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From: Guy B. <gb...@vu...> - 2008-03-19 14:22:41
|
Bruce Pennypacker wrote: > Thanks for the information. The apache account is a standard unix > account, however its login shell is set to /sbin/nologin by default. The apache account should, for security reasons, indeed be in "nologin". But I wanted to say that the end user, who is going to run EMBOSS programs over the Web, does need a standard UNIX account of his own. Guy |
From: Bruce P. <bru...@gm...> - 2008-03-19 14:11:08
|
Guy, Thanks for the information. The apache account is a standard unix account, however its login shell is set to /sbin/nologin by default. I did change it to /bin/bash so that I could su to it and run catch manually to see what happens. It's home directory is also defined (they default it to /var/www) and it does have full read/write access there. -Bruce On Wed, Mar 19, 2008 at 9:53 AM, Guy Bottu <gb...@vu...> wrote: > Dear Bruce, > > Do you have a classic UNIX user account ? wEMBOSS uses the mechanism > defined in > the httpd server to do the authentication but then the process catch, > which > starts up run by the user that runs httpd, must do a setuid to the user > and thsi > user needs to have a home directory. > > Guy Bottu, > BEN > |
From: Guy B. <gb...@vu...> - 2008-03-19 13:54:28
|
Dear Bruce, Do you have a classic UNIX user account ? wEMBOSS uses the mechanism defined in the httpd server to do the authentication but then the process catch, which starts up run by the user that runs httpd, must do a setuid to the user and thsi user needs to have a home directory. Guy Bottu, BEN |
From: Bruce P. <bru...@gm...> - 2008-03-19 13:24:54
|
Hi all, I'm trying to install wEMBOSS on a new RedHat 5 system that I just installed EMBOSS on, and I'm running into an odd problem. The installs of both EMBOSS and wEMBOSS went fine. I pretty much used the default settings for both. I also set up my Apache httpd.conf and it's doing basic authentication against our LDAP server. All of that is working fine. However when I try to access wEMBOSS from a browser I get a bunch of 500 (internal server error) messages. I see the following in my syslog: Mar 19 09:16:18 emboss kernel: catch[26397]: segfault at 0000000000000000 rip 00 002aaaaaac1bb5 rsp 00007fffc9d425d0 error 4 I also see the following in my Apache error log: [Wed Mar 19 09:20:21 2008] [error] [client 192.168.2.22] Premature end of script headers: catch, referer: http://192.168.2.27/wEMBOSS.html In trying to troubleshoot this I tried running catch manually. As both root and from my own account, I get the following: [brucep@emboss:~] /usr/local/wEMBOSS/cgi-bin/catch Content-type: text/html error, catch: <P>Sorry, the owner of this process is not allowed to run catch program, ask wEMBOSS manager! However if I run catch as the apache user (the account that httpd is running under) I get the following: $ /usr/local/wEMBOSS/cgi-bin/catch Segmentation fault So why does catch run properly under root and other unprivileged accounts but segfault when running under the apache account? Here's the permissions of catch: [brucep@emboss:~] ls -l /usr/local/wEMBOSS/cgi-bin/catch -rwsr-xr-x 1 root root 10219 Mar 18 15:20 catch Any suggestions? -Bruce |
From: Christian N. <chr...@we...> - 2008-03-10 13:06:10
|
Hallo, I just set up a new server with EMBOSS and wEMBOSS as a frontend. Everything works fine (for once:-). I only have a small problem regarding the email notification in wEMBOSS. If I type in an email into the corresponding field I get this message: Running blast... You will be receive email at cn@localhost when blast has finished running, or you can check here periodically... Which is fine. If I leave the window open the job finishes and I get an email afterwards. However, when I close this window before the job is finished I never get an email and the job gets killed. Does anyone have an idea what to do? regards Christian _____________________________________________________________________ Unbegrenzter Speicherplatz für Ihr E-Mail Postfach? Jetzt aktivieren! http://freemail.web.de/club/landingpage.htm/?mc=025555 |
From: Christian N. <chr...@we...> - 2008-03-02 13:39:47
|
> Hi, > i compiled wEMBOSS on a Centos 5 x64 machine. The compile went fine without errors. But wenn I try to access the site I get the following errors in syslog: > > catch[14898]: segfault at 0000000000000000 rip 00002aaaaaacdbb5 rsp 00007fff9d34fae0 error 4 Here I am again... This error was my mistake. I hadn't set up user auth yet. And on 64 bit systems segfaults are logged thats why I hadn' seen this before... Now it works fine. Keep up the good work. Regards Christian _____________________________________________________________________ Der WEB.DE SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! http://smartsurfer.web.de/?mc=100071&distributionid=000000000066 |
From: Christian N. <chr...@we...> - 2008-02-29 10:21:45
|
Hi, i compiled wEMBOSS on a Centos 5 x64 machine. The compile went fine without errors. But wenn I try to access the site I get the following errors in syslog: catch[14898]: segfault at 0000000000000000 rip 00002aaaaaacdbb5 rsp 00007fff9d34fae0 error 4 and Premature end of script headers: catch, referer: http://192.168.0.95/wEMBOSS/wEMBOSS.html in the apache error log. Any help is welcome. regards Christian _______________________________________________________________________ Jetzt neu! Schützen Sie Ihren PC mit McAfee und WEB.DE. 30 Tage kostenlos testen. http://www.pc-sicherheit.web.de/startseite/?mc=022220 |
From: Christian N. <chr...@we...> - 2007-12-06 16:07:27
|
> >>1: Where should the fastalibs file be located and what format should it have? And in what format should I but the database names when answering the > questions at installtime? > Well, it is explained in the "README" file. I will try to explain it in full detail. > The file must be called "fastlibs" and must be in the same directory as the > executables Good. It works now. I had a typo in mine that why it did not work... I was a little confused as with the old version you had to supply the path to the fastlibs file. > > This is a bug in wEMBOSS. wEMBOSS should hide only the file index.html but not > any other xxx.html. It will be repaired in the release scheduled for begin 2008. > In the mean time you can fix it by hacking the file iprscan.acd. > outfile: outfile [ > parameter: "Y" > extension: "@($(format) = raw : iprscan txt : iprscan html : > html xml : xml gff : gff)" > ] > Just replace "html : html" by "html : htm" or whatever. > Changed that and now it works! Thanks. regards Christian _________________________________________________________________________ In 5 Schritten zur eigenen Homepage. Jetzt Domain sichern und gestalten! Nur 3,99 EUR/Monat! http://www.maildomain.web.de/?mc=021114 |
