Installation problems - Githubissues

Greetings was installing MAPseq in ubuntu on windows wsl and when running make I got this error:

etable.cpp: In function ‘estrarrayof<etable> tablesLoad(const estr&, const evarhash&)’:
etable.cpp:242:3: error: ‘egzfile’ was not declared in this scope
   egzfile f;
   ^~~~~~~
etable.cpp:242:3: note: suggested alternative: ‘edcfile’
   egzfile f;
   ^~~~~~~
   edcfile
etable.cpp:260:8: error: ‘f’ was not declared in this scope
   if (!f.open(filename,"r")) { lerror(filename); return(ts); }
        ^
etable.cpp:271:15: error: ‘f’ was not declared in this scope
   if (header) f.readarr(line,headerarr,sep);
               ^
etable.cpp:273:10: error: ‘f’ was not declared in this scope
   while (f.readarr(line,arr,sep)){
          ^
etable.cpp:315:3: error: ‘f’ was not declared in this scope
   f.close();
   ^
etable.cpp: In function ‘etable etableLoad(const estr&, const evarhash&)’:
etable.cpp:362:3: error: ‘egzfile’ was not declared in this scope
   egzfile f;
   ^~~~~~~
etable.cpp:362:3: note: suggested alternative: ‘edcfile’
   egzfile f;
   ^~~~~~~
   edcfile
etable.cpp:372:8: error: ‘f’ was not declared in this scope
   if (!f.open(filename,"r")) { lerror(filename); return(t); }
        ^
etable.cpp:376:15: error: ‘f’ was not declared in this scope
   if (header) f.readarr(line,headerarr,sep);
               ^
etable.cpp:380:10: error: ‘f’ was not declared in this scope
   while (f.readarr(line,arr,sep)){
          ^
Makefile:1105: recipe for target 'etable.lo' failed
make[3]: *** [etable.lo] Error 1
make[3]: Leaving directory '/home/jcarrico/NGStools/MAPseq/libs/eutils'
Makefile:766: recipe for target 'all' failed
make[2]: *** [all] Error 2
make[2]: Leaving directory '/home/jcarrico/NGStools/MAPseq/libs/eutils'
Makefile:683: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/jcarrico/NGStools/MAPseq'
Makefile:461: recipe for target 'all' failed
make: *** [all] Error 2
(base)

Any idea how can this be solved?

Olá João,

Obrigado por entrares em contacto com esse problema. Uma maneira de resolver isso, se quiseres analisar ficheiros em formato fasta comprimidos (gz), é instalando a biblioteca zlib. Mas se não precisares dessa opção basta actualizares a biblioteca eutils (incluida com o mapseq) que eu já corrigi o erro (os scripts deveriam detectar que não tens essa biblioteca e evitar usa-la).

Para actualizares a biblioteca eutils (que se encontra na directoria libs/eutiils), basta mudares para essa directoria e executares o comando “svn update”.

Diz-me se encontrares mais algum problema.

João

On 11 Mar 2020, at 12:11, João André Carriço notifications@github.com wrote:

Greetings was installing MAPseq in ubuntu on windows wsl and whenrunning mak I got this error:

etable.cpp: In function ‘estrarrayof tablesLoad(const estr&, const evarhash&)’: etable.cpp:242:3: error: ‘egzfile’ was not declared in this scope egzfile f; ^~~ etable.cpp:242:3: note: suggested alternative: ‘edcfile’ egzfile f; ^~~ edcfile etable.cpp:260:8: error: ‘f’ was not declared in this scope if (!f.open(filename,"r")) { lerror(filename); return(ts); } ^ etable.cpp:271:15: error: ‘f’ was not declared in this scope if (header) f.readarr(line,headerarr,sep); ^ etable.cpp:273:10: error: ‘f’ was not declared in this scope while (f.readarr(line,arr,sep)){ ^ etable.cpp:315:3: error: ‘f’ was not declared in this scope f.close(); ^ etable.cpp: In function ‘etable etableLoad(const estr&, const evarhash&)’: etable.cpp:362:3: error: ‘egzfile’ was not declared in this scope egzfile f; ^~~ etable.cpp:362:3: note: suggested alternative: ‘edcfile’ egzfile f; ^~~ edcfile etable.cpp:372:8: error: ‘f’ was not declared in this scope if (!f.open(filename,"r")) { lerror(filename); return(t); } ^ etable.cpp:376:15: error: ‘f’ was not declared in this scope if (header) f.readarr(line,headerarr,sep); ^ etable.cpp:380:10: error: ‘f’ was not declared in this scope while (f.readarr(line,arr,sep)){ ^ Makefile:1105: recipe for target 'etable.lo' failed make[3]: [etable.lo] Error 1 make[3]: Leaving directory '/home/jcarrico/NGStools/MAPseq/libs/eutils' Makefile:766: recipe for target 'all' failed make[2]: [all] Error 2 make[2]: Leaving directory '/home/jcarrico/NGStools/MAPseq/libs/eutils' Makefile:683: recipe for target 'all-recursive' failed make[1]: [all-recursive] Error 1 make[1]: Leaving directory '/home/jcarrico/NGStools/MAPseq' Makefile:461: recipe for target 'all' failed make: [all] Error 2 (base) Any idea how can this be solved?

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Olá João. voltei a correr tudo desde o setup apos fazer o'svn update' como sugeristes e agora o erro que aparece é o seguinte:

ibtool: error: '/home/msarahan/miniconda2/conda-bld/compilers_linux-64_1507259624353/work/gcc_built/x86_64-conda_cos6-linux-gnu/lib/../lib/lib stdc++.la' is not a valid libtool archive make[3]: [Makefile:870: libeutils.la] Error 1 make[3]: Leaving directory '/home/jcarrico/NGStools/MAPseq/libs/eutils' make[2]: [Makefile:766: all] Error 2 make[2]: Leaving directory '/home/jcarrico/NGStools/MAPseq/libs/eutils' make[1]: [Makefile:683: all-recursive] Error 1 make[1]: Leaving directory '/home/jcarrico/NGStools/MAPseq' make: [Makefile:461: all] Error `

Obrigado desde já pela ajuda. JAC

Olá João,

Não sei bem o que está a causar esse problema. Parece que o programa "libtool" não reconhece uma das bibliotecas instaladas no teu sistema. Uma sugestão que vi noutro site, indica que se deve remover esse ficheiro (sugiro mudar o nome para o caso de outra coisa quebrar), o ficheiro em causa seria: /home/msarahan/miniconda2/conda-bld/compilers_linux-64_1507259624353/work/gcc_built/x86_64-conda_cos6-linux-gnu/lib/../lib/lib stdc++.la

Aqui está o link: https://www.linuxquestions.org/questions/linux-from-scratch-13/lfs-6-14-gmp-6-1-0-libtool-error-libstdc-ls-is-not-a-valid-libtool-archive-4175586676/

Espero que ajude. As versões precompiladas para linux não funcionam no teu sistema? O Ubuntu que falas em windows é só a consola se não me engano? Posso tentar criar uma versão precompilada para windows daqui a uns dias.

jfmrod / MAPseq

Installation problems #15