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

[Andreas Tille]

Hi Aaron,

I guess that's due to the new version of ncbi-tools+.  Any suggested
patch for this problem?

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
>        `-


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