From: Guy B. <gb...@vu...> - 2007-12-06 13:14:12
|
Christian Naumer wrote: >>I now installed the required autoconf version and now the wrappers compile fine. So, it was the old problem with the autoconf/automake version, as noted by Martin Sarachu. Good to know that just installing a new version helps. >>1: Where should the fastalibs file be located and what format should it have? And in what format should I but the database names when answering the questions at installtime? Well, it is explained in the "README" file. I will try to explain it in full detail. The file must be called "fastlibs" and must be in the same directory as the executables of the "naked" fasta version 3. The "naked" fasta allows you to put the file where you like and point at it with an environment variable or with a command line parameter -l, but the "wrapper" counts on you to do it in a certain way. The file fastlibs must contain lines in the style : SwissProt (protein)$0+sw+/usr/data/swiss.fasta and at installation time you must answer to the scipt : sw: SwissProt (highly annotated protein databank) Here : "SwissProt (protein)" will not be used "0" stands for protein databank, for nucleic put "1" "sw" is the shortname for the databank, used by the "naked" program as well as by the "wrapper" ; it is important that you type in twice the same. "/usr/data/swiss.fasta" is the databank as file in fastA format. fasta supports multiple file databanks : use e.g. "@usr/data/uniprot.lib" where "usr/data/uniprot.lib" is a file with on each line a filename (of a databank in fastA format, you cannot nest libraries like with BLAST) "SwissProt (highly annotated protein databank)" is the longname for the databank. It will appear under wEMBOSS in the selector. >>2: iprscan runs fine on the commandline but from wEMBOSS it just displays an empty html page. Any aliases or other config that needs to be done here? This is a bug in wEMBOSS. wEMBOSS should hide only the file index.html but not any other xxx.html. It will be repaired in the release scheduled for begin 2008. In the mean time you can fix it by hacking the file iprscan.acd. outfile: outfile [ parameter: "Y" extension: "@($(format) = raw : iprscan txt : iprscan html : html xml : xml gff : gff)" ] Just replace "html : html" by "html : htm" or whatever. Regards, Guy Bottu, BEN |
From: Christian N. <chr...@we...> - 2007-12-06 08:56:33
|
> I now installed the required autoconf version and now the wrappers compi= le fine. > But now I have some other problems. > 1: Where should the fastalibs file be located and what format should it = have=3F And in what format should I but the database names when answering th= e questions at installtime=3F >=20 > 2: iprscan runs fine on the commandline but from wEMBOSS it just display= s an empty html page. Any aliases or other config that needs to be done he= re=3F A small update here: Text-output works in the webinterface. The html-file is in the results dir= ectory it just isn't displayed in the webinterface. There is no reference = in the index.html to the result html file anywhere. Hope this helps to find the problem. regards Christian=20 =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F Jetzt neu! Sch=FCtzen Sie Ihren PC mit McAfee und WEB.DE. 3 Monate kostenlos testen. http://www.pc-sicherheit.web.de/startseite/=3Fmc=3D022220 |
From: Christian N. <chr...@we...> - 2007-12-06 08:45:50
|
Hallo I now installed the required autoconf version and now the wrappers compile fine. But now I have some other problems. 1: Where should the fastalibs file be located and what format should it have? And in what format should I but the database names when answering the questions at installtime? 2: iprscan runs fine on the commandline but from wEMBOSS it just displays an empty html page. Any aliases or other config that needs to be done here? regards Christian _____________________________________________________________________ Der WEB.DE SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! http://smartsurfer.web.de/?mc=100071&distributionid=000000000066 |
From: Christian N. <chr...@we...> - 2007-12-05 16:37:31
|
> The problem seems related to the graphical libraries. > > > /bin/sh ../libtool --mode=link --tag=CC gcc -O2 -o blast blast.o -L/usr/local/emboss/lib -lnucleus -lajaxg -lajax -leplplot -lm > > gcc -O2 -o blast blast.o -L/usr/local/emboss/lib /usr/local/emboss/lib/libnucleus.so /usr/local/emboss/lib/libajaxg.so /usr/local/emboss/lib/libajax.so /usr/local/emboss/lib/libeplplot.so -lpthread -lm -Wl,--rpath -Wl,/usr/local/emboss/lib -Wl,--rpath -Wl,/usr/local/emboss/lib > Strange that -lajaxg appears in the command line. It is not present in the > MYEMBOSS Makefile and I had to add it for the special case of compiling the EBI > Web Services wrappers, who need it. I think it has something to do with automake etc. Because the test programm myseq compiled just fine before I started with the wrappers. When I try to install the wrappers I rerun aclocal/autoconf/automake (libtoolize --copy --force prompted to rerun aclocal see error below) and after this myseq will not compile with the same errors. *****libtool error******** libtoolize --copy --force Using `AC_PROG_RANLIB' is rendered obsolete by `AC_PROG_LIBTOOL' libtoolize: `/usr/share/aclocal/libtool.m4' is serial 47, less than 48 in `aclocal.m4' To remain compatible, you should update your `aclocal.m4' by running aclocal. then I run aclocal ******libtool error******** > > > /usr/local/emboss/lib/libeplplot.so: undefined reference to `XFreePixmap' > > /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdImageColorAllocate' > These are related to X-window graphics. > > To understand what is going on : > > - can you run an EMBOSS program like pepwindow in a terminal and obtain X11 > graphics output ? Works. No problem there. > > - what does the file .../MYEMBOSS-3.0.0/source/Makefile.am contain ? > LDADD = -L${embprefix}/lib -lnucleus -lajax -leplplot $(XLIB) > or is -lajaxg also there ? This is the content of Makefile.am # SUBDIRS = source emboss_acd emboss_doc EXTRA_DIST = depcomp ltmain.sh install-sh config.sub config.guess # tar to pick up the other directories # then remove any CVS subdirectories dist-hook: tar cBf - emboss_acd | ( cd $(distdir); tar xBf - ; cd emboss_acd; rm -rf CVS) tar cBf - emboss_doc | ( cd $(distdir); tar xBf - ; cd emboss_doc; rm -rf CVS; rm -rf master) regards Christian _____________________________________________________________________ Der WEB.DE SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! http://smartsurfer.web.de/?mc=100071&distributionid=000000000066 |
From: Guy B. <gb...@vu...> - 2007-12-05 14:50:17
|
