to `field_opts_off' emnu.o: In function `make_field': emnu.o(.text+0x1093): undefined reference to `new_field' emnu.o(.text+0x10a7): undefined reference to `set_field_userptr' emnu.o(.text+0x10b5): undefined reference to `field_opts_off' emnu.o: In function `start_form': emnu.o(.text+0x17c9): undefined reference to `new_form' emnu.o(.text+0x17d5): undefined reference to `set_form_win' emnu.o(.text+0x17fe): undefined reference to `set_form_sub' emnu.o(.text+0x1817): undefined reference to `form_opts_off' emnu.o(.text+0x1823): undefined reference to `post_form' emnu.o(.text+0x1842): undefined reference to `form_win' emnu.o: In function `end_form': emnu.o(.text+0x1869): undefined reference to `form_win' emnu.o(.text+0x1874): undefined reference to `form_sub' emnu.o(.text+0x1882): undefined reference to `unpost_form' emnu.o: In function `populate_program_menus': emnu.o(.text+0x19ce): undefined reference to `new_item' emnu.o(.text+0x19fa): undefined reference to `new_item' emnu.o: In function `populate_menu': emnu.o(.text+0x1ab4): undefined reference to `new_item' emnu.o(.text+0x1ac8): undefined reference to `new_item' emnu.o(.text+0x1ae0): undefined reference to `new_item' emnu.o(.text+0x1af5): more undefined references to `new_item' follow emnu.o: In function `populate_menu': emnu.o(.text+0x1b36): undefined reference to `set_item_userptr' emnu.o(.text+0x1b48): undefined reference to `new_item' emnu.o(.text+0x1b60): undefined reference to `new_item' emnu.o(.text+0x1bb8): undefined reference to `new_item' emnu.o(.text+0x1bcd): undefined reference to `set_item_userptr' emnu.o(.text+0x1cd8): undefined reference to `new_item' emnu.o(.text+0x1cec): undefined reference to `new_item' emnu.o(.text+0x1d17): undefined reference to `new_item' emnu.o(.text+0x1d63): undefined reference to `item_userptr' emnu.o(.text+0x1d8d): undefined reference to `new_item' emnu.o(.text+0x1da1): undefined reference to `new_item' emnu.o(.text+0x1db9): undefined reference to `new_item' emnu.o(.text+0x1dc8): undefined reference to `item_userptr' emnu.o: In function `start_menu': emnu.o(.text+0x1e51): undefined reference to `new_menu' emnu.o(.text+0x1e71): undefined reference to `set_menu_mark' emnu.o(.text+0x1e8c): undefined reference to `menu_opts_off' emnu.o(.text+0x1ef3): undefined reference to `set_menu_format' emnu.o(.text+0x1f0d): undefined reference to `set_menu_win' emnu.o(.text+0x1f5e): undefined reference to `set_menu_sub' emnu.o(.text+0x1f77): undefined reference to `post_menu' emnu.o: In function `end_menu': emnu.o(.text+0x1fb5): undefined reference to `menu_items' emnu.o(.text+0x1fc0): undefined reference to `menu_win' emnu.o(.text+0x1fcf): undefined reference to `menu_sub' emnu.o(.text+0x1fda): undefined reference to `unpost_menu' emnu.o(.text+0x2007): undefined reference to `free_menu' emnu.o(.text+0x201e): undefined reference to `free_item' emnu.o: In function `store_file': emnu.o(.text+0x207d): undefined reference to `current_item' emnu.o(.text+0x2083): undefined reference to `item_name' emnu.o(.text+0x20b0): undefined reference to `current_item' emnu.o(.text+0x20b6): undefined reference to `item_name' emnu.o: In function `recall_file': emnu.o(.text+0x2120): undefined reference to `form_driver' emnu.o(.text+0x2173): undefined reference to `form_driver' emnu.o(.text+0x218d): undefined reference to `form_driver' emnu.o(.text+0x21bb): undefined reference to `form_driver' emnu.o(.text+0x21d5): undefined reference to `form_driver' emnu.o(.text+0x21e3): more undefined references to `form_driver' follow emnu.o: In function `get_default_file': emnu.o(.text+0x221a): undefined reference to `current_item' emnu.o(.text+0x2220): undefined reference to `item_name' emnu.o: In function `stuff_file': emnu.o(.text+0x2997): undefined reference to `form_driver' emnu.o(.text+0x29e7): undefined reference to `form_driver' emnu.o(.text+0x2a17): undefined reference to `form_driver' emnu.o(.text+0x2a31): undefined reference to `form_driver' emnu.o(.text+0x2a3f): undefined reference to `form_driver' emnu.o: In function `show_tfm_help': emnu.o(.text+0x2a73): undefined reference to `current_item' emnu.o(.text+0x2a79): undefined reference to `item_name' emnu.o(.text+0x2a85): undefined reference to `current_field' emnu.o(.text+0x2a8e): undefined reference to `set_field_buffer' emnu.o(.text+0x2a9f): undefined reference to `form_driver' emnu.o(.text+0x2ab0): undefined reference to `current_field' emnu.o(.text+0x2ab9): undefined reference to `field_buffer' emnu.o: In function `show_help': emnu.o(.text+0x2b8c): undefined reference to `current_field' emnu.o(.text+0x2b95): undefined reference to `field_buffer' emnu.o(.text+0x2e17): undefined reference to `current_item' emnu.o(.text+0x2e1d): undefined reference to `item_index' emnu.o: In function `command_virtualise': emnu.o(.text+0x36d5): undefined reference to `current_field' emnu.o(.text+0x36de): undefined reference to `field_buffer' emnu.o(.text+0x370a): undefined reference to `current_field' emnu.o(.text+0x3713): undefined reference to `field_buffer' emnu.o: In function `update_dir_menu': emnu.o(.text+0x3805): undefined reference to `menu_win' emnu.o(.text+0x3815): undefined reference to `current_item' emnu.o(.text+0x381b): undefined reference to `item_index' emnu.o(.text+0x386f): undefined reference to `menu_driver' emnu.o: In function `select_action': emnu.o(.text+0x3897): undefined reference to `menu_win' emnu.o(.text+0x38d4): undefined reference to `current_item' emnu.o(.text+0x38f0): undefined reference to `current_item' emnu.o(.text+0x38f6): undefined reference to `item_name' emnu.o(.text+0x3928): undefined reference to `current_item' emnu.o(.text+0x392e): undefined reference to `item_name' emnu.o(.text+0x3960): undefined reference to `current_item' emnu.o(.text+0x3966): undefined reference to `item_name' emnu.o(.text+0x39cf): undefined reference to `current_item' emnu.o(.text+0x39d5): undefined reference to `item_name' emnu.o(.text+0x3a14): undefined reference to `current_item' emnu.o(.text+0x3a1a): undefined reference to `item_name' emnu.o(.text+0x3a5f): undefined reference to `current_item' emnu.o(.text+0x3a65): undefined reference to `item_name' emnu.o: In function `stuff_shellout_files': emnu.o(.text+0x3adb): undefined reference to `form_driver' emnu.o(.text+0x3ae6): undefined reference to `form_driver' emnu.o(.text+0x3af4): undefined reference to `form_driver' emnu.o(.text+0x3aff): undefined reference to `form_driver' emnu.o(.text+0x3b0d): undefined reference to `form_driver' emnu.o(.text+0x3b18): more undefined references to `form_driver' follow emnu.o: In function `process_unknown_command': emnu.o(.text+0x3bc0): undefined reference to `form_win' emnu.o(.text+0x3bfb): undefined reference to `current_item' emnu.o(.text+0x3c01): undefined reference to `item_name' emnu.o(.text+0x3c10): undefined reference to `current_field' emnu.o(.text+0x3c19): undefined reference to `set_field_buffer' emnu.o(.text+0x3c2d): undefined reference to `form_driver' emnu.o(.text+0x3c8e): undefined reference to `current_item' emnu.o(.text+0x3c94): undefined reference to `item_name' emnu.o(.text+0x3ca3): undefined reference to `current_field' emnu.o(.text+0x3cac): undefined reference to `set_field_buffer' emnu.o(.text+0x3cc0): undefined reference to `form_driver' emnu.o(.text+0x3ce4): undefined reference to `current_field' emnu.o(.text+0x3ced): undefined reference to `field_buffer' emnu.o(.text+0x3d25): undefined reference to `pos_form_cursor' emnu.o(.text+0x3e5d): undefined reference to `current_item' emnu.o(.text+0x3e63): undefined reference to `item_name' emnu.o(.text+0x3e72): undefined reference to `current_field' emnu.o(.text+0x3e7b): undefined reference to `set_field_buffer' emnu.o(.text+0x3e8f): undefined reference to `form_driver' emnu.o: In function `run_form_menu': emnu.o(.text+0x410d): undefined reference to `menu_win' emnu.o(.text+0x415d): undefined reference to `current_item' emnu.o(.text+0x4163): undefined reference to `item_name' emnu.o(.text+0x4172): undefined reference to `current_field' emnu.o(.text+0x417b): undefined reference to `set_field_buffer' emnu.o(.text+0x418f): undefined reference to `form_driver' emnu.o(.text+0x419b): undefined reference to `pos_form_cursor' emnu.o(.text+0x41fc): undefined reference to `form_driver' emnu.o(.text+0x4232): undefined reference to `form_driver' emnu.o(.text+0x4246): undefined reference to `current_field' emnu.o(.text+0x424f): undefined reference to `field_buffer' emnu.o(.text+0x427e): undefined reference to `current_field' emnu.o(.text+0x4287): undefined reference to `field_buffer' emnu.o(.text+0x42a8): undefined reference to `set_menu_pattern' emnu.o(.text+0x42c2): undefined reference to `pos_form_cursor' emnu.o(.text+0x4358): undefined reference to `menu_driver' emnu.o(.text+0x4369): undefined reference to `pos_form_cursor' emnu.o(.text+0x4380): undefined reference to `current_item' emnu.o(.text+0x4386): undefined reference to `item_name' emnu.o(.text+0x43a5): undefined reference to `current_item' emnu.o(.text+0x43ab): undefined reference to `item_name' emnu.o(.text+0x43ba): undefined reference to `current_field' emnu.o(.text+0x43c3): undefined reference to `set_field_buffer' emnu.o(.text+0x43d7): undefined reference to `form_driver' ../../../plplot/.libs/libplplot.so: undefined reference to `XFreePixmap' ../../../plplot/.libs/libplplot.so: undefined reference to `XCheckWindowEvent' ../../../plplot/.libs/libplplot.so: undefined reference to `XCreateFontCursor' ../../../plplot/.libs/libplplot.so: undefined reference to `XSetWindowBackground' ../../../plplot/.libs/libplplot.so: undefined reference to `XSync' ../../../plplot/.libs/libplplot.so: undefined reference to `XDrawLines' ../../../plplot/.libs/libplplot.so: undefined reference to `XDefineCursor' ../../../plplot/.libs/libplplot.so: undefined reference to `XGetVisualInfo' ../../../plplot/.libs/libplplot.so: undefined reference to `XCloseDisplay' ../../../plplot/.libs/libplplot.so: undefined reference to `XPending' ../../../plplot/.libs/libplplot.so: undefined reference to `XSetForeground' ../../../plplot/.libs/libplplot.so: undefined reference to `XFillPolygon' ../../../plplot/.libs/libplplot.so: undefined reference to `XFreeGC' ../../../plplot/.libs/libplplot.so: undefined reference to `XCopyArea' ../../../plplot/.libs/libplplot.so: undefined reference to `XUndefineCursor' ../../../plplot/.libs/libplplot.so: undefined reference to `XStoreColor' ../../../plplot/.libs/libplplot.so: undefined reference to `XLookupString' ../../../plplot/.libs/libplplot.so: undefined reference to `XQueryPointer' ../../../plplot/.libs/libplplot.so: undefined reference to `XFree' ../../../plplot/.libs/libplplot.so: undefined reference to `XFreeColors' ../../../plplot/.libs/libplplot.so: undefined reference to `XSetErrorHandler' ../../../plplot/.libs/libplplot.so: undefined reference to `XAllocColorCells' ../../../plplot/.libs/libplplot.so: undefined reference to `XDestroyWindow' ../../../plplot/.libs/libplplot.so: undefined reference to `XSetWindowColormap' ../../../plplot/.libs/libplplot.so: undefined reference to `XSetBackground' ../../../plplot/.libs/libplplot.so: undefined reference to `XCreateColormap' ../../../plplot/.libs/libplplot.so: undefined reference to `XSynchronize' ../../../plplot/.libs/libplplot.so: undefined reference to `XDrawLine' ../../../plplot/.libs/libplplot.so: undefined reference to `XGetErrorText' ../../../plplot/.libs/libplplot.so: undefined reference to `XQueryColors' ../../../plplot/.libs/libplplot.so: undefined reference to `XAllocColor' ../../../plplot/.libs/libplplot.so: undefined reference to `XWindowEvent' ../../../plplot/.libs/libplplot.so: undefined reference to `XFlush' ../../../plplot/.libs/libplplot.so: undefined reference to `XCreateWindow' ../../../plplot/.libs/libplplot.so: undefined reference to `XSelectInput' ../../../plplot/.libs/libplplot.so: undefined reference to `XGetGeometry' ../../../plplot/.libs/libplplot.so: undefined reference to `XSetStandardProperties' ../../../plplot/.libs/libplplot.so: undefined reference to `XClearWindow' ../../../plplot/.libs/libplplot.so: undefined reference to `XFillRectangle' ../../../plplot/.libs/libplplot.so: undefined reference to `XWarpPointer' ../../../plplot/.libs/libplplot.so: undefined reference to `XCreatePixmap' ../../../plplot/.libs/libplplot.so: undefined reference to `XCreateGC' ../../../plplot/.libs/libplplot.so: undefined reference to `XOpenDisplay' ../../../plplot/.libs/libplplot.so: undefined reference to `XMapRaised' gmake: *** [emnu] Error 1 Script done on Tue Jan 23 14:46:28 2001 From gwilliam at hgmp.mrc.ac.uk Tue Jan 23 08:20:16 2001 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Tue, 23 Jan 2001 13:20:16 +0000 Subject: EMNU v1.0.0 References: <200101191125.LAA05913@tellurium.hgmp.mrc.ac.uk> <20010123145520.G52192@fling.sanbi.ac.za> Message-ID: <3A6D8510.C739AEBD@hgmp.mrc.ac.uk> Johann Visagie wrote: > > gwilliam at hgmp.mrc.ac.uk on 2001-01-19 (Fri) at 11:25:56 +0000: > > > > The simple character-based menu 'emnu' is now available from the EMBASSY > > FTP site: > > I'm having a bad day. :-) Compilation of EMNU fails for me in such a basic > way that I'm sure the answer to the problem is right in front of me, but for > the life of me I can't figure it out right now. > > I'm trying to compile on FreeBSD 5-CURRENT, which ships with ncurses 5.1. > > Attached is the output of running gmake in EMNU-1.0.0/source. As you can > see, emnu.o is compiled but upon trying to link it a whole bunch of undefined > references appear. Examination with nm(1) indicates that these symbols are > indeed undefined. The problem persists no matter how explicitly I enforce > linking in the Makefile (post-configure). It's as linking against libncurses > just fails silently. Very worrying. > > Any ideas or pointers? > > (The undefined references in libplplot is also worrying... but one problem > at a time...) > > -- Johann I think that you have not got the 'forms' and 'menu' libraries of curses set up on your machine. This appears to be more common than I had thought! The best course of action might be to set up a copy of 'ncurses' (a freeware version of System V curses). This includes the form and menu libraries. If you do not wish to overwrite your existing version of curses, the emnu INSTALL file gives details of the 'configure' option '--with-curses=' to allow you to specify the location of your curses libraries in a non-standard place: If you give `configure' the option `--with-curses=/usr/local/gnu', it will look for some form of curses in those directories. It will take ncurses if it's there otherwise it'll use curses. If you don't give this '--with-curses' option it will look in the standard places and, again, use ncurses in preference to curses. Gary -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From johann at egenetics.com Tue Jan 23 08:45:21 2001 From: johann at egenetics.com (Johann Visagie) Date: Tue, 23 Jan 2001 15:45:21 +0200 Subject: EMNU v1.0.0 In-Reply-To: <3A6D8510.C739AEBD@hgmp.mrc.ac.uk>; from gwilliam@hgmp.mrc.ac.uk on Tue, Jan 23, 2001 at 01:20:16PM +0000 References: <200101191125.LAA05913@tellurium.hgmp.mrc.ac.uk> <20010123145520.G52192@fling.sanbi.ac.za> <3A6D8510.C739AEBD@hgmp.mrc.ac.uk> Message-ID: <20010123154521.L52192@fling.sanbi.ac.za> Gary Williams, Tel 01223 494522 on 2001-01-23 (Tue) at 13:20:16 +0000: > > I think that you have not got the 'forms' and 'menu' libraries of curses > set up on your machine. -r--r--r-- 1 root wheel 16091 Sep 26 02:01 /usr/include/form.h -r--r--r-- 1 root wheel 10951 Nov 3 16:31 /usr/include/menu.h If I'd been missing those it would've complained during compilation, not linking, I think. > The best course of action might be to set up a copy of 'ncurses' (a > freeware version of System V curses). This includes the form and menu > libraries. FreeBSD versions at the heads of the 4 and 5 branches of the CVS tree have ncurses 5.1-20001009 integrated into the source tree as contributed software, so my "default" curses library is ncurses, and it resides in the /usr hierarchy. In fact, my curses.h and libcurses.{a,so} are symlinks to ncurses.h and libncurses.{a,so} respectively. :-) In short, the libraries are there, configure picks them up, I'm doing all I can think of to link them... but it doesn't work. Which is why I'm thinking I'm missing something *really* obvious... > If you give `configure' the option `--with-curses=/usr/local/gnu', it > will look for some form of curses in those directories. Just gave that a go as well (though configure has always picked up libncurses correctly) - no luck. :-( I'm out of ideas for the moment... -- Johann From sgmd at genetik.fu-berlin.de Tue Jan 23 09:33:46 2001 From: sgmd at genetik.fu-berlin.de (Thomas Siegmund) Date: Tue, 23 Jan 2001 15:33:46 +0100 Subject: EMNU v1.0.0, undefined reference in libplplot Message-ID: <01012315334600.12974@scarlet> Hi all, I too have the problem with undefined references in libplplot as Johann Visagie described. My system: SuSE linux 7.0 on i686. EMBOSS 1.9.0 and Phylip (Embassy) compiled and installed without problems. Best regards Thomas Siegmund __________________ Freie Universit?t Berlin Institut f?r Genetik Arnimallee 7 14195 Berlin Germany From a-aiyar at northwestern.edu Tue Jan 23 10:03:22 2001 From: a-aiyar at northwestern.edu (Ashok Aiyar) Date: Tue, 23 Jan 2001 09:03:22 -0600 Subject: EMNU v1.0.0, undefined reference in libplplot In-Reply-To: <01012315334600.12974@scarlet> References: <01012315334600.12974@scarlet> Message-ID: I too get the undefined references in libplplot. I do have both libmenu and libform installed .... perhaps they are too old? I have a home grown Linux system that started out as Slackware 3.0 Ashok From johann at egenetics.com Tue Jan 23 10:08:55 2001 From: johann at egenetics.com (Johann Visagie) Date: Tue, 23 Jan 2001 17:08:55 +0200 Subject: EMNU v1.0.0, undefined reference in libplplot In-Reply-To: <01012315334600.12974@scarlet>; from sgmd@genetik.fu-berlin.de on Tue, Jan 23, 2001 at 03:33:46PM +0100 References: <01012315334600.12974@scarlet> Message-ID: <20010123170855.A58449@fling.sanbi.ac.za> Hi Thomas, Thomas Siegmund on 2001-01-23 (Tue) at 15:33:46 +0100: > > I too have the problem with undefined references in libplplot as Johann > Visagie described. My system: SuSE linux 7.0 on i686. EMBOSS 1.9.0 and Phylip > (Embassy) compiled and installed without problems. My apologies. Gary Williams and I moved the conversation to private email after the first few postings to the EMBOSS list. Gary solved the problem relating to undefined references in emnu.o, and you'll see that he has made EMNU-1.0.0 available on their FTP site. The problem with undefined references in libplplot when compiling EMNU is due to the fact that anything that links against libplplot should also link against libX11. You can manually enforce this by editing EMNU-1.0.1/source/Makefile *after* running ./configure in the EMNU-1.0.1 directory. This is a bit of a kludge, and I'm sure Gary will solve the problem in a more elegant way than I did. :-) -- Johann From gwilliam at hgmp.mrc.ac.uk Tue Jan 23 10:14:03 2001 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Tue, 23 Jan 2001 15:14:03 +0000 Subject: EMNU v1.0.0, undefined reference in libplplot References: <01012315334600.12974@scarlet> <20010123170855.A58449@fling.sanbi.ac.za> Message-ID: <3A6D9FBA.6B0D27CF@hgmp.mrc.ac.uk> Johann Visagie wrote: > > Hi Thomas, > > Thomas Siegmund on 2001-01-23 (Tue) at 15:33:46 +0100: > > > > I too have the problem with undefined references in libplplot as Johann > > Visagie described. My system: SuSE linux 7.0 on i686. EMBOSS 1.9.0 and Phylip > > (Embassy) compiled and installed without problems. > > My apologies. Gary Williams and I moved the conversation to private email > after the first few postings to the EMBOSS list. > > Gary