This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository sra-sdk.
commit a3d8e304389f5195dfcf0efb1333a24060ff9591 Author: Andreas Tille <[email protected]> Date: Mon Jul 25 13:04:59 2016 +0200 Try to run test suite but failed. Since I probably need some help here I'm waiting until ncbi-vdb has passed new queue. --- debian/patches/series | 1 + debian/patches/set_explicit_path_to_schemata.patch | 186 +++++++++++++++++++++ debian/rules | 4 +- 3 files changed, 189 insertions(+), 2 deletions(-) diff --git a/debian/patches/series b/debian/patches/series index a606f84..029693f 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -8,3 +8,4 @@ link_debian_packaged_libz.patch link_debian_packaged_lmagic.patch dont_use_static_lib.patch fix_tests.patch +set_explicit_path_to_schemata.patch diff --git a/debian/patches/set_explicit_path_to_schemata.patch b/debian/patches/set_explicit_path_to_schemata.patch new file mode 100644 index 0000000..3b0817e --- /dev/null +++ b/debian/patches/set_explicit_path_to_schemata.patch @@ -0,0 +1,186 @@ +--- a/test/fastq-loader/test-fastq-loader.cpp ++++ b/test/fastq-loader/test-fastq-loader.cpp +@@ -146,7 +146,7 @@ public: + string dbName; + }; + const string TempFileFixture::TempDir = "./tmp"; +-const string TempFileFixture::SchemaPath = "align/align.vschema"; ++const string TempFileFixture::SchemaPath = "/usr/lib/ncbi-vdb/align/align.vschema"; + const string TempFileFixture::DbType = "NCBI:align:db:alignment_unsorted"; + + ///////////////////////////////////////////////// FASTQ-based tests for CommonWriter +--- a/test/general-loader/test-general-loader.cpp ++++ b/test/general-loader/test-general-loader.cpp +@@ -488,7 +488,7 @@ FIXTURE_TEST_CASE ( BadSchemaFileName_Lo + + FIXTURE_TEST_CASE ( BadSchemaName, GeneralLoaderFixture ) + { +- SetUpStream ( GetName(), "align/align.vschema", "bad schema name" ); ++ SetUpStream ( GetName(), "/usr/lib/ncbi-vdb/align/align.vschema", "bad schema name" ); + m_source . OpenStreamEvent(); + + REQUIRE ( Run ( m_source . MakeSource (), SILENT_RC ( rcVDB, rcMgr, rcCreating, rcSchema, rcNotFound ) ) ); +@@ -496,7 +496,7 @@ FIXTURE_TEST_CASE ( BadSchemaName, Gener + + FIXTURE_TEST_CASE ( BadSchemaName_Long, GeneralLoaderFixture ) + { +- SetUpStream ( GetName(), "align/align.vschema", string ( GeneralLoader :: MaxPackedString + 1, 'x' ) ); ++ SetUpStream ( GetName(), "/usr/lib/ncbi-vdb/align/align.vschema", string ( GeneralLoader :: MaxPackedString + 1, 'x' ) ); + m_source . OpenStreamEvent(); + + REQUIRE ( Run ( m_source . MakeSource (), SILENT_RC ( rcVDB, rcMgr, rcCreating, rcSchema, rcNotFound ) ) ); +--- a/test/general-loader/makeinputs.cpp ++++ b/test/general-loader/makeinputs.cpp +@@ -69,7 +69,7 @@ OneTableOneColumnWithDefaults( const str + TestSource source; + TestSource::packed = p_packed; + +- source . SchemaEvent ( "align/align.vschema", "NCBI:align:db:alignment_sorted" ); ++ source . SchemaEvent ( "/usr/lib/ncbi-vdb/align/align.vschema", "NCBI:align:db:alignment_sorted" ); + source . DatabaseEvent ( DatabasePath ( p_caseId, p_packed ) ); + + source . NewTableEvent ( 1, tableName ); +@@ -104,7 +104,7 @@ ErrorMessage( const string& p_caseId, bo + TestSource source; + TestSource::packed = p_packed; + +- source . SchemaEvent ( "align/align.vschema", "NCBI:align:db:alignment_sorted" ); ++ source . SchemaEvent ( "/usr/lib/ncbi-vdb/align/align.vschema", "NCBI:align:db:alignment_sorted" ); + source . DatabaseEvent ( DatabasePath ( p_caseId, p_packed ) ); + + source . NewTableEvent ( 1, tableName ); +@@ -123,7 +123,7 @@ EmptyDefaultValue( const string& p_caseI + TestSource source; + TestSource::packed = p_packed; + +- source . SchemaEvent ( "align/align.vschema", "NCBI:align:db:alignment_sorted" ); ++ source . SchemaEvent ( "/usr/lib/ncbi-vdb/align/align.vschema", "NCBI:align:db:alignment_sorted" ); + source . DatabaseEvent ( DatabasePath ( p_caseId, p_packed ) ); + + source . NewTableEvent ( 1, tableName ); +@@ -143,7 +143,7 @@ MoveAhead( const string& p_caseId, bool + TestSource source; + TestSource::packed = p_packed; + +- source . SchemaEvent ( "align/align.vschema", "NCBI:align:db:alignment_sorted" ); ++ source . SchemaEvent ( "/usr/lib/ncbi-vdb/align/align.vschema", "NCBI:align:db:alignment_sorted" ); + source . DatabaseEvent ( DatabasePath ( p_caseId, p_packed ) ); + + source . NewTableEvent ( 1, tableName ); +@@ -172,7 +172,7 @@ IntegerCompression( const string& p_case + TestSource source; + TestSource::packed = true; + +- source . SchemaEvent ( "align/align.vschema", "NCBI:align:db:alignment_sorted" ); ++ source . SchemaEvent ( "/usr/lib/ncbi-vdb/align/align.vschema", "NCBI:align:db:alignment_sorted" ); + source . DatabaseEvent ( DatabasePath ( p_caseId, p_packed ) ); + + source . NewTableEvent ( 1, tableName ); +@@ -194,7 +194,7 @@ SoftwareIdString( const string& p_caseId + TestSource source; + TestSource::packed = true; + +- source . SchemaEvent ( "align/align.vschema", "NCBI:align:db:alignment_sorted" ); ++ source . SchemaEvent ( "/usr/lib/ncbi-vdb/align/align.vschema", "NCBI:align:db:alignment_sorted" ); + source . DatabaseEvent ( DatabasePath ( p_caseId, p_packed ) ); + + source . SoftwareNameEvent ( string ( "some software" ), string ( "9.8.7654" ) ); +--- a/tools/fastq-loader/fastq-loader.c ++++ b/tools/fastq-loader/fastq-loader.c +@@ -253,7 +253,7 @@ rc_t CC Usage (const Args * args) + + /* MARK: Definitions and Globals */ + +-#define SCHEMAFILE "align/align.vschema" ++#define SCHEMAFILE "/usr/lib/ncbi-vdb/align/align.vschema" + + CommonWriterSettings G; + +--- a/tools/bam-loader/bam-loader.c ++++ b/tools/bam-loader/bam-loader.c +@@ -553,7 +553,7 @@ rc_t CC Usage (const Args * args) + + /* MARK: Definitions and Globals */ + +-#define SCHEMAFILE "align/align.vschema" ++#define SCHEMAFILE "/usr/lib/ncbi-vdb/align/align.vschema" + + Globals G; + +--- a/tools/sra-sort/run.c ++++ b/tools/sra-sort/run.c +@@ -78,7 +78,7 @@ bool map_typename_builtin ( const ctx_t + + #define ALIGN_EVIDENCE_MAP "NCBI:align:db:alignment_evidence_sorted" + #define ALIGN_UNSORTED_MAP "NCBI:align:db:alignment_sorted" +-#define ALIGN_SRC "align/align.vschema" ++#define ALIGN_SRC "/usr/lib/ncbi-vdb/align/align.vschema" + + if ( strcmp ( out, "NCBI/align/db/alignment_evidence" ) == 0 ) + copied = string_copy ( out, size, ALIGN_EVIDENCE_MAP, sizeof ALIGN_EVIDENCE_MAP - 1 ); +--- a/tools/cg-load/cg-load.c ++++ b/tools/cg-load/cg-load.c +@@ -1073,7 +1073,7 @@ rc_t CC KMain( int argc, char* argv[] ) + const XMLLogger* xml_logger = NULL; + SParam params; + memset(¶ms, 0, sizeof(params)); +- params.schema = "align/align.vschema"; ++ params.schema = "/usr/lib/ncbi-vdb/align/align.vschema"; + + params.argv0 = argv[0]; + +--- a/tools/util/sortreadtest.c ++++ b/tools/util/sortreadtest.c +@@ -21,11 +21,11 @@ + + /* + +- default file is "ncbi/seq.vschema" ++ default file is "/usr/lib/ncbi-vdb/ncbi/seq.vschema" + default table-spec "NCBI:tbl:base_space#2" + + */ +-#define SCHEMASPEC "ncbi/seq.vschema" ++#define SCHEMASPEC "/usr/lib/ncbi-vdb/ncbi/seq.vschema" + #define TYPESPEC "NCBI:tbl:base_space#2" + + const char UsageDefaultName[] = "sortreadtest"; +--- a/tools/vdb-copy/vdb-copy.kfg ++++ b/tools/vdb-copy/vdb-copy.kfg +@@ -25,11 +25,11 @@ + # matching legacy-tables with schema's to write to for vdb-copy + + # ILLUMINA +-/VDBCOPY/NCBI_SRA_Illumina_tbl_v0a_1/schema = "sra/illumina.vschema" ++/VDBCOPY/NCBI_SRA_Illumina_tbl_v0a_1/schema = "/usr/lib/ncbi-vdb/sra/illumina.vschema" + #/VDBCOPY/NCBI_SRA_Illumina_tbl_v0a_1/tab = "NCBI:SRA:Illumina:tbl:q4:v2" + #/VDBCOPY/NCBI_SRA_Illumina_tbl_v0a_1/tab = "NCBI:SRA:Illumina:tbl:q1:v2" + /VDBCOPY/NCBI_SRA_Illumina_tbl_v0a_1/tab = "NCBI:SRA:Illumina:tbl:phred:v2" +-/VDBCOPY/_ILLUMINA_/schema = "sra/illumina.vschema" ++/VDBCOPY/_ILLUMINA_/schema = "/usr/lib/ncbi-vdb/sra/illumina.vschema" + /VDBCOPY/_ILLUMINA_/tab = "NCBI:SRA:Illumina:tbl:phred:v2" + + +@@ -41,9 +41,9 @@ + + + # ABSOLID +-/VDBCOPY/NCBI_SRA_ABI_tbl_v1_1/schema = "sra/abi.vschema" ++/VDBCOPY/NCBI_SRA_ABI_tbl_v1_1/schema = "/usr/lib/ncbi-vdb/sra/abi.vschema" + /VDBCOPY/NCBI_SRA_ABI_tbl_v1_1/tab = "NCBI:SRA:ABI:tbl:v2" +-/VDBCOPY/_ABSOLID_/schema = "sra/abi.vschema" ++/VDBCOPY/_ABSOLID_/schema = "/usr/lib/ncbi-vdb/sra/abi.vschema" + /VDBCOPY/_ABSOLID_/tab = "NCBI:SRA:ABI:tbl:v2" + + +--- a/tools/pacbio-load/pl-context.h ++++ b/tools/pacbio-load/pl-context.h +@@ -52,7 +52,7 @@ extern "C" { + #define ALIAS_WITH_PROGRESS "p" + #define ALIAS_OUTPUT "o" + +-#define DFLT_SCHEMA "sra/pacbio.vschema" ++#define DFLT_SCHEMA "/usr/lib/ncbi-vdb/sra/pacbio.vschema" + #define PACBIO_SCHEMA_DB "NCBI:SRA:PacBio:smrt:db" + + diff --git a/debian/rules b/debian/rules index cccbb2b..dfad0a0 100755 --- a/debian/rules +++ b/debian/rules @@ -33,8 +33,8 @@ override_dh_install: done dh_install -override_dh_auto_test: - echo "FIXME: try activating tests!!!!!!!!!!!!!!!!!!!!!!!!" +#override_dh_auto_test: +# echo "FIXME: try activating tests!!!!!!!!!!!!!!!!!!!!!!!!" override_dh_prep: dh_prep -X debian/tmp -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/sra-sdk.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