Christian Naumer wrote: > Now for the problem I have: > I compiled EMBOSS 5.0 and installed it. Which worked fine without errors. I then tried to install the wrappers and configure ran fine but the make command put out some errors. The problem seems related to the graphical libraries. > /bin/sh ../libtool --mode=link --tag=CC gcc -O2 -o blast blast.o -L/usr/local/emboss/lib -lnucleus -lajaxg -lajax -leplplot -lm > gcc -O2 -o blast blast.o -L/usr/local/emboss/lib /usr/local/emboss/lib/libnucleus.so /usr/local/emboss/lib/libajaxg.so /usr/local/emboss/lib/libajax.so /usr/local/emboss/lib/libeplplot.so -lpthread -lm -Wl,--rpath -Wl,/usr/local/emboss/lib -Wl,--rpath -Wl,/usr/local/emboss/lib Strange that -lajaxg appears in the command line. It is not present in the MYEMBOSS Makefile and I had to add it for the special case of compiling the EBI Web Services wrappers, who need it. > /usr/local/emboss/lib/libeplplot.so: undefined reference to `XFreePixmap' > /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdImageColorAllocate' These are related to X-window graphics. To understand what is going on : - can you run an EMBOSS program like pepwindow in a terminal and obtain X11 graphics output ? - what does the file .../MYEMBOSS-3.0.0/source/Makefile.am contain ? LDADD = -L${embprefix}/lib -lnucleus -lajax -leplplot $(XLIB) or is -lajaxg also there ? Guy |
From: Christian N. <chr...@we...> - 2007-12-05 10:06:53
|
Hallo, first let me say I am sorry to hear of the death of Martin Sarachu.=20 Now for the problem I have: I compiled EMBOSS 5.0 and installed it. Which worked fine without errors. = I then tried to install the wrappers and configure ran fine but the make c= ommand put out some errors. Anyone got an idea what the problem is here=3F Thanks and best regards Christian Making all in source make[1]: Entering directory `/root/bioinf/EMBOSS/EMBOSS-5.0.0/embassy/MYEM= BOSS-3.0.0/source' cd .. && /bin/sh /root/bioinf/EMBOSS/EMBOSS-5.0.0/embassy/MYEMBOSS-3.0.0/= missing --run automake-1.9 --gnu source/Makefile cd .. && /bin/sh ./config.status source/Makefile depfiles config.status: creating source/Makefile config.status: executing depfiles commands make[1]: Leaving directory `/root/bioinf/EMBOSS/EMBOSS-5.0.0/embassy/MYEMB= OSS-3.0.0/source' make[1]: Entering directory `/root/bioinf/EMBOSS/EMBOSS-5.0.0/embassy/MYEM= BOSS-3.0.0/source' if gcc -DPACKAGE=5FNAME=3D\"\" -DPACKAGE=5FTARNAME=3D\"\" -DPACKAGE=5FVERSION=3D\"\" -= DPACKAGE=5FSTRING=3D\"\" -DPACKAGE=5FBUGREPORT=3D\"\" -DPACKAGE=3D\"MYEMBOSS\" -DVER= SION=3D\"3.0.0\" -DSTDC=5FHEADERS=3D1 -DHAVE=5FSYS=5FTYPES=5FH=3D1 -DHAVE=5FSYS=5FSTAT=5FH=3D1 -= DHAVE=5FSTDLIB=5FH=3D1 -DHAVE=5FSTRING=5FH=3D1 -DHAVE=5FMEMORY=5FH=3D1 -DHAVE=5FSTRINGS=5FH=3D1 -D= HAVE=5FINTTYPES=5FH=3D1 -DHAVE=5FSTDINT=5FH=3D1 -DHAVE=5FUNISTD=5FH=3D1 -DHAVE=5FDLFCN=5FH=3D1 -DH= AVE=5FDIRENT=5FH=3D1 -DSTDC=5FHEADERS=3D1 -DHAVE=5FUNISTD=5FH=3D1 -DGETPGRP=5FVOID=3D1 -DHAVE=5F= STRFTIME=3D1 -DHAVE=5FUNISTD=5FH=3D1 -DHAVE=5FFORK=3D1 -DHAVE=5FVFORK=3D1 -DHAVE=5FWORKING=5FV= FORK=3D1 -DHAVE=5FWORKING=5FFORK=3D1 -DHAVE=5FVPRINTF=3D1 -DHAVE=5FSTRDUP=3D1 -DHAVE=5FSTRST= R=3D1 -DHAVE=5FSTRCHR=3D1 -DHAVE=5FERAND48=3D1 -DHAVE=5FMEMMOVE=3D1 -DHAVE=5FLIBM=3D1 -I. -= I. -I../include -I/usr/local/emboss/include -I/usr/local/emboss/include/ep= lplot -DAJ=5FLinuxLF -D=5FFILE=5FOFFSET=5FBITS=3D64 -D=5FLARGEFILE=5FSOURCE -D=5FLARGEFIL= E64=5FSOURCE -DLENDIAN -O2 -MT blast.o -MD -MP -MF ".deps/blast.Tpo" -c -o= blast.o blast.c; \ then mv -f ".deps/blast.Tpo" ".deps/blast.Po"; else rm -f ".deps/blast.Tpo= "; exit 1; fi blast.c: In function `main': blast.c:47: Warnung: Verarbeiten des Argumentes 1 von =BBtime=AB von inkompati= blem Zeigertyp blast.c:50: Warnung: =BBajAcdGetListI=AB ist veraltet (deklariert bei /usr/loc= al/emboss/include/ajacd.h:99) blast.c:59: Warnung: =BBajAcdGetListI=AB ist veraltet (deklariert bei /usr/loc= al/emboss/include/ajacd.h:99) blast.c:64: Warnung: =BBajAcdGetListI=AB ist veraltet (deklariert bei /usr/loc= al/emboss/include/ajacd.h:99) blast.c:66: Warnung: =BBajAcdGetListI=AB ist veraltet (deklariert bei /usr/loc= al/emboss/include/ajacd.h:99) blast.c:74: Warnung: =BBajSeqFileNewOut=AB ist veraltet (deklariert bei /usr/l= ocal/emboss/include/ajseqwrite.h:180) blast.c:75: Warnung: =BBajSeqOutSetFormat=AB ist veraltet (deklariert bei /usr= /local/emboss/include/ajseqwrite.h:187) blast.c:77: Warnung: =BBajSeqToUpper=AB ist veraltet (deklariert bei /usr/loca= l/emboss/include/ajseq.h:343) blast.c:78: Warnung: =BBajSeqAllWrite=AB ist veraltet (deklariert bei /usr/loc= al/emboss/include/ajseqwrite.h:178) blast.c:80: Warnung: =BBajSeqWriteClose=AB ist veraltet (deklariert bei /usr/l= ocal/emboss/include/ajseqwrite.h:184) blast.c:83: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/em= boss/include/ajstr.h:566) blast.c:85: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/em= boss/include/ajstr.h:566) blast.c:87: Warnung: =BBajStrStr=AB ist veraltet (deklariert bei /usr/local/em= boss/include/ajstr.h:682) blast.c:91: Warnung: =BBajStrStr=AB ist veraltet (deklariert bei /usr/local/em= boss/include/ajstr.h:682) blast.c:103: Warnung: =BBajStrTrim=AB ist veraltet (deklariert bei /usr/local/= emboss/include/ajstr.h:699) blast.c:110: Warnung: =BBajStrTrim=AB ist veraltet (deklariert bei /usr/local/= emboss/include/ajstr.h:699) blast.c:119: Warnung: =BBajAcdGetSelectI=AB ist veraltet (deklariert bei /usr/= local/emboss/include/ajacd.h:100) blast.c:121: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:123: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:125: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:129: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:130: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:135: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:137: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:140: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:142: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:145: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:147: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:149: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:151: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:153: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:155: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:158: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:159: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:161: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:161: Warnung: =BBajAcdGetSelectI=AB ist veraltet (deklariert bei /usr/= local/emboss/include/ajacd.h:100) blast.c:163: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:164: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:167: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:167: Warnung: =BBajAcdGetListI=AB ist veraltet (deklariert bei /usr/lo= cal/emboss/include/ajacd.h:99) blast.c:170: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:170: Warnung: =BBajAcdGetListI=AB ist veraltet (deklariert