Bug#749367: htslib FTBFS on testing for mips/mipsel
Sure, I will upload the patches.
I am currently working on adapting the changes to the latest upstream version.
Also I have added a minor change to patch '02-fix-alignment.patch',
which you will find attached.
Best Regards
Aleksandar Zlicic
Index: htslib-0.2.0~rc3/sam.c
===
--- htslib-0.2.0~rc3.orig/sam.c
+++ htslib-0.2.0~rc3/sam.c
@@ -7,6 +7,7 @@
#include htslib/sam.h
#include htslib/bgzf.h
#include cram/cram.h
+#include cram/os.h
#include hfile.h
#include htslib/khash.h
@@ -726,18 +727,69 @@ int sam_format1(const bam_hdr_t *h, cons
s = bam_get_aux(b); // aux
while (s b-data + b-l_data) {
uint8_t type, key[2];
+ uint8_t tmpData[8];
+ int j;
key[0] = s[0]; key[1] = s[1];
s += 2; type = *s++;
kputc('\t', str); kputsn((char*)key, 2, str); kputc(':', str);
if (type == 'A') { kputsn(A:, 2, str); kputc(*s, str); ++s; }
else if (type == 'C') { kputsn(i:, 2, str); kputw(*s, str); ++s; }
else if (type == 'c') { kputsn(i:, 2, str); kputw(*(int8_t*)s, str); ++s; }
+#ifdef ALLOW_UAC
else if (type == 'S') { kputsn(i:, 2, str); kputw(*(uint16_t*)s, str); s += 2; }
else if (type == 's') { kputsn(i:, 2, str); kputw(*(int16_t*)s, str); s += 2; }
else if (type == 'I') { kputsn(i:, 2, str); kputuw(*(uint32_t*)s, str); s += 4; }
else if (type == 'i') { kputsn(i:, 2, str); kputw(*(int32_t*)s, str); s += 4; }
else if (type == 'f') { ksprintf(str, f:%g, *(float*)s); s += 4; }
else if (type == 'd') { ksprintf(str, d:%g, *(double*)s); s += 8; }
+#else
+ else if (type == 'S')
+{
+uint16_t *ptmpData = (uint16_t*)tmpData;
+for(j=0;j2;j++) tmpData[j]=s[j];
+kputsn(i:, 2, str);
+kputw(*ptmpData, str);
+s += 2;
+}
+ else if (type == 's')
+{
+int16_t *ptmpData = (int16_t*)tmpData;
+for(j=0;j2;j++) tmpData[j]=s[j];
+kputsn(i:, 2, str);
+kputw(*ptmpData, str);
+s += 2;
+}
+ else if (type == 'I')
+{
+uint32_t *ptmpData = (uint32_t*)tmpData;
+for(j=0;j4;j++) tmpData[j]=s[j];
+kputsn(i:, 2, str);
+kputuw(*ptmpData, str);
+s += 4;
+}
+ else if (type == 'i')
+{
+int32_t *ptmpData = (int32_t*)tmpData;
+for(j=0;j4;j++) tmpData[j]=s[j];
+kputsn(i:, 2, str);
+kputw(*ptmpData, str);
+s += 4;
+}
+ else if (type == 'f')
+{
+float *ptmpData = (float*)tmpData;
+for(j=0;j4;j++) tmpData[j]=s[j];
+ksprintf(str, f:%g, *ptmpData);
+s += 4;
+}
+ else if (type == 'd')
+{
+float *ptmpData = (float*)tmpData;
+for(j=0;j8;j++) tmpData[j]=s[j];
+ksprintf(str, d:%g, *ptmpData);
+s += 8;
+}
+#endif
else if (type == 'Z' || type == 'H') { kputc(type, str); kputc(':', str); while (*s) kputc(*s++, str); ++s; }
else if (type == 'B') {
uint8_t sub_type = *(s++);
@@ -749,11 +801,49 @@ int sam_format1(const bam_hdr_t *h, cons
kputc(',', str);
if ('c' == sub_type) { kputw(*(int8_t*)s, str); ++s; }
else if ('C' == sub_type) { kputw(*(uint8_t*)s, str); ++s; }
+#ifdef ALLOW_UAC
else if ('s' == sub_type) { kputw(*(int16_t*)s, str); s += 2; }
else if ('S' == sub_type) { kputw(*(uint16_t*)s, str); s += 2; }
else if ('i' == sub_type) { kputw(*(int32_t*)s, str); s += 4; }
else if ('I' == sub_type) { kputuw(*(uint32_t*)s, str); s += 4; }
