[EMBOSS] cannot compile a single program

[Derek Gatherer]

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