[med-svn] [Git][med-team/kissplice][master] Attempt to fix gcc-10 FTBFS

[Nilesh Patra]

Nilesh Patra pushed to branch master at Debian Med / kissplice


Commits:
7fa562e5 by Nilesh Patra at 2020-10-26T03:25:05+05:30
Attempt to fix gcc-10 FTBFS

- - - - -


2 changed files:

- + debian/patches/gcc10.patch
- debian/patches/series


Changes:

=====================================
debian/patches/gcc10.patch
=====================================
@@ -0,0 +1,87 @@
+--- a/thirdparty/kissreads/include/commons.h
++++ b/thirdparty/kissreads/include/commons.h
+@@ -49,28 +49,28 @@
+ #include<zlib.h>
+ typedef  uint64_t kmer_type;
+ //int artificial_overlap;
+-char comp ['t'+1];
+-char nuc [4];
+-char standard_fasta;
+-char silent;
+-char quality;
+-char only_print;
+-int kmer_size;
+-int size_seeds;
+-int minimal_read_overlap;
+-kmer_type mask_code_seed;
++__attribute__((__common__)) char comp ['t'+1];
++__attribute__((__common__)) char nuc [4];
++__attribute__((__common__)) char standard_fasta;
++__attribute__((__common__)) char silent;
++__attribute__((__common__)) char quality;
++__attribute__((__common__)) char only_print;
++__attribute__((__common__)) int kmer_size;
++__attribute__((__common__)) int size_seeds;
++__attribute__((__common__)) int minimal_read_overlap;
++__attribute__((__common__)) kmer_type mask_code_seed;
+ 
+ #ifdef INPUT_FROM_KISSPLICE
+-int kisspliceKmerSize;
+-int min_overlap;
+-int countingOption;
++__attribute__((__common__)) int kisspliceKmerSize;
++__attribute__((__common__)) int min_overlap;
++__attribute__((__common__)) int countingOption;
+ #endif
+ int valid_character(const char c);
+-int average_size_reads;
+-int nb_event_sets;
+-int number_of_read_sets;
+-int size_before_reads_starting; // see fragment_info.h
+-char * anykmer;
++extern int average_size_reads;
++extern int nb_event_sets;
++__attribute__((__common__)) int number_of_read_sets;
++extern int size_before_reads_starting; // see fragment_info.h
++__attribute__((__common__)) char * anykmer;
+ char **  sort_strings (char ** strings, int number);
+ void * mymalloc(const int size);
+ void * mycalloc(const int size, const int size_2);
+@@ -89,14 +89,14 @@
+ int get_next_sequence_and_comments_for_fastq (gzFile file, char * sequence, char * comment, char * quality, char * line);
+ int get_next_sequence_for_fastq (gzFile file, char * read, char * quality, char * readid, char * qualityid);
+ int number_of_sequences_in_file(gzFile file, char * line);
+-gzFile file;
++__attribute__((__common__)) gzFile file;
+ 
+-uint64_t sum_memory;
+-uint64_t sum_memory_strdup;
++__attribute__((__common__)) uint64_t sum_memory;
++__attribute__((__common__)) uint64_t sum_memory_strdup;
+ 
+-uint64_t  mask_nbseed ;
+-uint64_t  mask_offset_seed; 
+-unsigned int nbits_nbseeds;
++__attribute__((__common__)) uint64_t  mask_nbseed ;
++__attribute__((__common__)) uint64_t  mask_offset_seed; 
++__attribute__((__common__)) unsigned int nbits_nbseeds;
+ 
+ // macro to test if a variable is null (i.e., a malloc failed)
+ #define test_alloc( variable) {	if(variable == NULL){		fprintf(stderr,"cannot allocate memory for variable %s, exit\n",#variable);		exit(1);	}}
+--- a/thirdparty/kissreads/include/fragment_index.h
++++ b/thirdparty/kissreads/include/fragment_index.h
+@@ -49,10 +49,10 @@
+ #include <couple.h>
+ 
+ 
+-int number_of_starters;
+-hash_t seeds; // hash table seed -> (fragment id, position)
+-hash_t seeds_count;
+-couple * seed_table;
++__attribute__((__common__)) int number_of_starters;
++__attribute__((__common__)) hash_t seeds; // hash table seed -> (fragment id, position)
++__attribute__((__common__)) hash_t seeds_count;
++__attribute__((__common__)) couple * seed_table;
+ 
+ p_fragment_info * index_starters_from_input_file (const int k, int nb_events_per_set, const int nb_fragment_per_event, const char input_only_upper, const int index_stride);           // read and store all starters presents in the pointed file. Index by seeds of length k all these starters.
+ 


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
 fix-bcalm-install.patch
 tests-2to3.patch
 spelling.patch
+gcc10.patch



View it on GitLab: https://salsa.debian.org/med-team/kissplice/-/commit/7fa562e547544b6bf14a38fe3fe05bc0be309197

-- 
View it on GitLab: https://salsa.debian.org/med-team/kissplice/-/commit/7fa562e547544b6bf14a38fe3fe05bc0be309197
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20201025/be1d01e9/attachment-0001.html>