make error at develop branch

[wolf-Peng]

hello, I want to use the develop version of create_profmark.c and I run the command: git clone https://github.com/EddyRivasLab/hmmer cd hmmer git clone https://github.com/EddyRivasLab/easel git checkout develop autoconf ./configure make Then it raised an error esl_iset.c: In function ‘esl_iset_Cobalt’: esl_iset.c:368:5: error: ‘for’ loop initial declarations are only allowed in C99 mode for (int i = n; i < n+nb; i++){ ^ esl_iset.c:368:5: note: use option -std=c99 or -std=gnu99 to compile your code esl_iset.c: In function ‘esl_bi_iset_Cobalt’: esl_iset.c:491:9: error: ‘for’ loop initial declarations are only allowed in C99 mode for (int i = 2*n; i < 2*n+nb2; i++){ ^ esl_iset.c:526:7: error: ‘for’ loop initial declarations are only allowed in C99 mode for (int i = 2*n; i < 2*n+nb2; i++){ ^ esl_iset.c:538:9: error: ‘for’ loop initial declarations are only allowed in C99 mode for (int i = n; i < n+nb1; i++){ ^ make[1]: *** [esl_iset.o] Error 1 make: *** [all] Error 2 How to solve it ? Thank you.

[cryptogenomicon]

We are currently working on the develop branch version of create_profmark. Please be patient while we finish!

[npcarter]

This bug should now be fixed in the develop branch. Our autoconf/configure system should now detect that your compiler requires a flag to handle the C99 standard and insert it automatically. However, as Sean said, create_profmark is currently being revised so you may experience other problems.

-Nick

On Mon, Jun 20, 2022 at 1:34 AM wolf-Peng @.***> wrote:

hello, I want to use the develop version of create_profmark.c and I run the command: git clone https://github.com/EddyRivasLab/hmmer cd hmmer git clone https://github.com/EddyRivasLab/easel git checkout develop autoconf ./configure make Then it raised an error esl_iset.c: In function ‘esl_iset_Cobalt’: esl_iset.c:368:5: error: ‘for’ loop initial declarations are only allowed in C99 mode for (int i = n; i < n+nb; i++){ ^ esl_iset.c:368:5: note: use option -std=c99 or -std=gnu99 to compile your code esl_iset.c: In function ‘esl_bi_iset_Cobalt’: esl_iset.c:491:9: error: ‘for’ loop initial declarations are only allowed in C99 mode for (int i = 2n; i < 2n+nb2; i++){ ^ esl_iset.c:526:7: error: ‘for’ loop initial declarations are only allowed in C99 mode for (int i = 2n; i < 2n+nb2; i++){ ^ esl_iset.c:538:9: error: ‘for’ loop initial declarations are only allowed in C99 mode for (int i = n; i < n+nb1; i++){ ^ make[1]: [esl_iset.o] Error 1 make: [all] Error 2 How to solve it ? Thank you.

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[jrherr]

Just commenting here to get a ping if there are any updates to this issue.

I am also reinstalling on a M1 Mac. When I run:

git clone https://github.com/EddyRivasLab/hmmer
cd hmmer
git clone https://github.com/EddyRivasLab/easel
git checkout develop
autoconf
./configure
make

I then get the following error during compiling:

generic_vtrace.c:78:16: error: implicit declaration of function 'esl_FCompare_old' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
      if      (esl_FCompare_old(XMX(i, p7G_C), XMX(i-1, p7G_C) + gm->xsc[p7P_C][p7P_LOOP], tol) == eslOK)  scur = p7T_C; 
               ^
1 error generated.
make[1]: *** [generic_vtrace.o] Error 1
make: *** [all] Error 2

...any help is appreciated! Thanks!

[npcarter]

It looks to me like you’ve checked out the develop branch of HMMER, but not the develop branch of Easel, which the develop branch of HMMER requires. Could you please try checking out the develop branch of Easel as well, and let me know if that works?

-Nick

[0x1orz]

git clone -b develop  https://github.com/EddyRivasLab/hmmer
cd hmmer
git clone -b develop https://github.com/EddyRivasLab/easel
cd easel
autoconf
./configure
make
make check
cd ../
autoconf
./configure
make

when make at hmmer/, get the following error:

create-profmark.c:28:10: fatal error: 'esl_msa_iset.h' file not found
#include "esl_msa_iset.h"
         ^~~~~~~~~~~~~~~~
1 error generated.
make[1]: *** [create-profmark.o] Error 1
make: *** [all] Error 2

[cryptogenomicon]

Yes, our develop branch is currently not compiling, and we know about it.