[Debian-med-packaging] Bug#848394: metastudent-data: FTBFS: Error: Argument "dbtype". Mandatory value is missing: `String, `nucl', `prot''

[olivier sallou]

Le sam. 17 déc. 2016 11:45, Andreas Tille <tille at debian.org> a écrit :

> Hi Aaron,
>
> I guess that's due to the new version of ncbi-tools+.  Any suggested
> patch for this problem?
>
By the way, adding dbtype with prot or nuc value should do the job.
If dataset_201401/MFO/goasp.fasta contains only acgtn chars it is nuc
If it contains other letters it is prot

Patching script with the formatfb command should be ok

Olivier


> Kind regards
>
>      Andreas.
>
> On Sat, Dec 17, 2016 at 10:52:15AM +0100, Chris Lamb wrote:
> > Source: metastudent-data
> > Version: 2.0.1-1
> > Severity: serious
> > Justification: fails to build from source
> > User: reproducible-builds at lists.alioth.debian.org
> > Usertags: ftbfs
> > X-Debbugs-Cc: reproducible-bugs at lists.alioth.debian.org
> >
> > Dear Maintainer,
> >
> > metastudent-data fails to build from source in unstable/amd64:
> >
> >   […]
> >
> >      dh_auto_build -O--parallel
> >   dh_auto_build: Compatibility levels before 9 are deprecated (level 8
> in use)
> >       make -j9
> >   make[1]: Entering directory '«BUILDDIR»'
> >   mkdir -p dataset_201401/BPO/ && \
> >       formatdb -i "dataset_201401/BPO/goasp.fasta" -n
> "dataset_201401/BPO/goasp.fasta" && rm -f formatdb.log
> >   mkdir -p dataset_201401/MFO/ && \
> >       formatdb -i "dataset_201401/MFO/goasp.fasta" -n
> "dataset_201401/MFO/goasp.fasta" && rm -f formatdb.log
> >   mkdir -p dataset_201401/CCO/ && \
> >       formatdb -i "dataset_201401/CCO/goasp.fasta" -n
> "dataset_201401/CCO/goasp.fasta" && rm -f formatdb.log
> >   USAGE
> >     makeblastdb [-h] [-help] [-in input_file] [-input_type type]
> >       -dbtype molecule_type [-title database_title] [-parse_seqids]
> >       [-hash_index] [-mask_data mask_data_files] [-mask_id mask_algo_ids]
> >       [-mask_desc mask_algo_descriptions] [-gi_mask]
> >       [-gi_mask_name gi_based_mask_names] [-out database_name]
> >       [-max_file_sz number_of_bytes] [-logfile File_Name] [-taxid TaxID]
> >       [-taxid_map TaxIDMapFile] [-version]
> >
> >   DESCRIPTION
> >      Application to create BLAST databases, version 2.5.0+
> >
> >   Use '-help' to print detailed descriptions of command line arguments
> >
>  ========================================================================
> >
> >   Error: Argument "dbtype". Mandatory value is missing:  `String,
> `nucl', `prot''
> >   Error:  (CArgException::eNoArg) Argument "dbtype". Mandatory value is
> missing:  `String, `nucl', `prot''
> >   Program failed, try executing the command manually.
> >   Makefile:606: recipe for target 'dataset_201401/MFO/goasp.fasta.psq'
> failed
> >   make[1]: *** [dataset_201401/MFO/goasp.fasta.psq] Error 1
> >   make[1]: *** Waiting for unfinished jobs....
> >   USAGE
> >     makeblastdb [-h] [-help] [-in input_file] [-input_type type]
> >       -dbtype molecule_type [-title database_title] [-parse_seqids]
> >       [-hash_index] [-mask_data mask_data_files] [-mask_id mask_algo_ids]
> >       [-mask_desc mask_algo_descriptions] [-gi_mask]
> >       [-gi_mask_name gi_based_mask_names] [-out database_name]
> >       [-max_file_sz number_of_bytes] [-logfile File_Name] [-taxid TaxID]
> >       [-taxid_map TaxIDMapFile] [-version]
> >
> >   DESCRIPTION
> >      Application to create BLAST databases, version 2.5.0+
> >
> >   Use '-help' to print detailed descriptions of command line arguments
> >
>  ========================================================================
> >
> >   Error: Argument "dbtype". Mandatory value is missing:  `String,
> `nucl', `prot''
> >   Error:  (CArgException::eNoArg) Argument "dbtype". Mandatory value is
> missing:  `String, `nucl', `prot''
> >   Program failed, try executing the command manually.
> >   Makefile:606: recipe for target 'dataset_201401/BPO/goasp.fasta.psq'
> failed
> >   make[1]: *** [dataset_201401/BPO/goasp.fasta.psq] Error 1
> >   USAGE
> >     makeblastdb [-h] [-help] [-in input_file] [-input_type type]
> >       -dbtype molecule_type [-title database_title] [-parse_seqids]
> >       [-hash_index] [-mask_data mask_data_files] [-mask_id mask_algo_ids]
> >       [-mask_desc mask_algo_descriptions] [-gi_mask]
> >       [-gi_mask_name gi_based_mask_names] [-out database_name]
> >       [-max_file_sz number_of_bytes] [-logfile File_Name] [-taxid TaxID]
> >       [-taxid_map TaxIDMapFile] [-version]
> >
> >   DESCRIPTION
> >      Application to create BLAST databases, version 2.5.0+
> >
> >   Use '-help' to print detailed descriptions of command line arguments
> >
>  ========================================================================
> >
> >   Error: Argument "dbtype". Mandatory value is missing:  `String,
> `nucl', `prot''
> >   Error:  (CArgException::eNoArg) Argument "dbtype". Mandatory value is
> missing:  `String, `nucl', `prot''
> >   Program failed, try executing the command manually.
> >   Makefile:606: recipe for target 'dataset_201401/CCO/goasp.fasta.psq'
> failed
> >   make[1]: *** [dataset_201401/CCO/goasp.fasta.psq] Error 1
> >   make[1]: Leaving directory '«BUILDDIR»'
> >   dh_auto_build: make -j9 returned exit code 2
> >   debian/rules:8: recipe for target 'build' failed
> >   make: *** [build] Error 2
> >   dpkg-buildpackage: error: debian/rules build gave error exit status 2
> >
> >   […]
> >
> > The full build log is attached.
> >
> >
> > Regards,
> >
> > --
> >       ,''`.
> >      : :'  :     Chris Lamb
> >      `. `'`      lamby at debian.org / chris-lamb.co.uk
> >        `-
>
>
> > _______________________________________________
> > Debian-med-packaging mailing list
> > Debian-med-packaging at lists.alioth.debian.org
> >
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
>
>
> --
> http://fam-tille.de
>
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