solved the problem relating to undefined references in emnu.o, and > you'll see that he has made EMNU-1.0.0 available on their FTP site. > > The problem with undefined references in libplplot when compiling EMNU is due > to the fact that anything that links against libplplot should also link > against libX11. You can manually enforce this by editing > EMNU-1.0.1/source/Makefile *after* running ./configure in the EMNU-1.0.1 > directory. This is a bit of a kludge, and I'm sure Gary will solve the > problem in a more elegant way than I did. :-) > > -- Johann I wouldn't count on it :-) The quick and dirty fix that I'll commit soon is to add an explicit link to libX11 in configure.in (this will propagate to configure and Makefile). EMNU-1.0.2 should appear sometime this afternoon. Gary -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From johann at egenetics.com Tue Jan 23 10:29:29 2001 From: johann at egenetics.com (Johann Visagie) Date: Tue, 23 Jan 2001 17:29:29 +0200 Subject: EMNU v1.0.0, undefined reference in libplplot In-Reply-To: <3A6D9FBA.6B0D27CF@hgmp.mrc.ac.uk>; from gwilliam@hgmp.mrc.ac.uk on Tue, Jan 23, 2001 at 03:14:03PM +0000 References: <01012315334600.12974@scarlet> <20010123170855.A58449@fling.sanbi.ac.za> <3A6D9FBA.6B0D27CF@hgmp.mrc.ac.uk> Message-ID: <20010123172929.B59103@fling.sanbi.ac.za> Gary Williams, Tel 01223 494522 on 2001-01-23 (Tue) at 15:14:03 +0000: > > I wouldn't count on it :-) ;-) > The quick and dirty fix that I'll commit soon is to add an explicit link > to libX11 in configure.in (this will propagate to configure and > Makefile). > > EMNU-1.0.2 should appear sometime this afternoon. Looking forward to that, then! -- Johann From gwilliam at hgmp.mrc.ac.uk Tue Jan 23 11:07:01 2001 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Tue, 23 Jan 2001 16:07:01 +0000 Subject: EMNU v 1.0.2 Message-ID: <3A6DAC25.26EBB842@hgmp.mrc.ac.uk> OK folks, sorry for messing you all around. EMNU-1.0.2 is now available on the FTP site. ftp://ftp.uk.embnet.org/pub/EMBOSS/EMNU-1.0.2.tar.gz I hope this works better. We are forcing it to link to the curses menu and forms libraries and to the X11 library. Alan says he is going to try installing it on his home machine rather than our slightly non-standard setup here, so we should get a better idea of where any other problems for you might be. Gary -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From johann at egenetics.com Tue Jan 23 11:10:22 2001 From: johann at egenetics.com (Johann Visagie) Date: Tue, 23 Jan 2001 18:10:22 +0200 Subject: EMNU v1.0.0, undefined reference in libplplot In-Reply-To: <3A6D9FBA.6B0D27CF@hgmp.mrc.ac.uk>; from gwilliam@hgmp.mrc.ac.uk on Tue, Jan 23, 2001 at 03:14:03PM +0000 References: <01012315334600.12974@scarlet> <20010123170855.A58449@fling.sanbi.ac.za> <3A6D9FBA.6B0D27CF@hgmp.mrc.ac.uk> Message-ID: <20010123181022.A59653@fling.sanbi.ac.za> Gary Williams, Tel 01223 494522 on 2001-01-23 (Tue) at 15:14:03 +0000: > > The quick and dirty fix that I'll commit soon is to add an explicit link > to libX11 in configure.in (this will propagate to configure and > Makefile). > > EMNU-1.0.2 should appear sometime this afternoon. OK, I'm starting to nit-pick now since I can already get EMNU compiled on my system... but in the interests of having it build OOTB for everyone: If I do a straight ./configure and gmake for EMNU 1.0.2, I get: [ ... ] gcc -O -o .libs/emnu emnu.o ../../../plplot/.libs/libplplot.so -L/usr/lib -lm -L/usr/local/lib -lz -lgd -lpng ../../../ajax/.libs/libajax.so -lm -lz -lgd -lpng ../../../nucleus/.libs/libnucleus.so -lm -lz -lgd -lpng -lmenu -lform -lX11 -lm -lncurses -Wl,--rpath -Wl,/usr/local/lib /usr/libexec/elf/ld: cannot find -lX11 gmake: *** [emnu] Error 1 Specifying --x-libraries to ./configure doesn't seem to propagate to the Makefile either. Adding -L/usr/X11R6/lib manually to (say) CFLAGS in the Makefile works, though. -- Johann From johann at egenetics.com Tue Jan 23 11:21:24 2001 From: johann at egenetics.com (Johann Visagie) Date: Tue, 23 Jan 2001 18:21:24 +0200 Subject: EMNU v1.0.0, undefined reference in libplplot In-Reply-To: <20010123181022.A59653@fling.sanbi.ac.za>; from johann@egenetics.com on Tue, Jan 23, 2001 at 06:10:22PM +0200 References: <01012315334600.12974@scarlet> <20010123170855.A58449@fling.sanbi.ac.za> <3A6D9FBA.6B0D27CF@hgmp.mrc.ac.uk> <20010123181022.A59653@fling.sanbi.ac.za> Message-ID: <20010123182124.A60309@fling.sanbi.ac.za> Johann Visagie on 2001-01-23 (Tue) at 18:10:22 +0200: > > OK, I'm starting to nit-pick now since I can already get EMNU compiled on my > system... but in the interests of having it build OOTB for everyone: Actually, you might be able to scratch that nitpick. The FreeBSD EMBOSS port already works around some other EMBOSS building problems (such as the explicit -L/usr/local/lib which David Bauer mentioned), and pre-adding another -L to CPPFLAGS should not appreciably increase complexity or decrease elegance. :-) I'll report back if it works. -- Johann From bauer at genprofile.com Tue Jan 23 11:30:20 2001 From: bauer at genprofile.com (David Bauer) Date: Tue, 23 Jan 2001 17:30:20 +0100 Subject: EMNU v1.0.0, undefined reference in libplplot References: <01012315334600.12974@scarlet> <20010123170855.A58449@fling.sanbi.ac.za> <3A6D9FBA.6B0D27CF@hgmp.mrc.ac.uk> <20010123181022.A59653@fling.sanbi.ac.za> Message-ID: <3A6DB19C.4D605608@genprofile.com> > [ ... ] > gcc -O -o .libs/emnu emnu.o ../../../plplot/.libs/libplplot.so -L/usr/lib > -lm -L/usr/local/lib -lz -lgd -lpng ../../../ajax/.libs/libajax.so -lm -lz > -lgd -lpng ../../../nucleus/.libs/libnucleus.so -lm -lz -lgd -lpng -lmenu > -lform -lX11 -lm -lncurses -Wl,--rpath -Wl,/usr/local/lib > /usr/libexec/elf/ld: cannot find -lX11 > gmake: *** [emnu] Error 1 > > Specifying --x-libraries to ./configure doesn't seem to propagate to the > Makefile either. Adding -L/usr/X11R6/lib manually to (say) CFLAGS in the > Makefile works, though. I had to do the same hack to get 1.0.2 working. David. From gwilliam at hgmp.mrc.ac.uk Tue Jan 23 11:35:49 2001 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Tue, 23 Jan 2001 16:35:49 +0000 Subject: EMNU v1.0.0, undefined reference in libplplot References: <01012315334600.12974@scarlet> <20010123170855.A58449@fling.sanbi.ac.za> <3A6D9FBA.6B0D27CF@hgmp.mrc.ac.uk> <20010123181022.A59653@fling.sanbi.ac.za> <3A6DB19C.4D605608@genprofile.com> Message-ID: <3A6DB2E5.5171B41E@hgmp.mrc.ac.uk> David Bauer wrote: > > > [ ... ] > > gcc -O -o .libs/emnu emnu.o ../../../plplot/.libs/libplplot.so -L/usr/lib > > -lm -L/usr/local/lib -lz -lgd -lpng ../../../ajax/.libs/libajax.so -lm -lz > > -lgd -lpng ../../../nucleus/.libs/libnucleus.so -lm -lz -lgd -lpng -lmenu > > -lform -lX11 -lm -lncurses -Wl,--rpath -Wl,/usr/local/lib > > /usr/libexec/elf/ld: cannot find -lX11 > > gmake: *** [emnu] Error 1 > > > > Specifying --x-libraries to ./configure doesn't seem to propagate to the > > Makefile either. Adding -L/usr/X11R6/lib manually to (say) CFLAGS in the > > Makefile works, though. > > I had to do the same hack to get 1.0.2 working. Version 1.0.3 should be appearing later today or tomorrow morning... Thanks for your patience, Gary -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From bauer at genprofile.com Tue Jan 23 02:14:05 2001 From: bauer at genprofile.com (David Bauer) Date: Tue, 23 Jan 2001 08:14:05 +0100 Subject: EMBOSS 1.9.0 References: <200101221725.RAA21469@bromine.hgmp.mrc.ac.uk> Message-ID: <3A6D2F3D.6EBBFD56@genprofile.com> Hi, I had a minor build problem with this version. My gd,z and png libs are in /usr/local/lib. For some strange reason EMBOSS could not find the -lpng while compiling the ajax subdir. As workaround I just added -L/usr/local/lib to the CFLAGS in the ajax/Makefile and EMBOSS is happy now. David. -- Dr. David Bauer GenProfile AG, Max-Delbrueck-Center, Erwin-Negelein-Haus Robert-Roessle-Str. 10, D-13125 Berlin, Germany bauer at genprofile.com, Tel:49-30-94892165, FAX:49-30-94892151 From johann at egenetics.com Thu Jan 25 04:30:39 2001 From: johann at egenetics.com (Johann Visagie) Date: Thu, 25 Jan 2001 11:30:39 +0200 Subject: EMNU v1.0.0, undefined reference in libplplot In-Reply-To: <3A6DB19C.4D605608@genprofile.com>; from bauer@genprofile.com on Tue, Jan 23, 2001 at 05:30:20PM +0100 References: <01012315334600.12974@scarlet> <20010123170855.A58449@fling.sanbi.ac.za> <3A6D9FBA.6B0D27CF@hgmp.mrc.ac.uk> <20010123181022.A59653@fling.sanbi.ac.za> <3A6DB19C.4D605608@genprofile.com> Message-ID: <20010125113039.D99527@fling.sanbi.ac.za> David Bauer on 2001-01-23 (Tue) at 17:30:20 +0100: > > > Specifying --x-libraries to ./configure doesn't seem to propagate to the > > Makefile either. Adding -L/usr/X11R6/lib manually to (say) CFLAGS in the > > Makefile works, though. > > I had to do the same hack to get 1.0.2 working. Not so much a hack, since one can specify additions to make variables in the environment and you don't really need to edit any files. :-) FreeBSD port of EMBOSS 1.9.0 (incl. EMNU) has now been committed. I would _really_ appreciate it if FreeBSD-using EMBOSSers (David :) could test it sometime (if they the facilities to do so) and provide me with some feedback! http://www.freebsd.org/cgi/cvsweb.cgi/ports/biology/emboss/ -- Johann From ableasby at hgmp.mrc.ac.uk Thu Jan 25 12:06:25 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Thu, 25 Jan 2001 17:06:25 GMT Subject: EMBOSS 1.9.1 Message-ID: <200101251706.RAA15488@bromine.hgmp.mrc.ac.uk> This is a bugfix release. Programs affected in 1.9.0 are the supermatcher/diffseq/dottup family. Symptoms would be that under certain circumstances the programs would abort with an error. If the programs did not abort the results were correct. Particularly for Johann and FREEBSD: Files changed over 1.9.0 are (NEWS configure.in) ajax/ajlist.c nucleus/embword.c Alan From valenzi at iigb.na.cnr.it Mon Jan 8 16:01:39 2001 From: valenzi at iigb.na.cnr.it (Marco Valenzi) Date: Mon, 8 Jan 2001 17:01:39 +0100 Subject: RedHat 7.0 Message-ID: Does anyone know if Emboss is compatible with RedHat release 7.0 ? We must decide wich Red Hat release to install in our server . Thanks Marco Valenzi -- Marco Valenzi Istituto Internazionale di Genetica e Biofisica via Guglielmo Marconi 10 80125 Napoli E-mail valenzi at iigbna.iigb.na.cnr.it tel. 081-7257303 From mlahtela at csc.fi Tue Jan 9 05:06:26 2001 From: mlahtela at csc.fi (Maija Lahtela) Date: Tue, 9 Jan 2001 07:06:26 +0200 Subject: Installing EMBASSY Message-ID: Dear All, I would appreciate your help in my problem dealing with the installation of embassy. I have just installed EMBOSS 1.8.0 and it seems to work well, but as I tried to install phylip in our SGI Origin 2000 I ran it to difficulties. The procedure was following ./configure --prefix=/emboss/EMBOSS-1.8.0/EMBASSY/PHYLIP-3.573c make install During the installation several warning messages appeared ld32: WARNING 84 : /usr/lib32/libsocket.so is not used for resolving any symbol. And testing the program /emboss/EMBOSS-1.8.0/EMBASSY/PHYLIP-3.573c/src> ednaml test ld32: WARNING 84 : /usr/lib32/libsocket.so is not used for resolving any symbol. EMBOSS An error in ajacd.c at line 1143:acdfile '/emboss/EMBOSS-1.8.0/embassy/phylip/emboss_acd/ednaml.acd' not opened Thanks in advance! Yours, Maija Lahtela-Kakkonen ***************************************************** Maija Lahtela-Kakkonen, Researcher CSC-Scientific Computing Tekniikantie 15 a D, P.O.Box 405 FIN-02101 ESPOO FINLAND TEL 358-9-4572079 /050-3819506, FAX 358-9-4572302 E-MAIL mlahtela at csc.fi, Internet:www.csc.fi **************************************************** From mlahtela at csc.fi Tue Jan 9 05:13:17 2001 From: mlahtela at csc.fi (Maija Lahtela) Date: Tue, 9 Jan 2001 07:13:17 +0200 Subject: Installing Embassy package Message-ID: Dear All, I would appreciate your help in my problem dealing with the installation of embassy. I have just installed EMBOSS 1.8.0 and it seems to work well, but as I tried to install Phylip in our SGI Origin 2000 I ran it to difficulties. The procedure was following ./configure --prefix=/emboss/EMBOSS-1.8.0/EMBASSY/PHYLIP-3.573c make install During the installation several warning messages appeared ld32: WARNING 84 : /usr/lib32/libsocket.so is not used for resolving any symbol. And testing the program /emboss/EMBOSS-1.8.0/EMBASSY/PHYLIP-3.573c/src> ednaml test ld32: WARNING 84 : /usr/lib32/libsocket.so is not used for resolving any symbol. EMBOSS An error in ajacd.c at line 1143:acdfile '/emboss/EMBOSS-1.8.0/embassy/phylip/emboss_acd/ednaml.acd' not opened Thanks in advance! Yours, Maija Lahtela-Kakkonen ***************************************************** Maija Lahtela-Kakkonen, Researcher CSC-Scientific Computing Tekniikantie 15 a D, P.O.Box 405 FIN-02101 ESPOO FINLAND TEL 358-9-4572079 /050-3819506, FAX 358-9-4572302 E-MAIL mlahtela at csc.fi, Internet:www.csc.fi **************************************************** From mlahtela at csc.fi Tue Jan 16 05:35:55 2001 From: mlahtela at csc.fi (Maija Lahtela) Date: Tue, 16 Jan 2001 07:35:55 +0200 Subject: Application Entret Message-ID: Dear Emboss Users, While testing EMBOSS-1.8.0 we noticed that entret writes the all documentation but the sequence is missing. For example, entret embl:hsfau the end of hsfau.entret file is following RT combinatorial libraries"; RL J. Mol. Biol. 0:0-0(1993). XX FH Key Location/Qualifiers FH FT source 1. .408 FT /db_xref="taxon:9606" FT /sex="male" FT /organism="Homo sapiens" FT /cell_type="B-cell" FT /dev_stage="adult" FT /tissue_type="bone marrow" FT /tissue_lib="BMHIV" XX SQ Sequence 408 BP; 102 A; 101 C; 117 G; 88 T; 0 other; ~ ~ ~ What should be done to get sequence also in entret file as in example displayed in EMBOSS page ? Yours, Maija Lahtela-Kakkonen ***************************************************** Maija Lahtela-Kakkonen, Researcher CSC-Scientific Computing Tekniikantie 15 a D, P.O.Box 405 FIN-02101 ESPOO FINLAND TEL 358-9-4572079 /050-3819506, FAX 358-9-4572302 E-MAIL mlahtela at csc.fi, Internet:www.csc.fi **************************************************** From mlahtela at csc.fi Tue Jan 16 05:35:55 2001 From: mlahtela at csc.fi (Maija Lahtela) Date: Tue, 16 Jan 2001 07:35:55 +0200 Subject: Application Entret Message-ID: Dear Emboss Users, While testing EMBOSS-1.8.0 we noticed that entret writes the all documentation but the sequence is missing. For example, entret embl:hsfau the end of hsfau.entret file is following From bauer at genprofile.com Tue Jan 16 07:00:00 2001 From: bauer at genprofile.com (David Bauer) Date: Tue, 16 Jan 2001 08:00:00 +0100 Subject: Application Entret References: Message-ID: <3A63F170.645AA505@genprofile.com> Hi, I just tried to reproduce your problem, but I always get the whole entry WITH the sequence. So I think your problem is somewhere in your database retrieval configuration. I could get the hsfau entry from genbank and from embl while I have the following configuration entries for EMBL and GenBank in my emboss.default: #EMBL DB embldb [ type: N method: url format: embl url: "http://www.ebi.ac.uk/htbin/emblfetch?%s" comment: "EMBL via EBI WWW Server" ] #NCBI GenBank DB gb [ type: N method: url format: gb url: "http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=s&form=6&dopt=g&html=no&uid=%s" comment: "GenBank via Entrez WWW Server" ] I just don't remember all the emblfetch syntax but I'm nearly sure you can also specify that you want retrieve only the header and not the sequence. Maija Lahtela wrote: > > Dear Emboss Users, > > While testing EMBOSS-1.8.0 we noticed that entret writes > the all documentation but the sequence is missing. > For example, entret embl:hsfau the end of hsfau.entret file is following > RT combinatorial libraries"; > RL J. Mol. Biol. 0:0-0(1993). > XX > FH Key Location/Qualifiers > FH > FT source 1. .408 > FT /db_xref="taxon:9606" > FT /sex="male" > FT /organism="Homo sapiens" > FT /cell_type="B-cell" > FT /dev_stage="adult" > FT /tissue_type="bone marrow" > FT /tissue_lib="BMHIV" > XX > SQ Sequence 408 BP; 102 A; 101 C; 117 G; 88 T; 0 other; > ~ > ~ > ~ > What should be done to get sequence also in entret file as in example > displayed in EMBOSS page ? > > Yours, > Maija Lahtela-Kakkonen > ***************************************************** > Maija Lahtela-Kakkonen, Researcher > CSC-Scientific Computing > Tekniikantie 15 a D, P.O.Box 405 > FIN-02101 ESPOO FINLAND > TEL 358-9-4572079 /050-3819506, FAX 358-9-4572302 > E-MAIL mlahtela at csc.fi, Internet:www.csc.fi > **************************************************** -- Dr. David Bauer GenProfile AG, Max-Delbrueck-Center, Erwin-Negelein-Haus Robert-Roessle-Str. 10, D-13125 Berlin, Germany bauer at genprofile.com, Tel:49-30-94892165, FAX:49-30-94892151 From bauer at genprofile.com Tue Jan 16 07:00:00 2001 From: bauer at genprofile.com (David Bauer) Date: Tue, 16 Jan 2001 08:00:00 +0100 Subject: Application Entret References: Message-ID: <3A63F170.645AA505@genprofile.com> Hi, I just tried to reproduce your problem, but I always get the whole entry WITH the sequence. So I think your problem is somewhere in your database retrieval From ableasby at hgmp.mrc.ac.uk Tue Jan 16 07:46:36 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 16 Jan 2001 07:46:36 GMT Subject: Application Entret Message-ID: <200101160746.HAA25135@tin.hgmp.mrc.ac.uk> I suspect the "problem" is that you're using GCG indexed databases. Entret will currently only reproduce the original entry for databases which hold the whole entry in one file (e.g. the original flatfiles or SRS indexed databases). I originally announced the program mentioning this but it doesn't seem to be in the documentation; the one line description when the program is run does hint at this though. Alan From ableasby at hgmp.mrc.ac.uk Tue Jan 16 07:46:36 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 16 Jan 2001 07:46:36 GMT Subject: Application Entret Message-ID: <200101160746.HAA25135@tin.hgmp.mrc.ac.uk> I suspect the "problem" is that you're using GCG indexed databases. Entret will currently only reproduce the original entry for databases which hold the whole entry in one file (e.g. the original flatfiles or SRS indexed databases). From bauer at genprofile.com Tue Jan 16 07:52:56 2001 From: bauer at genprofile.com (David Bauer) Date: Tue, 16 Jan 2001 08:52:56 +0100 Subject: List Problem Message-ID: <3A63FDD8.5332008F@genprofile.com> Hi, the list manager software seems to have a problem. >From one email it creates a second copy which contains the first 5 lines of the complete message. David. From bauer at genprofile.com Tue Jan 16 07:52:56 2001 From: bauer at genprofile.com (David Bauer) Date: Tue, 16 Jan 2001 08:52:56 +0100 Subject: List Problem Message-ID: <3A63FDD8.5332008F@genprofile.com> Hi, the list manager software seems to have a problem. >From one email it creates a second copy which contains the first 5 lines of the complete message. From ableasby at hgmp.mrc.ac.uk Tue Jan 16 08:30:46 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 16 Jan 2001 08:30:46 GMT Subject: Test of EMBOSS after bounce fixes(?) Message-ID: <200101160830.IAA09113@bromine.hgmp.mrc.ac.uk> Apologies for the multiple messages. Hopefully this is now fixed. At least the list is free from bad addresses now. Alan From ableasby at hgmp.mrc.ac.uk Tue Jan 16 08:30:46 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 16 Jan 2001 08:30:46 GMT Subject: Test of EMBOSS after bounce fixes(?) Message-ID: <200101160830.IAA09113@bromine.hgmp.mrc.ac.uk> Apologies for the multiple messages. Hopefully this is now fixed. At least the list is free from bad addresses now. Alan From david.martin at biotek.uio.no Tue Jan 16 13:12:06 2001 From: david.martin at biotek.uio.no (David Martin) Date: Tue, 16 Jan 2001 13:12:06 +0000 Subject: Application Entret In-Reply-To: Message-ID: On Tue, 16 Jan 2001, Maija Lahtela wrote: > Hi, > > Our embl database is in gcg format. EMBL database is so hugh that we are > not able to habe both original and gcg format. So are there any > possibilities to change the code in entret program or should we use > embl and genabank databases through www ? I thought that was the case. Why not set up a second embl as a url method to extract the full sequence from a friendly SRS server which wil then work? ..d > > Yours, > Maija L.