bei /usr/lo= cal/emboss/include/ajacd.h:99) blast.c:173: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:173: Warnung: =BBajAcdGetListI=AB ist veraltet (deklariert bei /usr/lo= cal/emboss/include/ajacd.h:99) blast.c:174: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:174: Warnung: =BBajAcdGetListI=AB ist veraltet (deklariert bei /usr/lo= cal/emboss/include/ajacd.h:99) blast.c:180: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:182: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:185: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:187: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:189: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:190: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:191: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:192: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:192: Warnung: =BBajAcdGetListI=AB ist veraltet (deklariert bei /usr/lo= cal/emboss/include/ajacd.h:99) blast.c:200: Warnung: =BBajSeqToUpper=AB ist veraltet (deklariert bei /usr/loc= al/emboss/include/ajseq.h:343) blast.c:202: Warnung: =BBajSeqFileNewOut=AB ist veraltet (deklariert bei /usr/= local/emboss/include/ajseqwrite.h:180) blast.c:203: Warnung: =BBajSeqOutSetFormat=AB ist veraltet (deklariert bei /us= r/local/emboss/include/ajseqwrite.h:187) blast.c:204: Warnung: =BBajSeqWrite=AB ist veraltet (deklariert bei /usr/local= /emboss/include/ajseqwrite.h:182) blast.c:205: Warnung: =BBajSeqWriteClose=AB ist veraltet (deklariert bei /usr/= local/emboss/include/ajseqwrite.h:184) blast.c:208: Warnung: =BBajSeqGetName=AB ist veraltet (deklariert bei /usr/loc= al/emboss/include/ajseq.h:359) blast.c:209: Warnung: =BBajStrToLower=AB ist veraltet (deklariert bei /usr/loc= al/emboss/include/ajstr.h:694) blast.c:213: Warnung: =BBajStrSuffix=AB ist veraltet (deklariert bei /usr/loca= l/emboss/include/ajstr.h:691) blast.c:214: Warnung: =BBajStrCut=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:610) blast.c:214: Warnung: =BBajStrLen=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:629) blast.c:215: Warnung: =BBajStrLen=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:629) blast.c:215: Warnung: =BBajStrLen=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:629) blast.c:225: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:227: Warnung: =BBajStrApp=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:566) blast.c:229: Warnung: =BBajStrStr=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:682) blast.c:232: Warnung: =BBajSysUnlink=AB ist veraltet (deklariert bei /usr/loca= l/emboss/include/ajsys.h:78) blast.c:235: Warnung: =BBajStrStr=AB ist veraltet (deklariert bei /usr/local/e= mboss/include/ajstr.h:682) /bin/sh ../libtool --mode=3Dlink --tag=3DCC gcc -O2 -o blast blast.o -L/us= r/local/emboss/lib -lnucleus -lajaxg -lajax -leplplot -lm=20 gcc -O2 -o blast blast.o -L/usr/local/emboss/lib /usr/local/emboss/lib/li= bnucleus.so /usr/local/emboss/lib/libajaxg.so /usr/local/emboss/lib/libaja= x.so /usr/local/emboss/lib/libeplplot.so -lpthread -lm -Wl,--rpath -Wl,/us= r/local/emboss/lib -Wl,--rpath -Wl,/usr/local/emboss/lib /usr/local/emboss/lib/libeplplot.so: undefined reference to `XFreePixmap' /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdImageColorA= llocate' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XCheckWindowE= vent' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XCreateFontCu= rsor' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XSetWindowBac= kground' /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdImageGifPtr= ' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XSync' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XDrawLines' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XDefineCursor= ' /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdImageColorD= eallocate' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XGetVisualInf= o' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XCloseDisplay= ' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XPending' /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdImageSetThi= ckness' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XSetForegroun= d' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XFillPolygon'= /usr/local/emboss/lib/libeplplot.so: undefined reference to `XAllocNamedCo= lor' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XFreeGC' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XCopyArea' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XUndefineCurs= or' /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdImageDestro= y' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XGetImage' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XStoreColor' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XLookupString= ' /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdImagePngPtr= Ex' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XQueryPointer= ' /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdImageLine' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XFree' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XFreeColors' /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdImageFilled= Rectangle' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XSetErrorHand= ler' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XAllocColorCe= lls' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XDestroyWindo= w' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XSetWindowCol= ormap' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XSetBackgroun= d' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XCreateColorm= ap' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XSynchronize'= /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdImageCreate= ' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XDrawLine' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XGetErrorText= ' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XQueryColors'= /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdImageCreate= TrueColor' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XAllocColor' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XWindowEvent'= /usr/local/emboss/lib/libeplplot.so: undefined reference to `XSetFunction'= /usr/local/emboss/lib/libeplplot.so: undefined reference to `XFlush' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XCreateWindow= ' /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdImageFilled= Polygon' /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdFree' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XSelectInput'= /usr/local/emboss/lib/libeplplot.so: undefined reference to `XGetGeometry'= /usr/local/emboss/lib/libeplplot.so: undefined reference to `XSetLineAttri= butes' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XSetStandardP= roperties' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XClearWindow'= /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdImageSetAnt= iAliased' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XFillRectangl= e' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XWarpPointer'= /usr/local/emboss/lib/libeplplot.so: undefined reference to `XPutImage' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XCreatePixmap= ' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XCreateGC' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XOpenDisplay'= /usr/local/emboss/lib/libeplplot.so: undefined reference to `XMapRaised' collect2: ld returned 1 exit status make[1]: *** [blast] Fehler 1 make[1]: Leaving directory `/root/bioinf/EMBOSS/EMBOSS-5.0.0/embassy/MYEMB= OSS-3.0.0/source' make: *** [all-recursive] Fehler 1 Making install in source make[1]: Entering directory `/root/bioinf/EMBOSS/EMBOSS-5.0.0/embassy/MYEM= BOSS-3.0.0/source' /bin/sh ../libtool --mode=3Dlink --tag=3DCC gcc -O2 -o blast blast.o -L/us= r/local/emboss/lib -lnucleus -lajaxg -lajax -leplplot -lm=20 gcc -O2 -o blast blast.o -L/usr/local/emboss/lib /usr/local/emboss/lib/li= bnucleus.so /usr/local/emboss/lib/libajaxg.so /usr/local/emboss/lib/libaja= x.so /usr/local/emboss/lib/libeplplot.so -lpthread -lm -Wl,--rpath -Wl,/us= r/local/emboss/lib -Wl,--rpath -Wl,/usr/local/emboss/lib /usr/local/emboss/lib/libeplplot.so: undefined reference to `XFreePixmap' /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdImageColorA= llocate' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XCheckWindowE= vent' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XCreateFontCu= rsor' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XSetWindowBac= kground' /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdImageGifPtr= ' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XSync' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XDrawLines' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XDefineCursor= ' /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdImageColorD= eallocate' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XGetVisualInf= o' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XCloseDisplay= ' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XPending' /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdImageSetThi= ckness' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XSetForegroun= d' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XFillPolygon'= /usr/local/emboss/lib/libeplplot.so: undefined reference to `XAllocNamedCo= lor' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XFreeGC' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XCopyArea' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XUndefineCurs= or' /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdImageDestro= y' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XGetImage' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XStoreColor' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XLookupString= ' /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdImagePngPtr= Ex' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XQueryPointer= ' /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdImageLine' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XFree' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XFreeColors' /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdImageFilled= Rectangle' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XSetErrorHand= ler' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XAllocColorCe= lls' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XDestroyWindo= w' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XSetWindowCol= ormap' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XSetBackgroun= d' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XCreateColorm= ap' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XSynchronize'= /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdImageCreate= ' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XDrawLine' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XGetErrorText= ' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XQueryColors'= /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdImageCreate= TrueColor' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XAllocColor' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XWindowEvent'= /usr/local/emboss/lib/libeplplot.so: undefined reference to `XSetFunction'= /usr/local/emboss/lib/libeplplot.so: undefined reference to `XFlush' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XCreateWindow= ' /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdImageFilled= Polygon' /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdFree' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XSelectInput'= /usr/local/emboss/lib/libeplplot.so: undefined reference to `XGetGeometry'= /usr/local/emboss/lib/libeplplot.so: undefined reference to `XSetLineAttri= butes' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XSetStandardP= roperties' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XClearWindow'= /usr/local/emboss/lib/libeplplot.so: undefined reference to `gdImageSetAnt= iAliased' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XFillRectangl= e' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XWarpPointer'= /usr/local/emboss/lib/libeplplot.so: undefined reference to `XPutImage' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XCreatePixmap= ' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XCreateGC' /usr/local/emboss/lib/libeplplot.so: undefined reference to `XOpenDisplay'= /usr/local/emboss/lib/libeplplot.so: undefined reference to `XMapRaised' collect2: ld returned 1 exit status make[1]: *** [blast] Fehler 1 make[1]: Leaving directory `/root/bioinf/EMBOSS/EMBOSS-5.0.0/embassy/MYEMB= OSS-3.0.0/source' make: *** [install-recursive] Fehler 1 done! Cleaning up...done! All done! Enjoy the wrappers! =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F Der WEB.DE SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! http://smartsurfer.web.de/=3Fmc=3D100071&distributionid=3D000000000066 |
From: Guy B. <gb...@vu...> - 2007-11-30 11:16:02
|
