<br><br><div class="gmail_quote"><div dir="ltr">Le sam. 17 déc. 2016 11:45, Andreas Tille <<a href="mailto:tille@debian.org">tille@debian.org</a>> a écrit :<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Aaron,<br class="gmail_msg">
<br class="gmail_msg">
I guess that's due to the new version of ncbi-tools+. Any suggested<br class="gmail_msg">
patch for this problem?<br class="gmail_msg"></blockquote></div><div>Looks indeed related to a modification with formatdb.</div><div><br></div><div>I do not know the tool itself but looking at executed command and formatdb help, should be able to find difference for a patch.</div><div><br></div><div>Olivier</div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br class="gmail_msg">
Kind regards<br class="gmail_msg">
<br class="gmail_msg">
Andreas.<br class="gmail_msg">
<br class="gmail_msg">
On Sat, Dec 17, 2016 at 10:52:15AM +0100, Chris Lamb wrote:<br class="gmail_msg">
> Source: metastudent-data<br class="gmail_msg">
> Version: 2.0.1-1<br class="gmail_msg">
> Severity: serious<br class="gmail_msg">
> Justification: fails to build from source<br class="gmail_msg">
> User: <a href="mailto:reproducible-builds@lists.alioth.debian.org" class="gmail_msg" target="_blank">reproducible-builds@lists.alioth.debian.org</a><br class="gmail_msg">
> Usertags: ftbfs<br class="gmail_msg">
> X-Debbugs-Cc: <a href="mailto:reproducible-bugs@lists.alioth.debian.org" class="gmail_msg" target="_blank">reproducible-bugs@lists.alioth.debian.org</a><br class="gmail_msg">
><br class="gmail_msg">
> Dear Maintainer,<br class="gmail_msg">
><br class="gmail_msg">
> metastudent-data fails to build from source in unstable/amd64:<br class="gmail_msg">
><br class="gmail_msg">
> […]<br class="gmail_msg">
><br class="gmail_msg">
> dh_auto_build -O--parallel<br class="gmail_msg">
> dh_auto_build: Compatibility levels before 9 are deprecated (level 8 in use)<br class="gmail_msg">
> make -j9<br class="gmail_msg">
> make[1]: Entering directory '«BUILDDIR»'<br class="gmail_msg">
> mkdir -p dataset_201401/BPO/ && \<br class="gmail_msg">
> formatdb -i "dataset_201401/BPO/goasp.fasta" -n "dataset_201401/BPO/goasp.fasta" && rm -f formatdb.log<br class="gmail_msg">
> mkdir -p dataset_201401/MFO/ && \<br class="gmail_msg">
> formatdb -i "dataset_201401/MFO/goasp.fasta" -n "dataset_201401/MFO/goasp.fasta" && rm -f formatdb.log<br class="gmail_msg">
> mkdir -p dataset_201401/CCO/ && \<br class="gmail_msg">
> formatdb -i "dataset_201401/CCO/goasp.fasta" -n "dataset_201401/CCO/goasp.fasta" && rm -f formatdb.log<br class="gmail_msg">
> USAGE<br class="gmail_msg">
> makeblastdb [-h] [-help] [-in input_file] [-input_type type]<br class="gmail_msg">
> -dbtype molecule_type [-title database_title] [-parse_seqids]<br class="gmail_msg">
> [-hash_index] [-mask_data mask_data_files] [-mask_id mask_algo_ids]<br class="gmail_msg">
> [-mask_desc mask_algo_descriptions] [-gi_mask]<br class="gmail_msg">
> [-gi_mask_name gi_based_mask_names] [-out database_name]<br class="gmail_msg">
> [-max_file_sz number_of_bytes] [-logfile File_Name] [-taxid TaxID]<br class="gmail_msg">
> [-taxid_map TaxIDMapFile] [-version]<br class="gmail_msg">
><br class="gmail_msg">
> DESCRIPTION<br class="gmail_msg">
> Application to create BLAST databases, version 2.5.0+<br class="gmail_msg">
><br class="gmail_msg">
> Use '-help' to print detailed descriptions of command line arguments<br class="gmail_msg">
> ========================================================================<br class="gmail_msg">
><br class="gmail_msg">
> Error: Argument "dbtype". Mandatory value is missing: `String, `nucl', `prot''<br class="gmail_msg">
> Error: (CArgException::eNoArg) Argument "dbtype". Mandatory value is missing: `String, `nucl', `prot''<br class="gmail_msg">
> Program failed, try executing the command manually.<br class="gmail_msg">
> Makefile:606: recipe for target 'dataset_201401/MFO/goasp.fasta.psq' failed<br class="gmail_msg">
> make[1]: *** [dataset_201401/MFO/goasp.fasta.psq] Error 1<br class="gmail_msg">
> make[1]: *** Waiting for unfinished jobs....<br class="gmail_msg">
> USAGE<br class="gmail_msg">
