[EMBOSS] cannot compile a single program

Martín Sarachu mad at biol.unlp.edu.ar
Tue Feb 24 14:24:10 UTC 2004 

Hi

installed libtool-1.5.2 and yet the same errors

Regards,

martin

Derek Gatherer wrote:
> Hi
> 
> You will need libtool as well, by the looks of it.
> http://www.gnu.org/software/libtool/
> 
> Hope this helps
> Derek
> 
> 
> At 09:28 24/02/2004 -0300, you wrote:
> 
>> Hi Derek,
>>
>> thanks for your help. I've got other problems though, I followed your 
>> steps and when doing make I get
>>
>>> # make
>>> Making all in plplot
>>> make[1]: Entering directory `/home/work/EMBOSS/test/plplot'
>>> Making all in lib
>>> make[2]: Entering directory `/home/work/EMBOSS/test/plplot/lib'
>>> make[2]: Nothing to be done for `all'.
>>> make[2]: Leaving directory `/home/work/EMBOSS/test/plplot/lib'
>>> make[2]: Entering directory `/home/work/EMBOSS/test/plplot'
>>> source='pdfutils.c' object='pdfutils.lo' libtool=yes \
>>> depfile='.deps/pdfutils.Plo' tmpdepfile='.deps/pdfutils.TPlo' \
>>> depmode=gcc3 /bin/sh ../depcomp \
>>> /bin/sh ../libtool --mode=compile gcc -DPACKAGE_NAME=\"\" 
>>> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
>>> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"2.6.0\" 
>>> -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 
>>> -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 
>>> -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 
>>> -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 
>>> -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 
>>> -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 
>>> -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 
>>> -DHAVE_LIBM=1  -I. -I. -I/usr/X11R6/include -I./ -I/usr/include/gd    
>>> -g -O2 -c -o pdfutils.lo `test -f pdfutils.c || echo './'`pdfutils.c
>>> ../libtool: s%^.*/%%: No such file or directory
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> ../libtool: -e: command not found
>>> : compile: cannot determine name of library object from `'
>>> make[2]: *** [pdfutils.lo] Error 1
>>> make[2]: Leaving directory `/home/work/EMBOSS/test/plplot'
>>> make[1]: *** [all-recursive] Error 1
>>> make[1]: Leaving directory `/home/work/EMBOSS/test/plplot'
>>> make: *** [all-recursive] Error 1
>>> #
>>
>>
>> Can you help me with this? Thank you.
>>
>>
>> Regards,
>>
>> martin
>>
>>
>> Derek Gatherer wrote:
>>
>>> Hi
>>> You need to be working from the cvs version of emboss:
>>>  >cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/emboss login
>>>  >cvs
>>>  >cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/emboss 
>>> checkout emboss
>>>  >cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/emboss logout
>>> Assuming you have got this, you need to do what you did, ie. add the 
>>> code in the correct place and modify the makefile appropriately, and 
>>> then go to the correct directory and enter:
>>>  >aclocal -I m4
>>>  >autoconf -v
>>>  >automake -a
>>>  >./configure
>>>  >make
>>>  >make check
>>>  >make install
>>>  >make clean
>>> You'll need up to date versions of autoconf and automake.  We add 
>>> lots of local code - it's convoluted to do all this, but it always 
>>> works.
>>> Cheers
>>> Derek
>>> At 11:52 23/02/2004 -0300, you wrote:
>>>
>>>> Dear list,
>>>>
>>>> I'm trying to add a program to our EMBOSS-2.6.0 installation.
>>>> These are the steps I followed:
>>>> - added clustal.c into EMBOSS_distro/emboss dir and clustal.acd 
>>>> under EMBOSS_distro/emboss/acd
>>>> - then edited EMBOSS_distro/emboss/Makefile.am and added 'clustal' 
>>>> to the 'bin_PROGRAMS' section and the line 'clustal_SOURCES = 
>>>> clustal.c' to the same Makefile.am
>>>> - when doing a 'make clustal' into EMBOSS_distro/emboss dir I get this
>>>>
>>>>> # make clustal
>>>>> cd .. && /bin/sh ./config.status emboss/Makefile depfiles