Dear users of wEMBOSS, You might have noticed that the wEMBOSS SourceForge site had not been updated for quite a while. The reason is that our site manager and fellow developer Martin Sarachu suffered from leukemia and tragically passed away on 9 September 2007. The maintenance of the wEMBOSS project has now resumed and we can announce the release of a new version 2.0.0 of wrappers4EMBOSS. A new version of wEMBOSS (with version 2 of wrappers4EMBOSS included) is to be expected for begin 2008. An important change in wrappers4EMBOSS is that it now uses the EMBASSY module MYEMBOSS rather then EMBOSS itself for compiling and installing. This has two advantages : it goes much faster (which can be convenient if you need to redo it several times) and it avoids overwriting customizations you might have performed directly in the installed version of EMBOSS rather than in the source (addressing an issue raised by some users). Problem is that the manual in HTML format is now installed in .../share/EMBOSS/doc/html/embassy/myseq. A future version of wEMBOSS will fully address the problem of manual location ; for the moment users of wEMBOSS and some other GUI's might have to copy the manual entries "manually" to another location. There are two new modules : an interface to a local installation of the InterProScan server and an interface to a local installation of Maarten Hekkelman's MRS software for indexing databanks. The MRS module contains a program mrsindexsearch, which is much like the SRS based indexsearch. It also provides a tool to use a local MRS as sequence databank access mechanism for EMBOSS. For a complete list of changes, you can consult the Changelog http://sourceforge.net/project/shownotes.php?group_id=170030&release_id=557931 Regards, Belgian EMBnet Node - wEMBOSS development team, Guy Bottu |
From: Guy B. <gb...@vu...> - 2007-11-02 14:33:45
|
Charles A.Alexander wrote: > I have had the same problem and did the fix that was suggested. I get > the login window but when I login I get the same error. Which is... > > /error, catch > > can't reset GID/ Dear Charles, Maybe it is due to the fact that Macintoshed and some other UNIX platforms handle GID/UID settings in a different and incompatible way. We have not found a way to get around it. Go to the thread https://sourceforge.net/mailarchive/forum.php?thread_name=21533dc801e26f72e1a84854e1357604%40vanderbilt.edu&forum_name=wemboss-users You will see that Marc suggests to edit the file postambleJob and re-install. Does this help ? Guy Bottu |
From: Charles A. A. <cha...@va...> - 2007-11-01 21:57:08
|
Guy I have had the same problem and did the fix that was suggested. I get the login window but when I login I get the same error. Which is... error, catch can't reset GID My admin account protections look like this: -rwsrwxrwx 1 root root 8441 May 15 16:40 /var/emboss/wEMBOSS/cgi-bin/catch Maybe I am just not getting it, but I'd think this would work. My user for logging in is named wembtest. # grep wembtest /etc/passwd wembtest:x:529:532::/home/wembtest:/bin/bash User directory is also there: ls -al /home/wembtest total 88 drwx------ 4 wembtest wembtest 4096 Aug 21 11:05 . drwxr-xr-x 35 root root 4096 Aug 21 10:50 .. -rw------- 1 wembtest wembtest 5 Aug 21 11:05 .bash_history -rw-r--r-- 1 wembtest wembtest 24 May 14 17:36 .bash_logout -rw-r--r-- 1 wembtest wembtest 191 May 14 17:36 .bash_profile -rw-r--r-- 1 wembtest wembtest 124 May 14 17:36 .bashrc -rw-r--r-- 1 wembtest wembtest 383 May 14 17:36 .emacs -rw-r--r-- 1 wembtest wembtest 120 May 14 17:36 .gtkrc drwxr-xr-x 3 wembtest wembtest 4096 May 14 17:36 .kde drwxr-xr-x 2 wembtest wembtest 4096 May 14 17:36 .xemacs -rw-r--r-- 1 wembtest wembtest 658 May 14 17:36 .zshrc What am I doing wrong? Thanks much for your help. Charles On Oct 30, 2007, at 3:40 AM, Guy Bottu wrote: > Dear Sarah, > > Take a look in your wEMBOSS installation. ls -l .../wEMBOSS/cgi-bin > should give > something like > -rwsr-xr-x 1 admin admin 12941 Oct 26 15:27 catch > Indeed, the program catch must be executable by the fictive user who > runs the > WWW server (nologin, wwwrun or whoever) and have the 's' SEUID > setting. Indeed, > catch is started up by wwwrun and then changes owner to the user > who typed > in his username+password at the login box. This user must of course > also have a > valid UNIX home directory. > > Guy Bottu, > Belgian EMBnet Node > > > ----------------------------------------------------------------------- > -- > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > _______________________________________________ > wemboss-users mailing list > wem...@li... > https://lists.sourceforge.net/lists/listinfo/wemboss-users |
From: Guy B. <gb...@vu...> - 2007-10-30 09:40:41
|
Dear Sarah, Take a look in your wEMBOSS installation. ls -l .../wEMBOSS/cgi-bin should give something like -rwsr-xr-x 1 admin admin 12941 Oct 26 15:27 catch Indeed, the program catch must be executable by the fictive user who runs the WWW server (nologin, wwwrun or whoever) and have the 's' SEUID setting. Indeed, catch is started up by wwwrun and then changes owner to the user who typed in his username+password at the login box. This user must of course also have a valid UNIX home directory. Guy Bottu, Belgian EMBnet Node |
From: <Sar...@st...> - 2007-10-30 02:10:17
|
Hi, I get an error in each frame that reads: error, catch: Sorry, the owner of this process is not allowed to run catch program, ask wEMBOSS manager! when I try to run wEMBOSS in the browser. Can anyone please help me? Sarah |
From: Michael T. <mt...@us...> - 2007-10-07 09:47:22
|
Greetings - I am trying to install wEMBOSS 1.7.1. I got the installer to run and the index.html works but when I click on the start wEMBOSS button I am presented with a page that contains several Internal Server Error errors. The apache error.log and access.log files don't present me many clues as to what the problem can be. Any suggestions how to debug this? thanks Mike access.log 212.128.162.91 - - [07/Oct/2007:11:40:01 +0200] "GET /lab_resources/ wEMBOSS/images/but_pink_back.gif HTTP/1.1" 304 - 212.128.162.91 - - [07/Oct/2007:11:40:05 +0200] "GET /lab_resources/ wEMBOSS/wEMBOSS.html HTTP/1.1" 304 - 212.128.162.91 - - [07/Oct/2007:11:40:05 +0200] "GET /cgi-bin/wEMBOSS/ catch?_action=title HTTP/1.1" 500 535 212.128.162.91 - - [07/Oct/2007:11:40:05 +0200] "GET /cgi-bin/wEMBOSS/ catch?_action=mmenu_url HTTP/1.1" 500 535 212.128.162.91 - - [07/Oct/2007:11:40:06 +0200] "GET /cgi-bin/wEMBOSS/ catch?_action=mngt HTTP/1.1" 500 535 212.128.162.91 - - [07/Oct/2007:11:40:06 +0200] "GET /cgi-bin/wEMBOSS/ catch?_action=key HTTP/1.1" 500 535 error.log [Sun Oct 07 11:40:06 2007] [error] [client 212.128.162.91] Premature end of script headers: catch, referer: http:// bioinformatica.dep.usal.es/lab_resources/wEMBOSS/wEMBOSS.html [Sun Oct 07 11:40:06 2007] [error] [client 212.128.162.91] Premature end of script headers: catch, referer: http:// bioinformatica.dep.usal.es/lab_resources/wEMBOSS/wEMBOSS.html |
From: Guy B. <gb...@be...> - 2007-06-07 08:32:24
|
Dear Christian, The development of wEMBOSS+wrappers4EMBOSS is temporarily stalled because of health problems of one of the developers. So, it will take a little time before the next release. However, I can assure you that iprscan, a wrapper for a local installation of the InterProScan tool, will certainly be included. Regards, Guy Bottu, BEN + ULB |
From: Marc C. <Mar...@ul...> - 2007-06-05 07:34:47
