[med-svn] [Git][med-team/spaced][master] 2 commits: fix some build errors
Fabian Klötzl
gitlab at salsa.debian.org
Mon Jul 9 14:41:34 BST 2018
Fabian Klötzl pushed to branch master at Debian Med / spaced
Commits:
0269ac6f by Fabian Klötzl at 2018-07-09T15:13:09+02:00
fix some build errors
- - - - -
2cd54e11 by Fabian Klötzl at 2018-07-09T15:37:48+02:00
patch more signedness issues
- - - - -
5 changed files:
- + debian/patches/0005-fix-absolute-value-of-unsigned.patch
- + debian/patches/0006-include-random-header.patch
- + debian/patches/0007-remove-stray-semicolon.patch
- + debian/patches/0008-fix-some-more-signedness-issues.patch
- debian/patches/series
Changes:
=====================================
debian/patches/0005-fix-absolute-value-of-unsigned.patch
=====================================
--- /dev/null
+++ b/debian/patches/0005-fix-absolute-value-of-unsigned.patch
@@ -0,0 +1,39 @@
+From: =?utf-8?q?Fabian_Kl=C3=B6tzl?= <fabian at kloetzl.info>
+Date: Mon, 9 Jul 2018 14:49:11 +0200
+Subject: fix absolute value of unsigned
+
+---
+ src/patternset.cpp | 19 +++++++------------
+ 1 file changed, 7 insertions(+), 12 deletions(-)
+
+diff --git a/src/patternset.cpp b/src/patternset.cpp
+index 1b3e4f6..d859c92 100644
+--- a/src/patternset.cpp
++++ b/src/patternset.cpp
+@@ -188,19 +188,14 @@ void patternset::CheckParams(){
+ std::swap(max_dontcare,min_dontcare);
+ }
+ if(weight < 2){
+- if(weight < 0){
+- weight = std::abs(weight);
++ if(size != 1){
++ size = 1;
++ update = true;
+ }
+- else{
+- if(size != 1){
+- size = 1;
+- update = true;
+- }
+- if(max_dontcare != 0 || max_dontcare != 0){
+- min_dontcare = 0;
+- max_dontcare = 0;
+- update = true;
+- }
++ if(max_dontcare != 0 || max_dontcare != 0){
++ min_dontcare = 0;
++ max_dontcare = 0;
++ update = true;
+ }
+ }
+ if(weight == 2){
=====================================
debian/patches/0006-include-random-header.patch
=====================================
--- /dev/null
+++ b/debian/patches/0006-include-random-header.patch
@@ -0,0 +1,20 @@
+From: =?utf-8?q?Fabian_Kl=C3=B6tzl?= <fabian at kloetzl.info>
+Date: Mon, 9 Jul 2018 14:50:32 +0200
+Subject: include random header
+
+---
+ src/patternset.cpp | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/src/patternset.cpp b/src/patternset.cpp
+index d859c92..a910b8a 100644
+--- a/src/patternset.cpp
++++ b/src/patternset.cpp
+@@ -18,6 +18,7 @@
+ * @author: Lars Hahn - 12.05.2016, Georg-August-Universitaet Goettingen
+ * @version: 1.2.0 05/2016
+ */
++#include <random>
+ #include "patternset.h"
+
+
=====================================
debian/patches/0007-remove-stray-semicolon.patch
=====================================
--- /dev/null
+++ b/debian/patches/0007-remove-stray-semicolon.patch
@@ -0,0 +1,21 @@
+From: =?utf-8?q?Fabian_Kl=C3=B6tzl?= <fabian at kloetzl.info>
+Date: Mon, 9 Jul 2018 14:51:21 +0200
+Subject: remove stray semicolon
+
+---
+ src/spaced.cc | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/spaced.cc b/src/spaced.cc
+index 649997b..3f46d2e 100644
+--- a/src/spaced.cc
++++ b/src/spaced.cc
+@@ -186,7 +186,7 @@ int main(int argc, char *argv[]){
+ for(unsigned long long i=0; i<n;i++){
+ c=toupper(str[i]);
+ if(c=='>'){
+- while(str[++i]!='\n');
++ while(str[++i]!='\n')
+ seq++;
+ }
+ if(isalpha(c)){
=====================================
debian/patches/0008-fix-some-more-signedness-issues.patch
=====================================