else if ('f' == sub_type) { ksprintf(str, %g, *(float*)s); s += 4; }
+#else
+else if ('s' == sub_type)
+{
+int16_t *ptmpData = (int16_t*)tmpData;
+for(j=0;j2;j++) tmpData[j]=s[j];
+kputw(*ptmpData, str);
+s += 2;
+}
+else if ('S' == sub_type)
+{
+uint16_t *ptmpData = (uint16_t*)tmpData;
+for(j=0;j2;j++) tmpData[j]=s[j];
+kputw(*ptmpData, str);
+s += 2;
+}
+else if ('i' == sub_type)
+{
+int32_t *ptmpData = (int32_t*)tmpData;
+for(j=0;j4;j++) tmpData[j]=s[j];
+kputw(*ptmpData,
Bug#749367: htslib FTBFS on testing for mips/mipsel
Package: htslib
Version: 0.2.0~rc3-1
Tags: sid patch
Severity: important
Justification: FTBFS
User: debian-mips-dev-disc...@lists.alioth.debian.org
Usertags: mips-patch
While trying to build htslib on mips/mipsel, build fails on testing.
On mips, package fails with the following error:
./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.cram.sam_
./test_view -t xx.fa -C xx#unsorted.tmp.bam xx#unsorted.tmp.bam.cram
./test_view -b -D xx#unsorted.tmp.bam.cram xx#unsorted.tmp.bam.cram.bam
./test_view xx#unsorted.tmp.bam.cram.bam xx#unsorted.tmp.bam.cram.bam.sam_
./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_
Successes 235
Failures 5
make[2]: *** [test] Error 1
make[2]: Leaving directory `/«PKGBUILDDIR»'
dh_auto_test: make -j1 test returned exit code 2
make[1]: *** [override_dh_auto_test] Error 2
make[1]: Leaving directory `/«PKGBUILDDIR»'
make: *** [build-arch] Error 2
The reason for that are endianness related issues:
- system endianness is not detected properly
- function which converts multibyte data from big endian byte to little
endian byte order (and vice versa) has errors (this was partially fixed
in latest upstream release).
This is fixed in '01-fix-endianness.patch'.
After applying it, build fails with error:
./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.cram.sam_
./test_view -t xx.fa -C xx#unsorted.tmp.bam xx#unsorted.tmp.bam.cram
./test_view -b -D xx#unsorted.tmp.bam.cram xx#unsorted.tmp.bam.cram.bam
./test_view xx#unsorted.tmp.bam.cram.bam xx#unsorted.tmp.bam.cram.bam.sam_
./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_
make[2]: *** [test] Error 1
Successes 234
Failures 6
make[2]: Leaving directory `/«PKGBUILDDIR»'
dh_auto_test: make -j1 test returned exit code 2
make[1]: *** [override_dh_auto_test] Error 2
make[1]: Leaving directory `/«PKGBUILDDIR»'
make: *** [build-arch] Error 2
The same error appears on mipsel.
Reason for this is that unaligned memory access is not handled well
for achitectures that don't allow unaligned access, which causes bus errors
on both mips and mipsel.
This is fixed in '02-fix-alignment.patch'.
With these patches applied I have successfully built htslib on mips/mipsel.
Could you please consider including this patch?
Best regards,
Aleksandar Zlicic
--- a/cram/cram_encode.c
+++ b/cram/cram_encode.c
@@ -1858,6 +1858,12 @@
return rg;
}
+static inline int is_big_endian(){
+int x = 0x01;
+char *c = (char*)x;
+return (c[0] != 0x01);
+}
+
/*
* Encodes auxiliary data. Largely duplicated from above, but done so to
* keep it simple and avoid a myriad of version ifs.