-K. > > > > > > > In what format is your database. I don't think it is supposed to work > > unless everything is in strict EMBL format (GCG EMBL doesn't work) > > > > ..d > > > > > * Dr. David Martin Biotechnology Centre of Oslo * > > * Node Manager Gaustadalleen 21 * > > * The Norwegian EMBNet Node P.O. box 1125 Blindern * > > * tel +47 22 84 05 35 N-0317 Oslo * > > * fax +47 22 84 05 01 Norway * > > --------------------------------------------------------------------- > > > > ***************************************************** > Maija Lahtela-Kakkonen, Researcher > CSC-Scientific Computing > Tekniikantie 15 a D, P.O.Box 405 > FIN-02101 ESPOO FINLAND > TEL 358-9-4572079 /050-3819506, FAX 358-9-4572302 > E-MAIL mlahtela at csc.fi, Internet:www.csc.fi > **************************************************** > > > --------------------------------------------------------------------- * Dr. David Martin Biotechnology Centre of Oslo * * Node Manager Gaustadalleen 21 * * The Norwegian EMBNet Node P.O. box 1125 Blindern * * tel +47 22 84 05 35 N-0317 Oslo * * fax +47 22 84 05 01 Norway * --------------------------------------------------------------------- From gwilliam at hgmp.mrc.ac.uk Fri Jan 19 11:25:56 2001 From: gwilliam at hgmp.mrc.ac.uk (gwilliam at hgmp.mrc.ac.uk) Date: Fri, 19 Jan 2001 11:25:56 GMT Subject: EMNU v1.0.0 Message-ID: <200101191125.LAA05913@tellurium.hgmp.mrc.ac.uk> The simple character-based menu 'emnu' is now available from the EMBASSY FTP site: ftp://ftp.uk.embnet.org/pub/EMBOSS/EMNU-1.0.0.tar.gz For documentation see: http://www.hgmp.mrc.ac.uk/Software/EMBOSS/EMBASSY/EMNU/emnu.html This has been classed as an EMBASSY program, not an EMBOSS program, because it is interactive. emnu may be useful for users who dislike the UNIX command line and who are stuck on a telnet (or similar character-based) interface. Please comment on it freely. I hope there are not too many bugs left. I am sure there will be many features that people dislike intensely. :-) Please note that there are more GUIs in the pipeline, so emnu will be only one of several interfaces available. If you don't like emnu, use another interface. Bug reports to 'emboss-bug at embnet.org', please. Thanks, Gary Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From ableasby at hgmp.mrc.ac.uk Mon Jan 22 17:25:21 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Mon, 22 Jan 2001 17:25:21 GMT Subject: EMBOSS 1.9.0 Message-ID: <200101221725.RAA21469@bromine.hgmp.mrc.ac.uk> EMBOSS 1.9.0 is now available. New applications appear below (I may have missed some out but my colleagues will no doubt post if I have). Installation amendment: some sites were experiencing difficulties with autoconf. This was usually manifested by problems installing the ACD files. The installation files have been adjusted to solve this. List file reading: programs will now just give a warning for bad '@'file entries and carry on reading the list. This previously caused program termination Programming libraries: linked lists are now doubly linked. List iteration and string iteration functions have been rewritten. recode ------ This application scans a given nucleotide sequence for restriction sites. It reports single base positions in the restriction pattern which when mutated remove the restriction site whilst maintaining the same translation. Several restriction enzymes can be specified or alternatively all the enzymes in the REBASE database can be investigated. To find out whether the single point mutations found by 'recode', introduce new restriction sites, 'silent' should be run on the original sequence. ('Silent' searches for silent point mutation sites which maintain the same translation, see 'silent' documentation). The output for 'recode' is similar to the format used by 'silent'. abiview ------- This program graphically displays the results in an ABI file. The data for each nucleotide is plotted and the assigned nucleotide (G, A, T, C or N) in the ABI file is overlayed on the graphs. Alan From bauer at genprofile.com Tue Jan 23 07:14:05 2001 From: bauer at genprofile.com (David Bauer) Date: Tue, 23 Jan 2001 08:14:05 +0100 Subject: EMBOSS 1.9.0 References: <200101221725.RAA21469@bromine.hgmp.mrc.ac.uk> Message-ID: <3A6D2F3D.6EBBFD56@genprofile.com> Hi, I had a minor build problem with this version. My gd,z and png libs are in /usr/local/lib. For some strange reason EMBOSS could not find the -lpng while compiling the ajax subdir. As workaround I just added -L/usr/local/lib to the CFLAGS in the ajax/Makefile and EMBOSS is happy now. David. -- Dr. David Bauer GenProfile AG, Max-Delbrueck-Center, Erwin-Negelein-Haus Robert-Roessle-Str. 10, D-13125 Berlin, Germany bauer at genprofile.com, Tel:49-30-94892165, FAX:49-30-94892151 From ableasby at hgmp.mrc.ac.uk Tue Jan 23 07:49:47 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Tue, 23 Jan 2001 07:49:47 GMT Subject: EMBOSS 1.9.0 Message-ID: <200101230749.HAA11962@tin.hgmp.mrc.ac.uk> David writes: >For some strange reason EMBOSS could not find the -lpng while compiling >the ajax subdir. Very odd as I haven't (knowingly) changed the configure. >As workaround I just added -L/usr/local/lib to the CFLAGS in the >ajax/Makefile and EMBOSS is happy now. Whatever works I suppose but Makefile hacking is a little dicey as the makefile can be rewritten by auto configuration. Perhaps adding --with-pngdriver=/usr/local to the configure would have worked or, in your case make "CFLAGS= -L/usr/local/lib" might have been OK. I'd be interested to know whether anyone else has seen this /usr/local/lib problem. Cheers Alan From bauer at genprofile.com Tue Jan 23 07:50:33 2001 From: bauer at genprofile.com (David Bauer) Date: Tue, 23 Jan 2001 08:50:33 +0100 Subject: abiview References: <200101221725.RAA21469@bromine.hgmp.mrc.ac.uk> Message-ID: <3A6D37C9.3033C911@genprofile.com> Hi, abiview is nice but it suffers from a problem of plplots automatic character scaling. With larger windows (which still show a good readable plot) the sequence characters are too large to fit. Is there a way to change the size of the ploted sequence letters ? David. From johann at egenetics.com Tue Jan 23 12:55:20 2001 From: johann at egenetics.com (Johann Visagie) Date: Tue, 23 Jan 2001 14:55:20 +0200 Subject: EMNU v1.0.0 In-Reply-To: <200101191125.LAA05913@tellurium.hgmp.mrc.ac.uk>; from gwilliam@hgmp.mrc.ac.uk on Fri, Jan 19, 2001 at 11:25:56AM +0000 References: <200101191125.LAA05913@tellurium.hgmp.mrc.ac.uk> Message-ID: <20010123145520.G52192@fling.sanbi.ac.za> gwilliam at hgmp.mrc.ac.uk on 2001-01-19 (Fri) at 11:25:56 +0000: > > The simple character-based menu 'emnu' is now available from the EMBASSY > FTP site: I'm having a bad day. :-) Compilation of EMNU fails for me in such a basic way that I'm sure the answer to the problem is right in front of me, but for the life of me I can't figure it out right now. I'm trying to compile on FreeBSD 5-CURRENT, which ships with ncurses 5.1. Attached is the output of running gmake in EMNU-1.0.0/source. As you can see, emnu.o is compiled but upon trying to link it a whole bunch of undefined references appear. Examination with nm(1) indicates that these symbols are indeed undefined. The problem persists no matter how explicitly I enforce linking in the Makefile (post-configure). It's as linking against libncurses just fails silently. Very worrying. Any ideas or pointers? (The undefined references in libplplot is also worrying... but one problem at a time...) -- Johann -------------- next part -------------- Script started on Tue Jan 23 14:46:26 2001 cc -DPACKAGE=\"EMNU\" -DVERSION=\"1.0.0\" -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DHAVE_LIBM=1 -I. -I. -I../../../plplot -I../../../nucleus -I../../../ajax -I/usr/local/include/gd -O -c emnu.c /bin/sh ../libtool --mode=link cc -O -o emnu emnu.o ../../../plplot/libplplot.la ../../../ajax/libajax.la ../../../nucleus/libnucleus.la -lm -L/usr/local/lib -lncurses mkdir .libs cc -O -o .libs/emnu emnu.o ../../../plplot/.libs/libplplot.so -L/usr/lib -lm -L/usr/local/lib -lz -lgd -lpng ../../../ajax/.libs/libajax.so -lm -lz -lgd -lpng ../../../nucleus/.libs/libnucleus.so -lm -lz -lgd -lpng -lm -L/usr/local/lib -lncurses -Wl,--rpath -Wl,/usr/local/lib emnu.o: In function `prompt': emnu.o(.text+0x681): undefined reference to `new_field' emnu.o(.text+0x69a): undefined reference to `new_form' emnu.o(.text+0x6a9): undefined reference to `set_form_win' emnu.o(.text+0x6d0): undefined reference to `set_form_sub' emnu.o(.text+0x6ec): undefined reference to `form_opts_off' emnu.o(.text+0x6f8): undefined reference to `post_form' emnu.o(.text+0x71a): undefined reference to `form_win' emnu.o(.text+0x756): undefined reference to `form_driver' emnu.o(.text+0x78d): undefined reference to `form_driver' emnu.o(.text+0x79d): undefined reference to `field_buffer' emnu.o(.text+0x7c9): undefined reference to `field_buffer' emnu.o(.text+0x814): undefined reference to `unpost_form' emnu.o: In function `populate_file_menu': emnu.o(.text+0xe4e): undefined reference to `new_item' emnu.o(.text+0xe62): undefined reference to `new_item' emnu.o(.text+0xe7a): undefined reference to `new_item' emnu.o(.text+0xe8f): undefined reference to `new_item' emnu.o(.text+0xf49): undefined reference to `new_item' emnu.o(.text+0xf5d): more undefined references to `new_item' follow emnu.o: In function `make_label': emnu.o(.text+0x1049): undefined reference to `new_field' emnu.o(.text+0x105e): undefined