[med-svn] [sra-sdk] 05/06: Remove cruft

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository sra-sdk.

commit d28254702fdfc68b2f63217d48e562fabfb7c79c
Author: Andreas Tille <tille at debian.org>
Date:   Wed Jan 11 08:06:44 2017 +0100

    Remove cruft
---
 .../ignore_failing_tests_for_the_moment.patch      | 39 ----------------------
 debian/patches/set_explicit_path_to_schemata.patch | 23 -------------
 2 files changed, 62 deletions(-)

diff --git a/debian/patches/ignore_failing_tests_for_the_moment.patch b/debian/patches/ignore_failing_tests_for_the_moment.patch
index ba76818..7a565ca 100644
--- a/debian/patches/ignore_failing_tests_for_the_moment.patch
+++ b/debian/patches/ignore_failing_tests_for_the_moment.patch
@@ -70,42 +70,3 @@ Description: Exclude failing tests
  	kget            \
  	general-loader  \
  	vschema         \
---- a/test/fastq-loader/Makefile.rej
-+++ /dev/null
-@@ -1,36 +0,0 @@
----- test/fastq-loader/Makefile
--+++ test/fastq-loader/Makefile
--@@ -155,19 +155,19 @@ smalltests: $(TEST_TOOLS)
-- #           4.3 --cache-size        handled correctly
-- 	@echo "running 4.3"; export LD_LIBRARY_PATH=$(LIBDIR);$(BINDIR)/latf-load $(SRCDIR)/input/4.fastq --cache-size 10 -v -o actual/4.1.obj --quality PHRED_33 | grep "Cache size: 10M" >/dev/null
-- #           4.3.1 --cache-size      rejected if invalid
---	$(SMALLRUN) 4.3.1 3 $(SRCDIR)/input/4.fastq --cache-size BIG --quality PHRED_33
--+	# $(SMALLRUN) 4.3.1 3 $(SRCDIR)/input/4.fastq --cache-size BIG --quality PHRED_33
-- #           4.4 --max-rec-count     stops at the specified record #
-- 	$(SMALLRUN) 4.4 0 $(SRCDIR)/input/4.4.fastq --max-rec-count 3 --quality PHRED_33
-- #           4.5 --max-err-count     stops after the specified # of errors
---	$(SMALLRUN) 4.5 3 $(SRCDIR)/input/4.5.fastq --max-err-count 2 --quality PHRED_33
--+	# $(SMALLRUN) 4.5 3 $(SRCDIR)/input/4.5.fastq --max-err-count 2 --quality PHRED_33
-- #           4.5.1 --max-err-pct     fails if % of error records is too high
---	$(SMALLRUN) 4.5.1 3 $(SRCDIR)/input/4.5.1.fastq --quality PHRED_33  --max-err-count 10 --max-err-pct 20
--+	# $(SMALLRUN) 4.5.1 3 $(SRCDIR)/input/4.5.1.fastq --quality PHRED_33  --max-err-count 10 --max-err-pct 20
-- #           4.6 --platform          saves correct value in the PLATFORM column 
-- 	$(SMALLRUN) 4.6 0 $(SRCDIR)/input/4.fastq -p LS454 --quality PHRED_33
-- #           4.6.1 --platform        rejects invalid values
---	$(SMALLRUN) 4.6.1 3 $(SRCDIR)/input/4.fastq -p SOMETHINGELSE --quality PHRED_33
--+	# $(SMALLRUN) 4.6.1 3 $(SRCDIR)/input/4.fastq -p SOMETHINGELSE --quality PHRED_33
-- #           4.7 input file missing
---	$(SMALLRUN) 4.7 3 $(SRCDIR)/input/not_there --quality PHRED_33
--+	# $(SMALLRUN) 4.7 3 $(SRCDIR)/input/not_there --quality PHRED_33
-- #   Gzipped input
-- 	$(SMALLRUN) 5.0 0 $(SRCDIR)/input/5.0.fastq.gz --quality PHRED_33
-- #   Misparsed quality
--@@ -179,7 +179,7 @@ smalltests: $(TEST_TOOLS)
-- #   secondary read numbers other than 3
-- 	$(SMALLRUN) 8.0 0 $(SRCDIR)/input/8.0.fastq --quality PHRED_33
-- #   reject inconsistent secondary read numbers 
---	$(SMALLRUN) 8.1 3 $(SRCDIR)/input/8.1.fastq --quality PHRED_33
--+	# $(SMALLRUN) 8.1 3 $(SRCDIR)/input/8.1.fastq --quality PHRED_33
-- #   newest Illumina tag line variation ("_" instead of " /")
-- 	$(SMALLRUN) 9.0 0 $(SRCDIR)/input/9.0.fastq --quality PHRED_33
-- #   accepting ascii quality values up to 126
diff --git a/debian/patches/set_explicit_path_to_schemata.patch b/debian/patches/set_explicit_path_to_schemata.patch
index 64e458a..3020427 100644
--- a/debian/patches/set_explicit_path_to_schemata.patch
+++ b/debian/patches/set_explicit_path_to_schemata.patch
@@ -188,26 +188,3 @@ Description: In Debian */*.vschema is installed to /usr/lib/ncbi-vdb/
      m_source . OpenStreamEvent();
  
      REQUIRE ( Run ( m_source . MakeSource (), SILENT_RC ( rcVDB, rcMgr, rcCreating, rcSchema, rcNotFound ) ) );
---- a/test/general-loader/test-general-loader.cpp.rej
-+++ /dev/null
-@@ -1,20 +0,0 @@
----- test/general-loader/test-general-loader.cpp
--+++ 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 ) ) );

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/sra-sdk.git