fail to install at autoheader stage

[jrjhealey]

Hi, I'm attempting to install a local copy of ConSurf on to our linux machine but each time the process has failed at the autoheader stage:

autoheader: error: AC_CONFIG_HEADERS not found in configure.ac

Every step prior to this stage appeared to complete correctly (or at least failed silently!).

Any ideas? Do I perhaps need to edit some header files?

[juanmirocks]

@jrjhealey Thanks Joe -- we're a bit short of man power currently in our group. In general, we cannot provide maintenance for the software now. Anyway, I contact my colleagues in case they can help.

Ofc if you find a solution, we appreciate a contribution !

[jrjhealey]

Understandable! I don't have much experience compiling software, and less still with aclocal/autoheader etc. but if I stumble across something I'll be sure to post it up here!

[juanmirocks]

Dear @jrjhealey

in behalf of my colleague @BernhoferM I share his findings:

After a quick look at the repository and trying to install it, I've noticed a few things: 1) running 'autoheader' seems to be unnecessary and can be skipped (thus avoiding the error); However... 2) Makefile.am refers to "SUBDIRS = example output" which do not exist (probably have been renamed to 'old_1lk2_example' and 'old_1lk2_output') 3) configure.ac refers to "AC_CONFIG_FILES([Makefile example/Makefile output/Makefile])" (once again, the missing 'example' and 'output' directories) 4) 'CONSURF_CONSTANTS.pm.template' needs to be renamed to 'CONSURF_CONSTANTS.pm' and its content edited to reflect the local configuration

4 was once mentioned in the README.md, but later on got removed. Overall, it seems that nobody tried to acutally run and install everything to check if it still works after it was put on github.

After locally fixing #1-3 and just renaming #4 (without changing the paths) it installed on a VM

In theory, all that's needed would be to: 1) change the 'old1lk2*' directories back to 'example' and 'output' OR remove the references from 'Makefile.am' and 'configure.ac' 2) restore the hint about setting up 'CONSURF_CONSTANTS.pm' to the configuration section 3) remove the instruction to run 'autoheader'

Please give it a go :)

[jrjhealey]

Hi guys, I think it's working (compilation didn't error and the helpfile can be output)

Removing the references to the example and output files from Makefile.am and configure.ac seemed to work.

I had a few issues with the CONSURF_CONSTANTS.pm file though. Defining my own paths was causing errors. I added in the paths to each executable and tried it with single and double quotes, as well as with the string 3rd party software and 3rd\ party\ software as I'm not sure whether perl expects escaped whitespace? Using the default file seemed to remedy these errors, so it may be something I did wrong.

The errors looked like this:

 (Might be a runaway multi-line "" string starting on line 31)
        (Missing semicolon on previous line?)
Unquoted string "mnt" may clash with future reserved word at /usr/local/share/consurf/CONSURF_CONSTANTS.pm line 33.
Unquoted string "home" may clash with future reserved word at /usr/local/share/consurf/CONSURF_CONSTANTS.pm line 33.
Unquoted string "gcelniker" may clash with future reserved word at /usr/local/share/consurf/CONSURF_CONSTANTS.pm line 33.
Unquoted string "clustalw" may clash with future reserved word at /usr/local/share/consurf/CONSURF_CONSTANTS.pm line 33.
Unquoted string "home" may clash with future reserved word at /usr/local/share/consurf/CONSURF_CONSTANTS.pm line 34.
Unquoted string "ubuntu" may clash with future reserved word at /usr/local/share/consurf/CONSURF_CONSTANTS.pm line 34.
Bareword found where operator expected at /usr/local/share/consurf/CONSURF_CONSTANTS.pm line 34, near "3rd"

Here's what the file looked like before I used ' ' and escaped whitespace. I rarely use perl so maybe you can tell me if I've missed something stupid. Would it break internal path references if 3rd party software was renamed to 3rd_party_software?

#!/usr/bin/perl

package CONSURF_CONSTANTS; #don"t forget: a package must end with a return value (1; in the end)!!!!!

use constant MAXIMUM_MODIFIED_PERCENT => 0.15;
use constant FRAGMENT_REDUNDANCY_RATE => 95;
use constant FRAGMENT_OVERLAP => 0.10;
use constant FRAGMENT_MINIMUM_LENGTH => 0.60;
use constant MINIMUM_FRAGMENTS_FOR_MSA => 5;
use constant LOW_NUM_FRAGMENTS_FOR_MSA => 10;

use constant BAYES_INTERVAL => 3;