reference to `set_field_buffer' emnu.o(.text+0x1069): undefined reference to `field_opts_off' emnu.o: In function `make_field': emnu.o(.text+0x1093): undefined reference to `new_field' emnu.o(.text+0x10a7): undefined reference to `set_field_userptr' emnu.o(.text+0x10b5): undefined reference to `field_opts_off' emnu.o: In function `start_form': emnu.o(.text+0x17c9): undefined reference to `new_form' emnu.o(.text+0x17d5): undefined reference to `set_form_win' emnu.o(.text+0x17fe): undefined reference to `set_form_sub' emnu.o(.text+0x1817): undefined reference to `form_opts_off' emnu.o(.text+0x1823): undefined reference to `post_form' emnu.o(.text+0x1842): undefined reference to `form_win' emnu.o: In function `end_form': emnu.o(.text+0x1869): undefined reference to `form_win' emnu.o(.text+0x1874): undefined reference to `form_sub' emnu.o(.text+0x1882): undefined reference to `unpost_form' emnu.o: In function `populate_program_menus': emnu.o(.text+0x19ce): undefined reference to `new_item' emnu.o(.text+0x19fa): undefined reference to `new_item' emnu.o: In function `populate_menu': emnu.o(.text+0x1ab4): undefined reference to `new_item' emnu.o(.text+0x1ac8): undefined reference to `new_item' emnu.o(.text+0x1ae0): undefined reference to `new_item' emnu.o(.text+0x1af5): more undefined references to `new_item' follow emnu.o: In function `populate_menu': emnu.o(.text+0x1b36): undefined reference to `set_item_userptr' emnu.o(.text+0x1b48): undefined reference to `new_item' emnu.o(.text+0x1b60): undefined reference to `new_item' emnu.o(.text+0x1bb8): undefined reference to `new_item' emnu.o(.text+0x1bcd): undefined reference to `set_item_userptr' emnu.o(.text+0x1cd8): undefined reference to `new_item' emnu.o(.text+0x1cec): undefined reference to `new_item' emnu.o(.text+0x1d17): undefined reference to `new_item' emnu.o(.text+0x1d63): undefined reference to `item_userptr' emnu.o(.text+0x1d8d): undefined reference to `new_item' emnu.o(.text+0x1da1): undefined reference to `new_item' emnu.o(.text+0x1db9): undefined reference to `new_item' emnu.o(.text+0x1dc8): undefined reference to `item_userptr' emnu.o: In function `start_menu': emnu.o(.text+0x1e51): undefined reference to `new_menu' emnu.o(.text+0x1e71): undefined reference to `set_menu_mark' emnu.o(.text+0x1e8c): undefined reference to `menu_opts_off' emnu.o(.text+0x1ef3): undefined reference to `set_menu_format' emnu.o(.text+0x1f0d): undefined reference to `set_menu_win' emnu.o(.text+0x1f5e): undefined reference to `set_menu_sub' emnu.o(.text+0x1f77): undefined reference to `post_menu' emnu.o: In function `end_menu': emnu.o(.text+0x1fb5): undefined reference to `menu_items' emnu.o(.text+0x1fc0): undefined reference to `menu_win' emnu.o(.text+0x1fcf): undefined reference to `menu_sub' emnu.o(.text+0x1fda): undefined reference to `unpost_menu' emnu.o(.text+0x2007): undefined reference to `free_menu' emnu.o(.text+0x201e): undefined reference to `free_item' emnu.o: In function `store_file': emnu.o(.text+0x207d): undefined reference to `current_item' emnu.o(.text+0x2083): undefined reference to `item_name' emnu.o(.text+0x20b0): undefined reference to `current_item' emnu.o(.text+0x20b6): undefined reference to `item_name' emnu.o: In function `recall_file': emnu.o(.text+0x2120): undefined reference to `form_driver' emnu.o(.text+0x2173): undefined reference to `form_driver' emnu.o(.text+0x218d): undefined reference to `form_driver' emnu.o(.text+0x21bb): undefined reference to `form_driver' emnu.o(.text+0x21d5): undefined reference to `form_driver' emnu.o(.text+0x21e3): more undefined references to `form_driver' follow emnu.o: In function `get_default_file': emnu.o(.text+0x221a): undefined reference to `current_item' emnu.o(.text+0x2220): undefined reference to `item_name' emnu.o: In function `stuff_file': emnu.o(.text+0x2997): undefined reference to `form_driver' emnu.o(.text+0x29e7): undefined reference to `form_driver' emnu.o(.text+0x2a17): undefined reference to `form_driver' emnu.o(.text+0x2a31): undefined reference to `form_driver' emnu.o(.text+0x2a3f): undefined reference to `form_driver' emnu.o: In function `show_tfm_help': emnu.o(.text+0x2a73): undefined reference to `current_item' emnu.o(.text+0x2a79): undefined reference to `item_name' emnu.o(.text+0x2a85): undefined reference to `current_field' emnu.o(.text+0x2a8e): undefined reference to `set_field_buffer' emnu.o(.text+0x2a9f): undefined reference to `form_driver' emnu.o(.text+0x2ab0): undefined reference to `current_field' emnu.o(.text+0x2ab9): undefined reference to `field_buffer' emnu.o: In function `show_help': emnu.o(.text+0x2b8c): undefined reference to `current_field' emnu.o(.text+0x2b95): undefined reference to `field_buffer' emnu.o(.text+0x2e17): undefined reference to `current_item' emnu.o(.text+0x2e1d): undefined reference to `item_index' emnu.o: In function `command_virtualise': emnu.o(.text+0x36d5): undefined reference to `current_field' emnu.o(.text+0x36de): undefined reference to `field_buffer' emnu.o(.text+0x370a): undefined reference to `current_field' emnu.o(.text+0x3713): undefined reference to `field_buffer' emnu.o: In function `update_dir_menu': emnu.o(.text+0x3805): undefined reference to `menu_win' emnu.o(.text+0x3815): undefined reference to `current_item' emnu.o(.text+0x381b): undefined reference to `item_index' emnu.o(.text+0x386f): undefined reference to `menu_driver' emnu.o: In function `select_action': emnu.o(.text+0x3897): undefined reference to `menu_win' emnu.o(.text+0x38d4): undefined reference to `current_item' emnu.o(.text+0x38f0): undefined reference to `current_item' emnu.o(.text+0x38f6): undefined reference to `item_name' emnu.o(.text+0x3928): undefined reference to `current_item' emnu.o(.text+0x392e): undefined reference to `item_name' emnu.o(.text+0x3960): undefined reference to `current_item' emnu.o(.text+0x3966): undefined reference to `item_name' emnu.o(.text+0x39cf): undefined reference to `current_item' emnu.o(.text+0x39d5): undefined reference to `item_name' emnu.o(.text+0x3a14): undefined reference to `current_item' emnu.o(.text+0x3a1a): undefined reference to `item_name' emnu.o(.text+0x3a5f): undefined reference to `current_item' emnu.o(.text+0x3a65): undefined reference to `item_name' emnu.o: In function `stuff_shellout_files': emnu.o(.text+0x3adb): undefined reference to `form_driver' emnu.o(.text+0x3ae6): undefined reference to `form_driver' emnu.o(.text+0x3af4): undefined reference to `form_driver' emnu.o(.text+0x3aff): undefined reference to `form_driver' emnu.o(.text+0x3b0d): undefined reference to `form_driver' emnu.o(.text+0x3b18): more undefined references to `form_driver' follow emnu.o: In function `process_unknown_command': emnu.o(.text+0x3bc0): undefined reference to `form_win' emnu.o(.text+0x3bfb): undefined reference to `current_item' emnu.o(.text+0x3c01): undefined reference to `item_name' emnu.o(.text+0x3c10): undefined reference to `current_field' emnu.o(.text+0x3c19): undefined reference to `set_field_buffer' emnu.o(.text+0x3c2d): undefined reference to `form_driver' emnu.o(.text+0x3c8e): undefined reference to `current_item' emnu.o(.text+0x3c94): undefined reference to `item_name' emnu.o(.text+0x3ca3): undefined reference to `current_field' emnu.o(.text+0x3cac): undefined reference to `set_field_buffer' emnu.o(.text+0x3cc0): undefined reference to `form_driver' emnu.o(.text+0x3ce4): undefined reference to `current_field' emnu.o(.text+0x3ced): undefined reference to `field_buffer' emnu.o(.text+0x3d25): undefined reference to `pos_form_cursor' emnu.o(.text+0x3e5d): undefined reference to `current_item' emnu.o(.text+0x3e63): undefined reference to `item_name' emnu.o(.text+0x3e72): undefined reference to `current_field' emnu.o(.text+0x3e7b): undefined reference to `set_field_buffer' emnu.o(.text+0x3e8f): undefined reference to `form_driver' emnu.o: In function `run_form_menu': emnu.o(.text+0x410d): undefined reference to `menu_win' emnu.o(.text+0x415d): undefined reference to `current_item' emnu.o(.text+0x4163): undefined reference to `item_name' emnu.o(.text+0x4172): undefined reference to `current_field' emnu.o(.text+0x417b): undefined reference to `set_field_buffer' emnu.o(.text+0x418f): undefined reference to `form_driver' emnu.o(.text+0x419b): undefined reference to `pos_form_cursor' emnu.o(.text+0x41fc): undefined reference to `form_driver' emnu.o(.text+0x4232): undefined reference to `form_driver' emnu.o(.text+0x4246): undefined reference to `current_field' emnu.o(.text+0x424f): undefined reference to `field_buffer' emnu.o(.text+0x427e): undefined reference to `current_field' emnu.o(.text+0x4287): undefined reference to `field_buffer' emnu.o(.text+0x42a8): undefined reference to `set_menu_pattern' emnu.o(.text+0x42c2): undefined reference to `pos_form_cursor' emnu.o(.text+0x4358): undefined reference to `menu_driver' emnu.o(.text+0x4369): undefined reference to `pos_form_cursor' emnu.o(.text+0x4380): undefined reference to `current_item' emnu.o(.text+0x4386): undefined reference to `item_name' emnu.o(.text+0x43a5): undefined reference to `current_item' emnu.o(.text+0x43ab): undefined reference to `item_name' emnu.o(.text+0x43ba): undefined reference to `current_field' emnu.o(.text+0x43c3): undefined reference to `set_field_buffer' emnu.o(.text+0x43d7): undefined reference to `form_driver' ../../../plplot/.libs/libplplot.so: undefined reference to `XFreePixmap' ../../../plplot/.libs/libplplot.so: undefined reference to `XCheckWindowEvent' ../../../plplot/.libs/libplplot.so: undefined reference to `XCreateFontCursor' ../../../plplot/.libs/libplplot.so: undefined reference to `XSetWindowBackground' ../../../plplot/.libs/libplplot.so: undefined reference to `XSync' ../../../plplot/.libs/libplplot.so: undefined reference to `XDrawLines' ../../../plplot/.libs/libplplot.so: undefined reference to `XDefineCursor' ../../../plplot/.libs/libplplot.so: undefined reference to `XGetVisualInfo' ../../../plplot/.libs/libplplot.so: undefined reference to `XCloseDisplay' ../../../plplot/.libs/libplplot.so: undefined reference to `XPending' ../../../plplot/.libs/libplplot.so: undefined reference to `XSetForeground' ../../../plplot/.libs/libplplot.so: undefined reference to `XFillPolygon' ../../../plplot/.libs/libplplot.so: undefined reference to `XFreeGC' ../../../plplot/.libs/libplplot.so: undefined reference to `XCopyArea' ../../../plplot/.libs/libplplot.so: undefined reference to `XUndefineCursor' ../../../plplot/.libs/libplplot.so: undefined reference to `XStoreColor' ../../../plplot/.libs/libplplot.so: undefined reference to `XLookupString' ../../../plplot/.libs/libplplot.so: undefined reference to `XQueryPointer' ../../../plplot/.libs/libplplot.so: undefined reference to `XFree' ../../../plplot/.libs/libplplot.so: undefined reference to `XFreeColors' ../../../plplot/.libs/libplplot.so: undefined reference to `XSetErrorHandler' ../../../plplot/.libs/libplplot.so: undefined reference to `XAllocColorCells' ../../../plplot/.libs/libplplot.so: undefined reference to `XDestroyWindow' ../../../plplot/.libs/libplplot.so: undefined reference to `XSetWindowColormap' ../../../plplot/.libs/libplplot.so: undefined reference to `XSetBackground' ../../../plplot/.libs/libplplot.so: undefined reference to `XCreateColormap' ../../../plplot/.libs/libplplot.so: undefined reference to `XSynchronize' ../../../plplot/.libs/libplplot.so: undefined reference to `XDrawLine' ../../../plplot/.libs/libplplot.so: undefined reference to `XGetErrorText' ../../../plplot/.libs/libplplot.so: undefined reference to `XQueryColors' ../../../plplot/.libs/libplplot.so: undefined reference to `XAllocColor' ../../../plplot/.libs/libplplot.so: undefined reference to `XWindowEvent' ../../../plplot/.libs/libplplot.so: undefined reference to `XFlush' ../../../plplot/.libs/libplplot.so: undefined reference to `XCreateWindow' ../../../plplot/.libs/libplplot.so: undefined reference to `XSelectInput' ../../../plplot/.libs/libplplot.so: undefined reference to `XGetGeometry' ../../../plplot/.libs/libplplot.so: undefined reference to `XSetStandardProperties' ../../../plplot/.libs/libplplot.so: undefined reference to `XClearWindow' ../../../plplot/.libs/libplplot.so: undefined reference to `XFillRectangle' ../../../plplot/.libs/libplplot.so: undefined reference to `XWarpPointer' ../../../plplot/.libs/libplplot.so: undefined reference to `XCreatePixmap' ../../../plplot/.libs/libplplot.so: undefined reference to `XCreateGC' ../../../plplot/.libs/libplplot.so: undefined reference to `XOpenDisplay' ../../../plplot/.libs/libplplot.so: undefined reference to `XMapRaised' gmake: *** [emnu] Error 1 Script done on Tue Jan 23 14:46:28 2001 From gwilliam at hgmp.mrc.ac.uk Tue Jan 23 13:20:16 2001 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Tue, 23 Jan 2001 13:20:16 +0000 Subject: EMNU v1.0.0 References: <200101191125.LAA05913@tellurium.hgmp.mrc.ac.uk> <20010123145520.G52192@fling.sanbi.ac.za> Message-ID: <3A6D8510.C739AEBD@hgmp.mrc.ac.uk> Johann Visagie wrote: > > gwilliam at hgmp.mrc.ac.uk on 2001-01-19 (Fri) at 11:25:56 +0000: > > > > The simple character-based menu 'emnu' is now available from the EMBASSY > > FTP site: > > I'm having a bad day. :-) Compilation of EMNU fails for me in such a basic > way that I'm sure the answer to the problem is right in front of me, but for > the life of me I can't figure it out right now. > > I'm trying to compile on FreeBSD 5-CURRENT, which ships with ncurses 5.1. > > Attached is the output of running gmake in EMNU-1.0.0/source. As you can > see, emnu.o is compiled but upon trying to link it a whole bunch of undefined > references appear. Examination with nm(1) indicates that these symbols are > indeed undefined. The problem persists no matter how explicitly I enforce > linking in the Makefile (post-configure). It's as linking against libncurses > just fails silently. Very worrying. > > Any ideas or pointers? > > (The undefined references in libplplot is also worrying... but one problem > at a time...) > > -- Johann I think that you have not got the 'forms' and 'menu' libraries of curses set up on your machine. This appears to be more common than I had thought! The best course of action might be to set up a copy of 'ncurses' (a freeware version of System V curses). This includes the form and menu libraries. If you do not wish to overwrite your existing version of curses, the emnu INSTALL file gives details of the 'configure' option '--with-curses=' to allow you to specify the location of your curses libraries in a non-standard place: If you give `configure' the option `--with-curses=/usr/local/gnu', it will look for some form of curses in those directories. It will take ncurses if it's there otherwise it'll use curses. If you don't give this '--with-curses' option it will look in the standard places and, again, use ncurses in preference to curses. Gary -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From johann at egenetics.com Tue Jan 23 13:45:21 2001 From: johann at egenetics.com (Johann Visagie) Date: Tue, 23 Jan 2001 15:45:21 +0200 Subject: EMNU v1.0.0 In-Reply-To: <3A6D8510.C739AEBD@hgmp.mrc.ac.uk>; from gwilliam@hgmp.mrc.ac.uk on Tue, Jan 23, 2001 at 01:20:16PM +0000 References: <200101191125.LAA05913@tellurium.hgmp.mrc.ac.uk> <20010123145520.G52192@fling.sanbi.ac.za> <3A6D8510.C739AEBD@hgmp.mrc.ac.uk> Message-ID: <20010123154521.L52192@fling.sanbi.ac.za> Gary Williams, Tel 01223 494522 on 2001-01-23 (Tue) at 13:20:16 +0000: > > I think that you have not got the 'forms' and 'menu' libraries of curses > set up on your machine. -r--r--r-- 1 root wheel 16091 Sep 26 02:01 /usr/include/form.h -r--r--r-- 1 root wheel 10951 Nov 3 16:31 /usr/include/menu.h If I'd been missing those it would've complained during compilation, not linking, I think. > The best course of action might be to set up a copy of 'ncurses' (a > freeware version of System V curses). This includes the form and menu > libraries. FreeBSD versions at the heads of the 4 and 5 branches of the CVS tree have ncurses 5.1-20001009 integrated into the source tree as contributed software, so my "default" curses library is ncurses, and it resides in the /usr hierarchy. In fact, my curses.h and libcurses.{a,so} are symlinks to ncurses.h and libncurses.{a,so} respectively. :-) In short, the libraries are there, configure picks them up, I'm doing all I can think of to link them... but it doesn't work. Which is why I'm thinking I'm missing something *really* obvious... > If you give `configure' the option `--with-curses=/usr/local/gnu', it > will look for some form of curses in those directories. Just gave that a go as well (though configure has always picked up libncurses correctly) - no luck. :-( I'm out of ideas for the moment... -- Johann From sgmd at genetik.fu-berlin.de Tue Jan 23 14:33:46 2001 From: sgmd at genetik.fu-berlin.de (Thomas Siegmund) Date: Tue, 23 Jan 2001 15:33:46 +0100 Subject: EMNU v1.0.0, undefined reference in libplplot Message-ID: <01012315334600.12974@scarlet> Hi all, I too have the problem with undefined references in libplplot as Johann Visagie described. My system: SuSE linux 7.0 on i686. EMBOSS 1.9.0 and Phylip (Embassy) compiled and installed without problems. Best regards Thomas Siegmund __________________ Freie Universit?t Berlin Institut f?r Genetik Arnimallee 7 14195 Berlin Germany From a-aiyar at northwestern.edu Tue Jan 23 15:03:22 2001 From: a-aiyar at northwestern.edu (Ashok Aiyar) Date: Tue, 23 Jan 2001 09:03:22 -0600 Subject: EMNU v1.0.0, undefined reference in libplplot In-Reply-To: <01012315334600.12974@scarlet> References: <01012315334600.12974@scarlet> Message-ID: I too get the undefined references in libplplot. I do have both libmenu and libform installed .... perhaps they are too old? I have a home grown Linux system that started out as Slackware 3.0 Ashok From johann at egenetics.com Tue Jan 23 15:08:55 2001 From: johann at egenetics.com (Johann Visagie) Date: Tue, 23 Jan 2001 17:08:55 +0200 Subject: EMNU v1.0.0, undefined reference in libplplot In-Reply-To: <01012315334600.12974@scarlet>; from sgmd@genetik.fu-berlin.de on Tue, Jan 23, 2001 at 03:33:46PM +0100 References: <01012315334600.12974@scarlet> Message-ID: <20010123170855.A58449@fling.sanbi.ac.za> Hi Thomas, Thomas Siegmund on 2001-01-23 (Tue) at 15:33:46 +0100: > > I too have the problem with undefined references in libplplot as Johann > Visagie described. My system: SuSE linux 7.0 on i686. EMBOSS 1.9.0 and Phylip > (Embassy) compiled and installed without problems. My apologies. Gary Williams and I moved the conversation to private email after the first few postings to the EMBOSS list. Gary solved the problem relating to undefined references in emnu.o, and you'll see that he has made EMNU-1.0.0 available on their FTP site. The problem with undefined references in libplplot when compiling EMNU is due to the fact that anything that links against libplplot should also link against libX11. You can manually enforce this by editing EMNU-1.0.1/source/Makefile *after* running ./configure in the EMNU-1.0.1 directory. This is a bit of a kludge, and I'm sure Gary will solve the problem in a more elegant way than I did. :-) -- Johann From gwilliam at hgmp.mrc.ac.uk Tue Jan 23 15:14:03 2001 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Tue, 23 Jan 2001 15:14:03 +0000 Subject: EMNU v1.0.0, undefined reference in libplplot References: <01012315334600.12974@scarlet> <20010123170855.A58449@fling.sanbi.ac.za> Message-ID: <3A6D9FBA.6B0D27CF@hgmp.mrc.ac.uk> Johann Visagie wrote: > > Hi Thomas, > > Thomas Siegmund on 2001-01-23 (Tue) at 15:33:46 +0100: > > > > I too have the problem with undefined references in libplplot as Johann > > Visagie described. My system: SuSE linux 7.0 on i686. EMBOSS 1.9.0 and Phylip > > (Embassy) compiled and installed without problems. > > My apologies. Gary Williams and I moved the conversation to