> makeblastdb [-h] [-help] [-in input_file] [-input_type type]<br class="gmail_msg">
> -dbtype molecule_type [-title database_title] [-parse_seqids]<br class="gmail_msg">
> [-hash_index] [-mask_data mask_data_files] [-mask_id mask_algo_ids]<br class="gmail_msg">
> [-mask_desc mask_algo_descriptions] [-gi_mask]<br class="gmail_msg">
> [-gi_mask_name gi_based_mask_names] [-out database_name]<br class="gmail_msg">
> [-max_file_sz number_of_bytes] [-logfile File_Name] [-taxid TaxID]<br class="gmail_msg">
> [-taxid_map TaxIDMapFile] [-version]<br class="gmail_msg">
><br class="gmail_msg">
> DESCRIPTION<br class="gmail_msg">
> Application to create BLAST databases, version 2.5.0+<br class="gmail_msg">
><br class="gmail_msg">
> Use '-help' to print detailed descriptions of command line arguments<br class="gmail_msg">
> ========================================================================<br class="gmail_msg">
><br class="gmail_msg">
> Error: Argument "dbtype". Mandatory value is missing: `String, `nucl', `prot''<br class="gmail_msg">
> Error: (CArgException::eNoArg) Argument "dbtype". Mandatory value is missing: `String, `nucl', `prot''<br class="gmail_msg">
> Program failed, try executing the command manually.<br class="gmail_msg">
> Makefile:606: recipe for target 'dataset_201401/BPO/goasp.fasta.psq' failed<br class="gmail_msg">
> make[1]: *** [dataset_201401/BPO/goasp.fasta.psq] Error 1<br class="gmail_msg">
> USAGE<br class="gmail_msg">
> makeblastdb [-h] [-help] [-in input_file] [-input_type type]<br class="gmail_msg">
> -dbtype molecule_type [-title database_title] [-parse_seqids]<br class="gmail_msg">
> [-hash_index] [-mask_data mask_data_files] [-mask_id mask_algo_ids]<br class="gmail_msg">
> [-mask_desc mask_algo_descriptions] [-gi_mask]<br class="gmail_msg">
> [-gi_mask_name gi_based_mask_names] [-out database_name]<br class="gmail_msg">
> [-max_file_sz number_of_bytes] [-logfile File_Name] [-taxid TaxID]<br class="gmail_msg">
> [-taxid_map TaxIDMapFile] [-version]<br class="gmail_msg">
><br class="gmail_msg">
> DESCRIPTION<br class="gmail_msg">
> Application to create BLAST databases, version 2.5.0+<br class="gmail_msg">
><br class="gmail_msg">
> Use '-help' to print detailed descriptions of command line arguments<br class="gmail_msg">
> ========================================================================<br class="gmail_msg">
><br class="gmail_msg">
> Error: Argument "dbtype". Mandatory value is missing: `String, `nucl', `prot''<br class="gmail_msg">
> Error: (CArgException::eNoArg) Argument "dbtype". Mandatory value is missing: `String, `nucl', `prot''<br class="gmail_msg">
> Program failed, try executing the command manually.<br class="gmail_msg">
> Makefile:606: recipe for target 'dataset_201401/CCO/goasp.fasta.psq' failed<br class="gmail_msg">
> make[1]: *** [dataset_201401/CCO/goasp.fasta.psq] Error 1<br class="gmail_msg">
> make[1]: Leaving directory '«BUILDDIR»'<br class="gmail_msg">
> dh_auto_build: make -j9 returned exit code 2<br class="gmail_msg">
> debian/rules:8: recipe for target 'build' failed<br class="gmail_msg">
> make: *** [build] Error 2<br class="gmail_msg">
> dpkg-buildpackage: error: debian/rules build gave error exit status 2<br class="gmail_msg">
><br class="gmail_msg">
> […]<br class="gmail_msg">
><br class="gmail_msg">
> The full build log is attached.<br class="gmail_msg">
><br class="gmail_msg">
><br class="gmail_msg">
> Regards,<br class="gmail_msg">
><br class="gmail_msg">
> --<br class="gmail_msg">
> ,''`.<br class="gmail_msg">
> : :' : Chris Lamb<br class="gmail_msg">
> `. `'` <a href="mailto:lamby@debian.org" class="gmail_msg" target="_blank">lamby@debian.org</a> / <a href="http://chris-lamb.co.uk" rel="noreferrer" class="gmail_msg" target="_blank">chris-lamb.co.uk</a><br class="gmail_msg">
> `-<br class="gmail_msg">
<br class="gmail_msg">
<br class="gmail_msg">
> _______________________________________________<br class="gmail_msg">
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--<br class="gmail_msg">
<a href="http://fam-tille.de" rel="noreferrer" class="gmail_msg" target="_blank">http://fam-tille.de</a><br class="gmail_msg">
</blockquote></div>