#external databases
        # replace /biodb/PDB/data/structures/divided/pdb/ with your location of the PDB
use constant PDB_DIVIDED => "/mnt/project/rost_db/data/pdb/entries/";
        # replace /biodb/BLAST/Proteins/swissprot with your location of SwissProt database
use constant SWISSPROT_DB => "/home/ubuntu/Applications/ConSurf/databases/uniprot_sprot.fasta";
        # replace /biodb/BLAST/Proteins/uniprot with your location of UniProt Database
use constant UNIPROT_DB => "/home/ubuntu/Applications/ConSurf/databases/uniprot_trembl.fasta";

use constant UNIREF90_DB => "/mnt/project/rost_db/data/big/big_80";

use constant CLEAN_UNIPROT_DB => "/mnt/project/consurf/data/clean_uniprot";

use constant RCSB_WGET => "wget ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/pdb/";

#external programs

        #replace /usr/local/bin/muscle with the location of your muscle instalation
use constant MUSCLE => "/home/ubuntu/Applications/ConSurf/3rd party software/muscle3.8.31";

        # replace /usr/local/bin/clustalw with your locationion of your clustalw istalation
#use constant CLUSTALW =>            "/mnt/home/gcelniker/ConSurf_TEST/DB/clustalw/";
use constant CLUSTALW => "/home/ubuntu/Applications/ConSurf/3rd party software/clustalw-2.1/clustalw2";
        # replace /db1/Local/src/Rate4SiteSource/r4s_Nov_06_dev/rate4site.exe with the location of your rate4site instalation

use constant RATE4SITE => "/home/ubuntu/Applications/ConSurf/3rd party software/rate4site.3.2.source_fast/sourceMar09/rate4site";
        #replace /db1/Local/src/Rate4SiteSource/r4s_Nov_06_dev/rate4siteSlow.exe with the location of your rate4site_Slow instalation
use constant RATE4SITE_SLOW => "/home/ubuntu/Applications/ConSurf/3rd party software/rate4site.3.2.source_slow/sourceMar09/rate4site";
        #replace /db1/Local/src/cd-hit_redundency/ with the directory containing your instalation of CD-HIT

use constant CD_HIT_DIR => "/home/ubuntu/Applications/ConSurf/3rd party software/cdhit/";
        #replace /usr/local/bin/blastpgp with the location of your blastpgp instalation
use constant BLASTPGP => "/home/ubuntu/Applications/ConSurf/3rd party software/blast-2.2.26/bin/blastpgp";
# constant values
use constant BLAST_MAX_HOMOLOGUES_TO_DISPLAY => 50;

# external links
use constant RCSB_WEB => "http://www.rcsb.org/";

1;

I've tried running the example data 1lk2.pdb, however I keep getting a memory problem error. I really doubt this is a RAM issue as I'm using a HPC virtual machine with 96GB of RAM?

The calculation could not be completed due to memory problem, since the MSA is too large. Please run ConSurf again with fewer sequences.
ubuntu@protein-simulation-2:~/Applications/ConSurf$ consurf --PDB example/1lk2.pdb --CHAIN A --Out_Dir output -m --workdir workdir --BlastFile example/1lk2_A.protein_query.blast
defined(@array) is deprecated at /usr/local/bin/consurf line 1247.
        (Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/bin/consurf line 1255.
        (Maybe you should just omit the defined()?)
defined(@array) is deprecated at /usr/local/bin/consurf line 1267.
        (Maybe you should just omit the defined()?)

ConSurf Version 1.0.6
====================================
Process Started at 15:22:21

Output files could be found in output directory: output/

There are 49 PSI-BLAST hits, 19 of them are unique sequences.
The calculation is performed on the 19 unique sequences.

If you wish to view the list of sequences which produced significant alignments in blast, but were not chosen as hits please have a look at: 1lk2_A.rejected_homolougs.fas

 unable to open output file for writing.

 unable to open output file for writing.
System Error: No such file or directory
System Error: No such file or directory
rate4site: errorMsg.cpp:40: static void errorMsg::reportError(const string&, int): Assertion `0' failed.
Aborted (core dumped)

Warning: The given MSA is very large, therefore it will take longer for ConSurf calculation to finish. The calculation continues nevertheless.

 unable to open output file for writing.

 unable to open output file for writing.
System Error: No such file or directory
System Error: No such file or directory
rate4site: errorMsg.cpp:40: static void errorMsg::reportError(const string&, int): Assertion `0' failed.
Aborted (core dumped)
Use of uninitialized value in concatenation (.) or string at /usr/local/bin/consurf line 1391.

EXIT on error:
The calculation could not be completed due to memory problem, since the MSA is too large. Please run ConSurf again with fewer sequences.