>>>>> config.status: creating emboss/Makefile
>>>>> config.status: executing depfiles commands
>>>>> Makefile:2179: aaindexextract.Po: No such file or directory
>>>>> Makefile:2180: abiview.Po: No such file or directory
>>>>> Makefile:2181: acdc.Po: No such file or directory
>>>>> Makefile:2182: ajtest.Po: No such file or directory
>>>>> Makefile:2183: antigenic.Po: No such file or directory
>>>>> Makefile:2184: backtranseq.Po: No such file or directory
>>>>> Makefile:2185: banana.Po: No such file or directory
>>>>> Makefile:2186: biosed.Po: No such file or directory
>>>>> Makefile:2187: btwisted.Po: No such file or directory
>>>>> Makefile:2188: cai.Po: No such file or directory
>>>>> Makefile:2189: chaos.Po: No such file or directory
>>>>> Makefile:2190: charge.Po: No such file or directory
>>>>> Makefile:2191: checktrans.Po: No such file or directory
>>>>> Makefile:2192: chips.Po: No such file or directory
>>>>> Makefile:2193: cirdna.Po: No such file or directory
>>>>> Makefile:2194: clustal.Po: No such file or directory
>>>>> Makefile:2195: codcmp.Po: No such file or directory
>>>>> Makefile:2196: coderet.Po: No such file or directory
>>>>> Makefile:2197: complex.Po: No such file or directory
>>>>> Makefile:2198: compseq.Po: No such file or directory
>>>>> Makefile:2199: cons.Po: No such file or directory
>>>>> Makefile:2200: corbatest.Po: No such file or directory
>>>>> Makefile:2201: cpgplot.Po: No such file or directory
>>>>> Makefile:2202: cpgreport.Po: No such file or directory
>>>>> Makefile:2203: cusp.Po: No such file or directory
>>>>> Makefile:2204: cutgextract.Po: No such file or directory
>>>>> Makefile:2205: cutseq.Po: No such file or directory
>>>>> Makefile:2206: dan.Po: No such file or directory
>>>>> Makefile:2207: dbiblast.Po: No such file or directory
>>>>> Makefile:2208: dbifasta.Po: No such file or directory
>>>>> Makefile:2209: dbiflat.Po: No such file or directory
>>>>> Makefile:2210: dbigcg.Po: No such file or directory
>>>>> Makefile:2211: degapseq.Po: No such file or directory
>>>>> Makefile:2212: demoalign.Po: No such file or directory
>>>>> Makefile:2213: demofeatures.Po: No such file or directory
>>>>> Makefile:2214: demolist.Po: No such file or directory
>>>>> Makefile:2215: demoreport.Po: No such file or directory
>>>>> Makefile:2216: demosequence.Po: No such file or directory
>>>>> Makefile:2217: demostring.Po: No such file or directory
>>>>> Makefile:2218: demotable.Po: No such file or directory
>>>>> Makefile:2219: descseq.Po: No such file or directory
>>>>> Makefile:2220: diffseq.Po: No such file or directory
>>>>> Makefile:2221: digest.Po: No such file or directory
>>>>> Makefile:2222: distmat.Po: No such file or directory
>>>>> Makefile:2223: dotmatcher.Po: No such file or directory
>>>>> Makefile:2224: dotpath.Po: No such file or directory
>>>>> Makefile:2225: dottup.Po: No such file or directory
>>>>> Makefile:2226: dreg.Po: No such file or directory
>>>>> Makefile:2227: einverted.Po: No such file or directory
>>>>> Makefile:2228: embossdata.Po: No such file or directory
>>>>> Makefile:2229: embossversion.Po: No such file or directory
>>>>> Makefile:2230: emma.Po: No such file or directory
>>>>> Makefile:2231: emowse.Po: No such file or directory
>>>>> Makefile:2232: entrails.Po: No such file or directory
>>>>> Makefile:2233: entret.Po: No such file or directory
>>>>> Makefile:2234: eprimer3.Po: No such file or directory
>>>>> Makefile:2235: equicktandem.Po: No such file or directory
>>>>> Makefile:2236: est2genome.Po: No such file or directory
>>>>> Makefile:2237: etandem.Po: No such file or directory
>>>>> Makefile:2238: extractfeat.Po: No such file or directory
>>>>> Makefile:2239: extractseq.Po: No such file or directory