|
Charles, Try the suggestion I did send you a few days ago, your box is not a Mac but it sounds it could be the same problem. Marc Charles A. Alexander a écrit : > Hi Guy > > i Tried this and still no luck. > > I installed wEMBOSS here (/home/wEMBOSS was not workable due to > extensive permissions problems): > > /var/emboss/wEMBOSS/ > > The catch file has the following permissions: > > ls -l /var/emboss/wEMBOSS/cgi-bin > > -rwsrwxrwx 1 root root 8441 May 15 16:40 catch > -rwxrwxrwx 1 root root 3548 May 15 16:40 catch.c > -rwxrwxrwx 1 root root 3448 May 15 16:40 catch.o > -rwxrwxrwx 1 root root 1675 May 15 16:40 emboss.pl > -rwxrwxrwx 1 root root 479 May 15 16:53 hello.cgi > -rwxrwxrwx 1 root root 438 May 15 16:40 _jalview_ps2pdf > -rwxrwxrwx 1 root root 111 May 15 16:40 makefile > > The user is wembtest and with a real directory. The error I get is > still: > > error, catch > > can't reset GID > > According to logs: > > access_log -> > > 120.nnn.nnn.nnn - - [04/Jun/2007:15:24:53 -0500] "GET > /wEMBOSS/wEMBOSS.html HTTP/1.1" 200 1010 "-" "Mozilla/5.0 (Macintosh; > U; PPC Mac OS X Mac > h-O; en-US; rv:1.8.0.10) Gecko/20070216 Firefox/1.5.0.10" > 120.nnn.nnn.nnn - - [04/Jun/2007:15:24:53 -0500] "GET > /wEMBOSS/wEMBOSS.css HTTP/1.1" 200 4259 > "http://myserver.mydomain.mysite.inst/wEMBOSS/wEM > BOSS.html" "Mozilla/5.0 (Macintosh; U; PPC Mac OS X Mach-O; en-US; > rv:1.8.0.10) Gecko/20070216 Firefox/1.5.0.10" > 120.nnn.nnn.nnn - - [04/Jun/2007:15:24:53 -0500] "GET > /wEMBOSS/EMBOSS.js HTTP/1.1" 200 23129 > "http://myserver.mydomain.mysite.inst/wEMBOSS/wEMB > OSS.html" "Mozilla/5.0 (Macintosh; U; PPC Mac OS X Mach-O; en-US; > rv:1.8.0.10) Gecko/20070216 Firefox/1.5.0.10" > 120.nnn.nnn.nnn - - [04/Jun/2007:15:24:53 -0500] "GET > /wEMBOSS_cgi/catch?_action=title HTTP/1.1" 401 496 > "http://myserver.mydomain.mysite.inst/ > wEMBOSS/wEMBOSS.html" "Mozilla/5.0 (Macintosh; U; PPC Mac OS X Mach-O; > en-US; rv:1.8.0.10) Gecko/20070216 Firefox/1.5.0.10" > 120.nnn.nnn.nnn - - [04/Jun/2007:15:24:53 -0500] "GET > /wEMBOSS_cgi/catch?_action=mmenu_url HTTP/1.1" 401 496 > "http://myserver.mydomain.mysite.inst. > edu/wEMBOSS/wEMBOSS.html" "Mozilla/5.0 (Macintosh; U; PPC Mac OS X > Mach-O; en-US; rv:1.8.0.10) Gecko/20070216 Firefox/1.5.0.10" > 120.nnn.nnn.nnn - - [04/Jun/2007:15:24:53 -0500] "GET > /wEMBOSS_cgi/catch?_action=key HTTP/1.1" 401 496 > "http://myserver.mydomain.mysite.inst/wE > MBOSS/wEMBOSS.html" "Mozilla/5.0 (Macintosh; U; PPC Mac OS X Mach-O; > en-US; rv:1.8.0.10) Gecko/20070216 Firefox/1.5.0.10" > 120.nnn.nnn.nnn - - [04/Jun/2007:15:24:53 -0500] "GET > /wEMBOSS_cgi/catch?_action=mngt HTTP/1.1" 401 496 > "http://myserver.mydomain.mysite.inst/w > EMBOSS/wEMBOSS.html" "Mozilla/5.0 (Macintosh; U; PPC Mac OS X Mach-O; > en-US; rv:1.8.0.10) Gecko/20070216 Firefox/1.5.0.10" > 120.nnn.nnn.nnn - wembtest [04/Jun/2007:15:25:04 -0500] "GET > /wEMBOSS_cgi/catch?_action=title HTTP/1.1" 200 33 > "http://fisher.bioinfo.vanderbil > t/wEMBOSS/wEMBOSS.html" "Mozilla/5.0 (Macintosh; U; PPC Mac OS X > Mach-O; en-US; rv:1.8.0.10) Gecko/20070216 Firefox/1.5.0.10" > 120.nnn.nnn.nnn - wembtest [04/Jun/2007:15:25:04 -0500] "GET > /wEMBOSS_cgi/catch?_action=mmenu_url HTTP/1.1" 200 33 > "http://fisher.bioinfo.vande > rbilt/wEMBOSS/wEMBOSS.html" "Mozilla/5.0 (Macintosh; U; PPC Mac OS X > Mach-O; en-US; rv:1.8.0.10) Gecko/20070216 Firefox/1.5.0.10" > 120.nnn.nnn.nnn - wembtest [04/Jun/2007:15:25:04 -0500] "GET > /wEMBOSS_cgi/catch?_action=key HTTP/1.1" 200 33 > "http://myserver.mydomain.mysite.inst. > edu/wEMBOSS/wEMBOSS.html" "Mozilla/5.0 (Macintosh; U; PPC Mac OS X > Mach-O; en-US; rv:1.8.0.10) Gecko/20070216 Firefox/1.5.0.10" > 120.nnn.nnn.nnn - wembtest [04/Jun/2007:15:25:04 -0500] "GET > /wEMBOSS_cgi/catch?_action=mngt HTTP/1.1" 200 33 > "http://myserver.mydomain.mysite.inst > /wEMBOSS/wEMBOSS.html" "Mozilla/5.0 (Macintosh; U; PPC Mac OS X Mach-O; > en-US; rv:1.8.0.10) Gecko/20070216 Firefox/1.5.0.10" > 120.nnn.nnn.nnn - - [04/Jun/2007:15:25:04 -0500] "GET /favicon.ico > HTTP/1.1" 404 304 "-" "Mozilla/5.0 (Macintosh; U; PPC Mac OS X Mach-O; > en-US > ; rv:1.8.0.10) Gecko/20070216 Firefox/1.5.0.10" > > error_log -> > > [Mon Jun 04 15:25:04 2007] [error] [client 120.nnn.nnn.nnn] File does > not exist: /var/www/html/favicon.ico > > I don't think the favicon.ico is a big deal. Is it? > > Thanks > > Cahrles > > On Jun 4, 2007, at 4:15 AM, Guy Bottu wrote: > > >> Dear Charles, >> >> If it is not the Mac specific problem it could be the following : The >> current version of wEMBOSS uses classic UNIX user directories and the >> program catch starts up with as owner the user that runs the Web server >> and then performs a SUID to the user that owns the directory. So : >> >> - check that the user name typed in when starting wEMBOSS corresponds >> to >> a user really existing in the computer and having a home directory >> >> - do a ls -l in the directory where the program catch is installed (by >> default /home/wEMBOSS/cgi-dir, but it depends on what you chose during >> install). You should have : >> -rwsr-xr-x 1 root root 12941 2007-04-06 10:02 catch >> Maybe the installation procedure somehow failed to set the permission >> 'rws' correctly. You can try to set it "manually" by doing >> chmod 'u+x' catch >> chmod 'u+s' catch >> >> Guy Bottu, >> Belgian EMBnet Node >> >> >> ----------------------------------------------------------------------- >> -- >> This SF.net email is sponsored by DB2 Express >> Download DB2 Express C - the FREE version of DB2 express and take >> control of your XML. No limits. Just data. Click to get it now. >> http://sourceforge.net/powerbar/db2/ >> _______________________________________________ >> wemboss-users mailing list >> wem...@li... >> https://lists.sourceforge.net/lists/listinfo/wemboss-users >> > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > wemboss-users mailing list > wem...@li... > https://lists.sourceforge.net/lists/listinfo/wemboss-users > -- ==================================================================== Marc Colet IBMM UNIVERSITE LIBRE DE BRUXELLES Rue des Professeurs Jeneer et Brachet 12 B6041 Charleroi Belgium E-mail: Mar...@ul... Tel: 32 2 6509977 Fax: 32 2 6509998 ==================================================================== |
From: Charles A. A. <cha...@va...> - 2007-06-04 20:39:04
|