private email > after the first few postings to the EMBOSS list. > > Gary solved the problem relating to undefined references in emnu.o, and > you'll see that he has made EMNU-1.0.0 available on their FTP site. > > The problem with undefined references in libplplot when compiling EMNU is due > to the fact that anything that links against libplplot should also link > against libX11. You can manually enforce this by editing > EMNU-1.0.1/source/Makefile *after* running ./configure in the EMNU-1.0.1 > directory. This is a bit of a kludge, and I'm sure Gary will solve the > problem in a more elegant way than I did. :-) > > -- Johann I wouldn't count on it :-) The quick and dirty fix that I'll commit soon is to add an explicit link to libX11 in configure.in (this will propagate to configure and Makefile). EMNU-1.0.2 should appear sometime this afternoon. Gary -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From johann at egenetics.com Tue Jan 23 15:29:29 2001 From: johann at egenetics.com (Johann Visagie) Date: Tue, 23 Jan 2001 17:29:29 +0200 Subject: EMNU v1.0.0, undefined reference in libplplot In-Reply-To: <3A6D9FBA.6B0D27CF@hgmp.mrc.ac.uk>; from gwilliam@hgmp.mrc.ac.uk on Tue, Jan 23, 2001 at 03:14:03PM +0000 References: <01012315334600.12974@scarlet> <20010123170855.A58449@fling.sanbi.ac.za> <3A6D9FBA.6B0D27CF@hgmp.mrc.ac.uk> Message-ID: <20010123172929.B59103@fling.sanbi.ac.za> Gary Williams, Tel 01223 494522 on 2001-01-23 (Tue) at 15:14:03 +0000: > > I wouldn't count on it :-) ;-) > The quick and dirty fix that I'll commit soon is to add an explicit link > to libX11 in configure.in (this will propagate to configure and > Makefile). > > EMNU-1.0.2 should appear sometime this afternoon. Looking forward to that, then! -- Johann From gwilliam at hgmp.mrc.ac.uk Tue Jan 23 16:07:01 2001 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Tue, 23 Jan 2001 16:07:01 +0000 Subject: EMNU v 1.0.2 Message-ID: <3A6DAC25.26EBB842@hgmp.mrc.ac.uk> OK folks, sorry for messing you all around. EMNU-1.0.2 is now available on the FTP site. ftp://ftp.uk.embnet.org/pub/EMBOSS/EMNU-1.0.2.tar.gz I hope this works better. We are forcing it to link to the curses menu and forms libraries and to the X11 library. Alan says he is going to try installing it on his home machine rather than our slightly non-standard setup here, so we should get a better idea of where any other problems for you might be. Gary -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From johann at egenetics.com Tue Jan 23 16:10:22 2001 From: johann at egenetics.com (Johann Visagie) Date: Tue, 23 Jan 2001 18:10:22 +0200 Subject: EMNU v1.0.0, undefined reference in libplplot In-Reply-To: <3A6D9FBA.6B0D27CF@hgmp.mrc.ac.uk>; from gwilliam@hgmp.mrc.ac.uk on Tue, Jan 23, 2001 at 03:14:03PM +0000 References: <01012315334600.12974@scarlet> <20010123170855.A58449@fling.sanbi.ac.za> <3A6D9FBA.6B0D27CF@hgmp.mrc.ac.uk> Message-ID: <20010123181022.A59653@fling.sanbi.ac.za> Gary Williams, Tel 01223 494522 on 2001-01-23 (Tue) at 15:14:03 +0000: > > The quick and dirty fix that I'll commit soon is to add an explicit link > to libX11 in configure.in (this will propagate to configure and > Makefile). > > EMNU-1.0.2 should appear sometime this afternoon. OK, I'm starting to nit-pick now since I can already get EMNU compiled on my system... but in the interests of having it build OOTB for everyone: If I do a straight ./configure and gmake for EMNU 1.0.2, I get: [ ... ] gcc -O -o .libs/emnu emnu.o ../../../plplot/.libs/libplplot.so -L/usr/lib -lm -L/usr/local/lib -lz -lgd -lpng ../../../ajax/.libs/libajax.so -lm -lz -lgd -lpng ../../../nucleus/.libs/libnucleus.so -lm -lz -lgd -lpng -lmenu -lform -lX11 -lm -lncurses -Wl,--rpath -Wl,/usr/local/lib /usr/libexec/elf/ld: cannot find -lX11 gmake: *** [emnu] Error 1 Specifying --x-libraries to ./configure doesn't seem to propagate to the Makefile either. Adding -L/usr/X11R6/lib manually to (say) CFLAGS in the Makefile works, though. -- Johann From johann at egenetics.com Tue Jan 23 16:21:24 2001 From: johann at egenetics.com (Johann Visagie) Date: Tue, 23 Jan 2001 18:21:24 +0200 Subject: EMNU v1.0.0, undefined reference in libplplot In-Reply-To: <20010123181022.A59653@fling.sanbi.ac.za>; from johann@egenetics.com on Tue, Jan 23, 2001 at 06:10:22PM +0200 References: <01012315334600.12974@scarlet> <20010123170855.A58449@fling.sanbi.ac.za> <3A6D9FBA.6B0D27CF@hgmp.mrc.ac.uk> <20010123181022.A59653@fling.sanbi.ac.za> Message-ID: <20010123182124.A60309@fling.sanbi.ac.za> Johann Visagie on 2001-01-23 (Tue) at 18:10:22 +0200: > > OK, I'm starting to nit-pick now since I can already get EMNU compiled on my > system... but in the interests of having it build OOTB for everyone: Actually, you might be able to scratch that nitpick. The FreeBSD EMBOSS port already works around some other EMBOSS building problems (such as the explicit -L/usr/local/lib which David Bauer mentioned), and pre-adding another -L to CPPFLAGS should not appreciably increase complexity or decrease elegance. :-) I'll report back if it works. -- Johann From bauer at genprofile.com Tue Jan 23 16:30:20 2001 From: bauer at genprofile.com (David Bauer) Date: Tue, 23 Jan 2001 17:30:20 +0100 Subject: EMNU v1.0.0, undefined reference in libplplot References: <01012315334600.12974@scarlet> <20010123170855.A58449@fling.sanbi.ac.za> <3A6D9FBA.6B0D27CF@hgmp.mrc.ac.uk> <20010123181022.A59653@fling.sanbi.ac.za> Message-ID: <3A6DB19C.4D605608@genprofile.com> > [ ... ] > gcc -O -o .libs/emnu emnu.o ../../../plplot/.libs/libplplot.so -L/usr/lib > -lm -L/usr/local/lib -lz -lgd -lpng ../../../ajax/.libs/libajax.so -lm -lz > -lgd -lpng ../../../nucleus/.libs/libnucleus.so -lm -lz -lgd -lpng -lmenu > -lform -lX11 -lm -lncurses -Wl,--rpath -Wl,/usr/local/lib > /usr/libexec/elf/ld: cannot find -lX11 > gmake: *** [emnu] Error 1 > > Specifying --x-libraries to ./configure doesn't seem to propagate to the > Makefile either. Adding -L/usr/X11R6/lib manually to (say) CFLAGS in the > Makefile works, though. I had to do the same hack to get 1.0.2 working. David. From gwilliam at hgmp.mrc.ac.uk Tue Jan 23 16:35:49 2001 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Tue, 23 Jan 2001 16:35:49 +0000 Subject: EMNU v1.0.0, undefined reference in libplplot References: <01012315334600.12974@scarlet> <20010123170855.A58449@fling.sanbi.ac.za> <3A6D9FBA.6B0D27CF@hgmp.mrc.ac.uk> <20010123181022.A59653@fling.sanbi.ac.za> <3A6DB19C.4D605608@genprofile.com> Message-ID: <3A6DB2E5.5171B41E@hgmp.mrc.ac.uk> David Bauer wrote: > > > [ ... ] > > gcc -O -o .libs/emnu emnu.o ../../../plplot/.libs/libplplot.so -L/usr/lib > > -lm -L/usr/local/lib -lz -lgd -lpng ../../../ajax/.libs/libajax.so -lm -lz > > -lgd -lpng ../../../nucleus/.libs/libnucleus.so -lm -lz -lgd -lpng -lmenu > > -lform -lX11 -lm -lncurses -Wl,--rpath -Wl,/usr/local/lib > > /usr/libexec/elf/ld: cannot find -lX11 > > gmake: *** [emnu] Error 1 > > > > Specifying --x-libraries to ./configure doesn't seem to propagate to the > > Makefile either. Adding -L/usr/X11R6/lib manually to (say) CFLAGS in the > > Makefile works, though. > > I had to do the same hack to get 1.0.2 working. Version 1.0.3 should be appearing later today or tomorrow morning... Thanks for your patience, Gary -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From bauer at genprofile.com Tue Jan 23 07:14:05 2001 From: bauer at genprofile.com (David Bauer) Date: Tue, 23 Jan 2001 08:14:05 +0100 Subject: EMBOSS 1.9.0 References: <200101221725.RAA21469@bromine.hgmp.mrc.ac.uk> Message-ID: <3A6D2F3D.6EBBFD56@genprofile.com> Hi, I had a minor build problem with this version. My gd,z and png libs are in /usr/local/lib. For some strange reason EMBOSS could not find the -lpng while compiling the ajax subdir. As workaround I just added -L/usr/local/lib to the CFLAGS in the ajax/Makefile and EMBOSS is happy now. David. -- Dr. David Bauer GenProfile AG, Max-Delbrueck-Center, Erwin-Negelein-Haus Robert-Roessle-Str. 10, D-13125 Berlin, Germany bauer at genprofile.com, Tel:49-30-94892165, FAX:49-30-94892151 From johann at egenetics.com Thu Jan 25 09:30:39 2001 From: johann at egenetics.com (Johann Visagie) Date: Thu, 25 Jan 2001 11:30:39 +0200 Subject: EMNU v1.0.0, undefined reference in libplplot In-Reply-To: <3A6DB19C.4D605608@genprofile.com>; from bauer@genprofile.com on Tue, Jan 23, 2001 at 05:30:20PM +0100 References: <01012315334600.12974@scarlet> <20010123170855.A58449@fling.sanbi.ac.za> <3A6D9FBA.6B0D27CF@hgmp.mrc.ac.uk> <20010123181022.A59653@fling.sanbi.ac.za> <3A6DB19C.4D605608@genprofile.com> Message-ID: <20010125113039.D99527@fling.sanbi.ac.za> David Bauer on 2001-01-23 (Tue) at 17:30:20 +0100: > > > Specifying --x-libraries to ./configure doesn't seem to propagate to the > > Makefile either. Adding -L/usr/X11R6/lib manually to (say) CFLAGS in the > > Makefile works, though. > > I had to do the same hack to get 1.0.2 working. Not so much a hack, since one can specify additions to make variables in the environment and you don't really need to edit any files. :-) FreeBSD port of EMBOSS 1.9.0 (incl. EMNU) has now been committed. I would _really_ appreciate it if FreeBSD-using EMBOSSers (David :) could test it sometime (if they the facilities to do so) and provide me with some feedback! http://www.freebsd.org/cgi/cvsweb.cgi/ports/biology/emboss/ -- Johann From ableasby at hgmp.mrc.ac.uk Thu Jan 25 17:06:25 2001 From: ableasby at hgmp.mrc.ac.uk (ableasby at hgmp.mrc.ac.uk) Date: Thu, 25 Jan 2001 17:06:25 GMT Subject: EMBOSS 1.9.1 Message-ID: <200101251706.RAA15488@bromine.hgmp.mrc.ac.uk> This is a bugfix release. Programs affected in 1.9.0 are the supermatcher/diffseq/dottup family. Symptoms would be that under certain circumstances the programs would abort with an error. If the programs did not abort the results were correct. Particularly for Johann and FREEBSD: Files changed over 1.9.0 are (NEWS configure.in) ajax/ajlist.c nucleus/embword.c Alan