>>>>> Makefile:2240: findkm.Po: No such file or directory
>>>>> Makefile:2241: freak.Po: No such file or directory
>>>>> Makefile:2242: fuzznuc.Po: No such file or directory
>>>>> Makefile:2243: fuzzpro.Po: No such file or directory
>>>>> Makefile:2244: fuzztran.Po: No such file or directory
>>>>> Makefile:2245: garnier.Po: No such file or directory
>>>>> Makefile:2246: geecee.Po: No such file or directory
>>>>> Makefile:2247: getorf.Po: No such file or directory
>>>>> Makefile:2248: helixturnhelix.Po: No such file or directory
>>>>> Makefile:2249: histogramtest.Po: No such file or directory
>>>>> Makefile:2250: hmoment.Po: No such file or directory
>>>>> Makefile:2251: iep.Po: No such file or directory
>>>>> Makefile:2252: infoalign.Po: No such file or directory
>>>>> Makefile:2253: infoseq.Po: No such file or directory
>>>>> Makefile:2254: intconv.Po: No such file or directory
>>>>> Makefile:2255: isochore.Po: No such file or directory
>>>>> Makefile:2256: jembossctl.Po: No such file or directory
>>>>> Makefile:2257: lindna.Po: No such file or directory
>>>>> Makefile:2258: listor.Po: No such file or directory
>>>>> Makefile:2259: marscan.Po: No such file or directory
>>>>> Makefile:2260: maskfeat.Po: No such file or directory
>>>>> Makefile:2261: maskseq.Po: No such file or directory
>>>>> Makefile:2262: matcher.Po: No such file or directory
>>>>> Makefile:2263: megamerger.Po: No such file or directory
>>>>> Makefile:2264: merger.Po: No such file or directory
>>>>> Makefile:2265: msbar.Po: No such file or directory
>>>>> Makefile:2266: mwcontam.Po: No such file or directory
>>>>> Makefile:2267: mwfilter.Po: No such file or directory
>>>>> Makefile:2268: needle.Po: No such file or directory
>>>>> Makefile:2269: newcpgreport.Po: No such file or directory
>>>>> Makefile:2270: newcpgseek.Po: No such file or directory
>>>>> Makefile:2271: newseq.Po: No such file or directory
>>>>> Makefile:2272: noreturn.Po: No such file or directory
>>>>> Makefile:2273: notseq.Po: No such file or directory
>>>>> Makefile:2274: nthseq.Po: No such file or directory
>>>>> Makefile:2275: octanol.Po: No such file or directory
>>>>> Makefile:2276: oddcomp.Po: No such file or directory
>>>>> Makefile:2277: palindrome.Po: No such file or directory
>>>>> Makefile:2278: pasteseq.Po: No such file or directory
>>>>> Makefile:2279: patmatdb.Po: No such file or directory
>>>>> Makefile:2280: patmatmotifs.Po: No such file or directory
>>>>> Makefile:2281: patmattest.Po: No such file or directory
>>>>> Makefile:2282: pepcoil.Po: No such file or directory
>>>>> Makefile:2283: pepinfo.Po: No such file or directory
>>>>> Makefile:2284: pepnet.Po: No such file or directory
>>>>> Makefile:2285: pepstats.Po: No such file or directory
>>>>> Makefile:2286: pepwheel.Po: No such file or directory
>>>>> Makefile:2287: pepwindow.Po: No such file or directory
>>>>> Makefile:2288: pepwindowall.Po: No such file or directory
>>>>> Makefile:2289: pestfind.Po: No such file or directory
>>>>> Makefile:2290: plotcon.Po: No such file or directory
>>>>> Makefile:2291: plotorf.Po: No such file or directory
>>>>> Makefile:2292: polydot.Po: No such file or directory
>>>>> Makefile:2293: preg.Po: No such file or directory
>>>>> Makefile:2294: prettyplot.Po: No such file or directory
>>>>> Makefile:2295: prettyseq.Po: No such file or directory
>>>>> Makefile:2296: prima.Po: No such file or directory
>>>>> Makefile:2297: primers.Po: No such file or directory
>>>>> Makefile:2298: primersearch.Po: No such file or directory
>>>>> Makefile:2299: printsextract.Po: No such file or directory
>>>>> Makefile:2300: profit.Po: No such file or directory
>>>>> Makefile:2301: prophecy.Po: No such file or directory
>>>>> Makefile:2302: prophet.Po: No such file or directory