Hi Guy i Tried this and still no luck. I installed wEMBOSS here (/home/wEMBOSS was not workable due to extensive permissions problems): /var/emboss/wEMBOSS/ The catch file has the following permissions: ls -l /var/emboss/wEMBOSS/cgi-bin -rwsrwxrwx 1 root root 8441 May 15 16:40 catch -rwxrwxrwx 1 root root 3548 May 15 16:40 catch.c -rwxrwxrwx 1 root root 3448 May 15 16:40 catch.o -rwxrwxrwx 1 root root 1675 May 15 16:40 emboss.pl -rwxrwxrwx 1 root root 479 May 15 16:53 hello.cgi -rwxrwxrwx 1 root root 438 May 15 16:40 _jalview_ps2pdf -rwxrwxrwx 1 root root 111 May 15 16:40 makefile The user is wembtest and with a real directory. The error I get is still: error, catch can't reset GID According to logs: access_log -> 120.nnn.nnn.nnn - - [04/Jun/2007:15:24:53 -0500] "GET /wEMBOSS/wEMBOSS.html HTTP/1.1" 200 1010 "-" "Mozilla/5.0 (Macintosh; U; PPC Mac OS X Mac h-O; en-US; rv:1.8.0.10) Gecko/20070216 Firefox/1.5.0.10" 120.nnn.nnn.nnn - - [04/Jun/2007:15:24:53 -0500] "GET /wEMBOSS/wEMBOSS.css HTTP/1.1" 200 4259 "http://myserver.mydomain.mysite.inst/wEMBOSS/wEM BOSS.html" "Mozilla/5.0 (Macintosh; U; PPC Mac OS X Mach-O; en-US; rv:1.8.0.10) Gecko/20070216 Firefox/1.5.0.10" 120.nnn.nnn.nnn - - [04/Jun/2007:15:24:53 -0500] "GET /wEMBOSS/EMBOSS.js HTTP/1.1" 200 23129 "http://myserver.mydomain.mysite.inst/wEMBOSS/wEMB OSS.html" "Mozilla/5.0 (Macintosh; U; PPC Mac OS X Mach-O; en-US; rv:1.8.0.10) Gecko/20070216 Firefox/1.5.0.10" 120.nnn.nnn.nnn - - [04/Jun/2007:15:24:53 -0500] "GET /wEMBOSS_cgi/catch?_action=title HTTP/1.1" 401 496 "http://myserver.mydomain.mysite.inst/ wEMBOSS/wEMBOSS.html" "Mozilla/5.0 (Macintosh; U; PPC Mac OS X Mach-O; en-US; rv:1.8.0.10) Gecko/20070216 Firefox/1.5.0.10" 120.nnn.nnn.nnn - - [04/Jun/2007:15:24:53 -0500] "GET /wEMBOSS_cgi/catch?_action=mmenu_url HTTP/1.1" 401 496 "http://myserver.mydomain.mysite.inst. edu/wEMBOSS/wEMBOSS.html" "Mozilla/5.0 (Macintosh; U; PPC Mac OS X Mach-O; en-US; rv:1.8.0.10) Gecko/20070216 Firefox/1.5.0.10" 120.nnn.nnn.nnn - - [04/Jun/2007:15:24:53 -0500] "GET /wEMBOSS_cgi/catch?_action=key HTTP/1.1" 401 496 "http://myserver.mydomain.mysite.inst/wE MBOSS/wEMBOSS.html" "Mozilla/5.0 (Macintosh; U; PPC Mac OS X Mach-O; en-US; rv:1.8.0.10) Gecko/20070216 Firefox/1.5.0.10" 120.nnn.nnn.nnn - - [04/Jun/2007:15:24:53 -0500] "GET /wEMBOSS_cgi/catch?_action=mngt HTTP/1.1" 401 496 "http://myserver.mydomain.mysite.inst/w EMBOSS/wEMBOSS.html" "Mozilla/5.0 (Macintosh; U; PPC Mac OS X Mach-O; en-US; rv:1.8.0.10) Gecko/20070216 Firefox/1.5.0.10" 120.nnn.nnn.nnn - wembtest [04/Jun/2007:15:25:04 -0500] "GET /wEMBOSS_cgi/catch?_action=title HTTP/1.1" 200 33 "http://fisher.bioinfo.vanderbil t/wEMBOSS/wEMBOSS.html" "Mozilla/5.0 (Macintosh; U; PPC Mac OS X Mach-O; en-US; rv:1.8.0.10) Gecko/20070216 Firefox/1.5.0.10" 120.nnn.nnn.nnn - wembtest [04/Jun/2007:15:25:04 -0500] "GET /wEMBOSS_cgi/catch?_action=mmenu_url HTTP/1.1" 200 33 "http://fisher.bioinfo.vande rbilt/wEMBOSS/wEMBOSS.html" "Mozilla/5.0 (Macintosh; U; PPC Mac OS X Mach-O; en-US; rv:1.8.0.10) Gecko/20070216 Firefox/1.5.0.10" 120.nnn.nnn.nnn - wembtest [04/Jun/2007:15:25:04 -0500] "GET /wEMBOSS_cgi/catch?_action=key HTTP/1.1" 200 33 "http://myserver.mydomain.mysite.inst. edu/wEMBOSS/wEMBOSS.html" "Mozilla/5.0 (Macintosh; U; PPC Mac OS X Mach-O; en-US; rv:1.8.0.10) Gecko/20070216 Firefox/1.5.0.10" 120.nnn.nnn.nnn - wembtest [04/Jun/2007:15:25:04 -0500] "GET /wEMBOSS_cgi/catch?_action=mngt HTTP/1.1" 200 33 "http://myserver.mydomain.mysite.inst /wEMBOSS/wEMBOSS.html" "Mozilla/5.0 (Macintosh; U; PPC Mac OS X Mach-O; en-US; rv:1.8.0.10) Gecko/20070216 Firefox/1.5.0.10" 120.nnn.nnn.nnn - - [04/Jun/2007:15:25:04 -0500] "GET /favicon.ico HTTP/1.1" 404 304 "-" "Mozilla/5.0 (Macintosh; U; PPC Mac OS X Mach-O; en-US ; rv:1.8.0.10) Gecko/20070216 Firefox/1.5.0.10" error_log -> [Mon Jun 04 15:25:04 2007] [error] [client 120.nnn.nnn.nnn] File does not exist: /var/www/html/favicon.ico I don't think the favicon.ico is a big deal. Is it? Thanks Cahrles On Jun 4, 2007, at 4:15 AM, Guy Bottu wrote: > Dear Charles, > > If it is not the Mac specific problem it could be the following : The > current version of wEMBOSS uses classic UNIX user directories and the > program catch starts up with as owner the user that runs the Web server > and then performs a SUID to the user that owns the directory. So : > > - check that the user name typed in when starting wEMBOSS corresponds > to > a user really existing in the computer and having a home directory > > - do a ls -l in the directory where the program catch is installed (by > default /home/wEMBOSS/cgi-dir, but it depends on what you chose during > install). You should have : > -rwsr-xr-x 1 root root 12941 2007-04-06 10:02 catch > Maybe the installation procedure somehow failed to set the permission > 'rws' correctly. You can try to set it "manually" by doing > chmod 'u+x' catch > chmod 'u+s' catch > > Guy Bottu, > Belgian EMBnet Node > > > ----------------------------------------------------------------------- > -- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > wemboss-users mailing list > wem...@li... > https://lists.sourceforge.net/lists/listinfo/wemboss-users |
From: Charles A. A. <cha...@va...> - 2007-06-04 13:37:26
|
Thanks, Guy. I will try this. Charles On Jun 4, 2007, at 4:15 AM, Guy Bottu wrote: > Dear Charles, > > If it is not the Mac specific problem it could be the following : The > current version of wEMBOSS uses classic UNIX user directories and the > program catch starts up with as owner the user that runs the Web server > and then performs a SUID to the user that owns the directory. So : > > - check that the user name typed in when starting wEMBOSS corresponds > to > a user really existing in the computer and having a home directory > > - do a ls -l in the directory where the program catch is installed (by > default /home/wEMBOSS/cgi-dir, but it depends on what you chose during > install). You should have : > -rwsr-xr-x 1 root root 12941 2007-04-06 10:02 catch > Maybe the installation procedure somehow failed to set the permission > 'rws' correctly. You can try to set it "manually" by doing > chmod 'u+x' catch > chmod 'u+s' catch > > Guy Bottu, > Belgian EMBnet Node > > > ----------------------------------------------------------------------- > -- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > wemboss-users mailing list > wem...@li... > https://lists.sourceforge.net/lists/listinfo/wemboss-users |
From: Guy B. <gb...@be...> - 2007-06-04 09:15:52
|
Dear Charles, If it is not the Mac specific problem it could be the following : The current version of wEMBOSS uses classic UNIX user directories and the program catch starts up with as owner the user that runs the Web server and then performs a SUID to the user that owns the directory. So : - check that the user name typed in when starting wEMBOSS corresponds to a user really existing in the computer and having a home directory - do a ls -l in the directory where the program catch is installed (by default /home/wEMBOSS/cgi-dir, but it depends on what you chose during install). You should have : -rwsr-xr-x 1 root root 12941 2007-04-06 10:02 catch Maybe the installation procedure somehow failed to set the permission 'rws' correctly. You can try to set it "manually" by doing chmod 'u+x' catch chmod 'u+s' catch Guy Bottu, Belgian EMBnet Node |