diff options
Diffstat (limited to 'var')
5 files changed, 100 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/bamutil/libstatgen-issue-17.patch b/var/spack/repos/builtin/packages/bamutil/libstatgen-issue-17.patch new file mode 100644 index 0000000000..94758152a2 --- /dev/null +++ b/var/spack/repos/builtin/packages/bamutil/libstatgen-issue-17.patch @@ -0,0 +1,16 @@ +diff --git a/general/Makefile b/general/Makefile +index ed39442..d828c6b 100755 +--- a/libStatGen/general/Makefile ++++ b/libStatGen/general/Makefile +@@ -8,7 +8,10 @@ ifeq ($(UNAME), Linux) + # an error, but allow unused results and variables for the + # time being. + # +- USER_WARNINGS ?= -Werror $(shell if [ X$(CCVERSION) \> X4.2.0 ] ; then echo " -Wno-strict-overflow" ; fi) ++ # Disable format-truncation check because StringBasics specifically tests ++ # to make sure snprintf truncates as expected. ++ USER_WARNINGS ?= -Werror -Wno-format-truncation $(shell if [ X$(CCVERSION) \> X7.0.0 ] ; then echo " -Wno-strict-overflow -Wno-format-truncation" ; elif [ X$(CCVERSION) \> X4.2.0 ] ; then echo " -Wno-strict-overflow" ; fi) ++# USER_WARNINGS ?= -Werror $(shell if [ X$(CCVERSION) \> X4.2.0 ] ; then echo " -Wno-strict-overflow" ; fi) + #-Wno-strict-overflow + # -Wno-unused-variable $(shell if [ X$(CCVERSION) \> X4.2.0 ] ; then echo " -Wno-unused-result" ; fi) + endif diff --git a/var/spack/repos/builtin/packages/bamutil/libstatgen-issue-19.patch b/var/spack/repos/builtin/packages/bamutil/libstatgen-issue-19.patch new file mode 100644 index 0000000000..86beb5c34e --- /dev/null +++ b/var/spack/repos/builtin/packages/bamutil/libstatgen-issue-19.patch @@ -0,0 +1,29 @@ +From 3a10afe08c209dbacc3eca7794a5a8c0a42ee566 Mon Sep 17 00:00:00 2001 +From: jonathonl <jonathonl@users.noreply.github.com> +Date: Thu, 20 Sep 2018 11:57:06 -0400 +Subject: [PATCH] Removes erroneous deletes in Chromosome constructor. + +--- + general/Chromosome.cpp | 2 -- + 1 file changed, 2 deletions(-) + +diff --git a/general/Chromosome.cpp b/general/Chromosome.cpp +index ac2ff5c..2d773e8 100644 +--- a/libStatGen/general/Chromosome.cpp ++++ b/libStatGen/general/Chromosome.cpp +@@ -27,7 +27,6 @@ Chromosome::Chromosome(GenomeSequence* gs, const char* chromosomeName) + Chromosome::Chromosome(const char* genomseSequenceFileName, unsigned int chromosomeIndex, bool isColorSpace) + { + std::string s(genomseSequenceFileName); +- if (this->gs) delete gs; + gs = new GenomeSequence; + assert(gs); + gs->setReferenceName(s); +@@ -39,7 +38,6 @@ Chromosome::Chromosome(const char* genomseSequenceFileName, unsigned int chromos + + Chromosome::Chromosome(const std::string& genomseSequenceFileName, unsigned int chromosomeIndex, bool isColorSpace) + { +- if (this->gs) delete gs; + gs = new GenomeSequence; + assert(gs); + gs->setReferenceName(genomseSequenceFileName); diff --git a/var/spack/repos/builtin/packages/bamutil/libstatgen-issue-7.patch b/var/spack/repos/builtin/packages/bamutil/libstatgen-issue-7.patch new file mode 100644 index 0000000000..8ccc585e27 --- /dev/null +++ b/var/spack/repos/builtin/packages/bamutil/libstatgen-issue-7.patch @@ -0,0 +1,22 @@ +From 2f1876e53ac6c31c8e459a4c4543ab801d1dd705 Mon Sep 17 00:00:00 2001 +From: Jonathon LeFaive <jonathonl@users.noreply.github.com> +Date: Fri, 21 Jul 2017 10:41:10 -0400 +Subject: [PATCH] Fixes #15 + +--- + general/Parameters.cpp | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/general/Parameters.cpp b/general/Parameters.cpp +index 1dc4571..ca2c946 100644 +--- a/libStatGen/general/Parameters.cpp ++++ b/libStatGen/general/Parameters.cpp +@@ -553,7 +553,7 @@ void LongParameters::Status() + int line_len = 0; + + bool legacy_parameters = false; +- bool legacy_count = 0; ++ int legacy_count = 0; + + for (LongParameterList * ptr = list + 1; ptr->description != NULL; ptr++) + if (ptr->type == LP_LEGACY_PARAMETERS) diff --git a/var/spack/repos/builtin/packages/bamutil/package.py b/var/spack/repos/builtin/packages/bamutil/package.py index 73a2d322ca..e256601efd 100644 --- a/var/spack/repos/builtin/packages/bamutil/package.py +++ b/var/spack/repos/builtin/packages/bamutil/package.py @@ -22,6 +22,12 @@ class Bamutil(MakefilePackage): # Looks like this will be fixed in 1.0.14. # https://github.com/statgen/libStatGen/issues/9 patch('libstatgen-issue-9.patch', when='@1.0.13:') + # These are fixed in the standalone libStatGen, + # but bamutil@1.0.13 embeds its own copy, so fix 'em here. + patch('libstatgen-issue-19.patch', when='@1.0.13') + patch('libstatgen-issue-17.patch', when='@1.0.13') + patch('libstatgen-issue-7.patch', when='@1.0.13') + patch('verifybamid-issue-8.patch', when='@1.0.13') parallel = False diff --git a/var/spack/repos/builtin/packages/bamutil/verifybamid-issue-8.patch b/var/spack/repos/builtin/packages/bamutil/verifybamid-issue-8.patch new file mode 100644 index 0000000000..efb14f2f81 --- /dev/null +++ b/var/spack/repos/builtin/packages/bamutil/verifybamid-issue-8.patch @@ -0,0 +1,27 @@ +From 29805376613c680dee344726ce5c583daf11872f Mon Sep 17 00:00:00 2001 +From: mktrost <mktrost@umich.edu> +Date: Tue, 3 Mar 2015 13:30:21 -0500 +Subject: [PATCH] VCF - add missing include for c++11 + +--- + vcf/VcfRecordDiscardRules.h | 6 ++++++ + 1 file changed, 6 insertions(+) + +diff --git a/vcf/VcfRecordDiscardRules.h b/vcf/VcfRecordDiscardRules.h +index 1cc6fa7..53d2509 100644 +--- a/libStatGen/vcf/VcfRecordDiscardRules.h ++++ b/libStatGen/vcf/VcfRecordDiscardRules.h +@@ -19,7 +19,13 @@ + #define __VCF_RECORD_DISCARD_RULES_H__ + + #include <vector> ++ ++#ifdef __GXX_EXPERIMENTAL_CXX0X__ ++#include <unordered_set> ++#else + #include <set> ++#endif ++ + #include <string> + #include "VcfHeader.h" + |