@@ -1949,10 +1955,21 @@
case 'B': {
int type = aux[3], blen;
- uint32_t count = (uint32_t)unsigned char *)aux)[4] 0) +
+uint32_t count;
+if(is_big_endian())
+{
+ count = (uint32_t)unsigned char *)aux)[7] 0) +
+ (((unsigned char *)aux)[6] 8) +
+ (((unsigned char *)aux)[5]16) +
+ (((unsigned char *)aux)[4]24));
+}
+else
+{
+ count = (uint32_t)unsigned char *)aux)[4] 0) +
(((unsigned char *)aux)[5] 8) +
(((unsigned char *)aux)[6]16) +
(((unsigned char *)aux)[7]24));
+}
// skip TN field
aux+=3;
--- a/cram/os.h
+++ b/cram/os.h
@@ -88,8 +88,15 @@
* processor type too.
*/
-/* Set by autoconf */
-#define SP_LITTLE_ENDIAN
+#if !defined(SP_BIG_ENDIAN) !defined(SP_LITTLE_ENDIAN)
+
+# if __BYTE_ORDER == __BIG_ENDIAN
+# define SP_BIG_ENDIAN
+#elif __BYTE_ORDER == __LITTLE_ENDIAN
+# define SP_LITTLE_ENDIAN
+#endif
+
+#endif
/* Mac FAT binaries or unknown. Auto detect based on CPU type */
#if !defined(SP_BIG_ENDIAN) !defined(SP_LITTLE_ENDIAN)
--- a/sam.c
+++ b/sam.c
@@ -216,7 +216,12 @@
else return 0;
}
-static void swap_data(const bam1_core_t *c, int l_data, uint8_t *data)
+typedef enum swap_data_rw {
+SWAP_DATA_READ,
+SWAP_DATA_WRITE
+}swap_data_rw_t;
+
+static void swap_data(const bam1_core_t *c, int l_data, uint8_t *data, swap_data_rw_t rw_mode)
{
uint8_t *s;
uint32_t *cigar = (uint32_t*)(data + c-l_qname);
@@ -234,15 +239,23 @@
else if (type == 'Z' || type == 'H') { while (*s) ++s; ++s; }
else if (type == 'B') {
int32_t n, Bsize = aux_type2size(*s);
+ if(SWAP_DATA_READ == rw_mode)
+ {
+ed_swap_4p(s+1);
+ }
memcpy(n, s + 1, 4);
if (Bsize == 2) {
-for (i = 0; i n; i += 2)
+for (i = 0; i n*Bsize; i += 2)
ed_swap_2p(s + 5 + i);
} else if (Bsize == 4) {
-for (i = 0; i n; i += 4)
+for (i = 0; i n*Bsize; i += 4)
ed_swap_4p(s + 5 + i);
}
- ed_swap_4p(s+1);
+ if(SWAP_DATA_WRITE == rw_mode)
+ {
+ed_swap_4p(s+1);
+ }
+ s += (4 + Bsize * n + 1);
}
}
}
@@ -274,7 +287,7 @@
}
if (bgzf_read(fp, b-data, b-l_data) != b-l_data) return -4;
//b-l_aux = b-l_data - c-n_cigar * 4 - c-l_qname - c-l_qseq - (c-l_qseq+1)/2;
- if (fp-is_be) swap_data(c,
Bug#749367: [Debian-med-packaging] Bug#749367: htslib FTBFS on testing for mips/mipsel
Control: severity -1 wishlist (Adujsting severity since this is not a regression). Le Mon, May 26, 2014 at 03:53:17PM +, Aleksandar Zlicic a écrit : Package: htslib Version: 0.2.0~rc3-1 Tags: sid patch Severity: important Justification: FTBFS User: debian-mips-dev-disc...@lists.alioth.debian.org Usertags: mips-patch With these patches applied I have successfully built htslib on mips/mipsel. Hi, can you sumbit the patches in upstream's issue tracker ? On my side do not feel qualified to review them. https://github.com/samtools/htslib/issues Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