>>>>> Makefile:2303: prosextract.Po: No such file or directory
>>>>> Makefile:2304: pscan.Po: No such file or directory
>>>>> Makefile:2305: rebaseextract.Po: No such file or directory
>>>>> Makefile:2306: recoder.Po: No such file or directory
>>>>> Makefile:2307: redata.Po: No such file or directory
>>>>> Makefile:2308: remap.Po: No such file or directory
>>>>> Makefile:2309: restover.Po: No such file or directory
>>>>> Makefile:2310: restrict.Po: No such file or directory
>>>>> Makefile:2311: revseq.Po: No such file or directory
>>>>> Makefile:2312: seealso.Po: No such file or directory
>>>>> Makefile:2313: seqinfo.Po: No such file or directory
>>>>> Makefile:2314: seqmatchall.Po: No such file or directory
>>>>> Makefile:2315: seqret.Po: No such file or directory
>>>>> Makefile:2316: seqretall.Po: No such file or directory
>>>>> Makefile:2317: seqretallfeat.Po: No such file or directory
>>>>> Makefile:2318: seqretset.Po: No such file or directory
>>>>> Makefile:2319: seqretsingle.Po: No such file or directory
>>>>> Makefile:2320: seqretsplit.Po: No such file or directory
>>>>> Makefile:2321: showalign.Po: No such file or directory
>>>>> Makefile:2322: showdb.Po: No such file or directory
>>>>> Makefile:2323: showfeat.Po: No such file or directory
>>>>> Makefile:2324: showorf.Po: No such file or directory
>>>>> Makefile:2325: showseq.Po: No such file or directory
>>>>> Makefile:2326: shuffleseq.Po: No such file or directory
>>>>> Makefile:2327: sigcleave.Po: No such file or directory
>>>>> Makefile:2328: silent.Po: No such file or directory
>>>>> Makefile:2329: sirna.Po: No such file or directory
>>>>> Makefile:2330: sixpack.Po: No such file or directory
>>>>> Makefile:2331: skipseq.Po: No such file or directory
>>>>> Makefile:2332: splitter.Po: No such file or directory
>>>>> Makefile:2333: stretcher.Po: No such file or directory
>>>>> Makefile:2334: stssearch.Po: No such file or directory
>>>>> Makefile:2335: supermatcher.Po: No such file or directory
>>>>> Makefile:2336: syco.Po: No such file or directory
>>>>> Makefile:2337: testplot.Po: No such file or directory
>>>>> Makefile:2338: textsearch.Po: No such file or directory
>>>>> Makefile:2339: tfextract.Po: No such file or directory
>>>>> Makefile:2340: tfm.Po: No such file or directory
>>>>> Makefile:2341: tfscan.Po: No such file or directory
>>>>> Makefile:2342: tmap.Po: No such file or directory
>>>>> Makefile:2343: tranalign.Po: No such file or directory
>>>>> Makefile:2344: transeq.Po: No such file or directory
>>>>> Makefile:2345: treetypedisplay.Po: No such file or directory
>>>>> Makefile:2346: trimest.Po: No such file or directory
>>>>> Makefile:2347: trimseq.Po: No such file or directory
>>>>> Makefile:2348: twofeat.Po: No such file or directory
>>>>> Makefile:2349: union.Po: No such file or directory
>>>>> Makefile:2350: vectorstrip.Po: No such file or directory
>>>>> Makefile:2351: water.Po: No such file or directory
>>>>> Makefile:2352: whichdb.Po: No such file or directory
>>>>> Makefile:2353: wobble.Po: No such file or directory
>>>>> Makefile:2354: wordcount.Po: No such file or directory
>>>>> Makefile:2355: wordmatch.Po: No such file or directory
>>>>> Makefile:2356: wossname.Po: No such file or directory
>>>>> Makefile:2357: yank.Po: No such file or directory
>>>>> make: *** No rule to make target `yank.Po'.  Stop.
>>>>> #
>>>>
>>>>
>>>>
>>>> What am I missing?
>>>>
>>>> Regards,
>>>>
>>>> martin
>>>>
>>>> -- 
>>>> Martín Sarachu
>>>> mad at biol.unlp.edu.ar
>>>> EMBNet Argentina
>>>> http://www.ar.embnet.org
>>>
>>>
>>
>> -- 
>> Martín Sarachu
>> mad at biol.unlp.edu.ar
>> EMBNet Argentina
>> http://www.ar.embnet.org
> 
> 
> 

-- 
Martín Sarachu
mad at biol.unlp.edu.ar
EMBNet Argentina
http://www.ar.embnet.org

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