--- /dev/null
+++ b/debian/patches/0008-fix-some-more-signedness-issues.patch
@@ -0,0 +1,80 @@
+From: =?utf-8?q?Fabian_Kl=C3=B6tzl?= <fabian at kloetzl.info>
+Date: Mon, 9 Jul 2018 15:28:43 +0200
+Subject: fix some more signedness issues
+
+---
+ src/patternset.cpp | 8 ++++----
+ src/sort.h | 10 +++++-----
+ 2 files changed, 9 insertions(+), 9 deletions(-)
+
+diff --git a/src/patternset.cpp b/src/patternset.cpp
+index a910b8a..55b9b25 100644
+--- a/src/patternset.cpp
++++ b/src/patternset.cpp
+@@ -456,13 +456,13 @@ bool patternset::VerifyPatternCondition(){
+
+ weight = first_weight;
+
+- min_dontcare -= weight;
+- max_dontcare -= weight;
+-
+- if(min_dontcare < 0 || max_dontcare < 0){
++ if(min_dontcare < weight || max_dontcare < weight){
+ pattern_error = true;
+ }
+
++ min_dontcare -= weight;
++ max_dontcare -= weight;
++
+ return pattern_error;
+ }
+
+diff --git a/src/sort.h b/src/sort.h
+index 86ba729..8edaafd 100644
+--- a/src/sort.h
++++ b/src/sort.h
+@@ -80,7 +80,7 @@ void getFirstBits(vector<unsigned char>&pattern, unsigned char* firstBits, unsig
+ unsigned char p0,p1,p2,p3;
+ p0=pattern[0];p1=pattern[1];p2=pattern[2];p3=pattern[3];
+ if(weight>=4){
+- for(int i=0; i<length;i++){
++ for(unsigned int i=0; i<length;i++){
+ w=0;
+ unsigned char* tmp=&seqData[i+pos];
+ w|=alphabet[*(tmp+p0)] << 6;
+@@ -93,7 +93,7 @@ void getFirstBits(vector<unsigned char>&pattern, unsigned char* firstBits, unsig
+ else if (weight==3){
+ unsigned char p0,p1,p2;
+ p0=pattern[0];p1=pattern[1];p2=pattern[2];
+- for(int i=0; i<length;i++){
++ for(unsigned int i=0; i<length;i++){
+ w=0;
+ unsigned char* tmp=&seqData[i+pos];
+ w|=alphabet[*(tmp+p0)] << 4;
+@@ -105,7 +105,7 @@ void getFirstBits(vector<unsigned char>&pattern, unsigned char* firstBits, unsig
+ else if(weight==2){
+ unsigned char p0,p1;
+ p0=pattern[0];p1=pattern[1];
+- for(int i=0; i<length;i++){
++ for(unsigned int i=0; i<length;i++){
+ w=0;
+ unsigned char* tmp=&seqData[i+pos];
+ w|=alphabet[*(tmp+p0)] << 2;
+@@ -117,7 +117,7 @@ void getFirstBits(vector<unsigned char>&pattern, unsigned char* firstBits, unsig
+ else{
+ unsigned char p0;
+ p0=pattern[0];
+- for(int i=0; i<length;i++){
++ for(unsigned int i=0; i<length;i++){
+ unsigned char* tmp=&seqData[i+pos];
+ w=alphabet[*(tmp+p0)];
+ firstBits[i]=w;
+@@ -217,7 +217,7 @@ void spacedDNA(vector<string>& patternSet, unsigned char* seqData, uint n, int d
+ sequences.back().seqWordEnd=totalSeqLength-(weight+dontCare)+1;
+ seqNum=sequences.size();
+ uint cnt=0;
+- for(uint i=0; i<seqNum;i++){
++ for(int i=0; i<seqNum;i++){
+ uint start=sequences[i].seqStart;
+ uint end=sequences[i].seqEnd-1;
+ sequences[i].revCompStart=cnt+totalSeqLength;
=====================================
debian/patches/series
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,7 @@
0002-Fix-FTBFS-without-OpenMP.patch
0003-Add-autotools-buildsystem.patch
0004-signed.patch
+0005-fix-absolute-value-of-unsigned.patch
+0006-include-random-header.patch
+0007-remove-stray-semicolon.patch
+0008-fix-some-more-signedness-issues.patch
View it on GitLab: https://salsa.debian.org/med-team/spaced/compare/a06a4376dedf082728363932937136ced76a1f87...2cd54e1123894a6f82375a63be9996eb4182d964
--
View it on GitLab: https://salsa.debian.org/med-team/spaced/compare/a06a4376dedf082728363932937136ced76a1f87...2cd54e1123894a6f82375a63be9996eb4182d964
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