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biology/smithwaterman: Smith-waterman-gotoh alignment algorithm
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Authored by jwb on Apr 15 2018, 5:25 AM.
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jrm
wen
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rP467402: biology/smithwaterman: Smith-waterman-gotoh alignment algorithm
Summary

biology/smithwaterman: Smith-waterman-gotoh alignment algorithm
Approved by jrm (mentor) or wen (mentor)
Differential to be added to commit message

Test Plan

portlint -AC: looks fine
Passed poudriere on {10.3,11.1}-{amd64,i386}
Tested in production

Diff Detail

Repository
rP FreeBSD ports repository
Lint
Lint Not Applicable
Unit
Tests Not Applicable

Event Timeline

jwb created this revision.Apr 15 2018, 5:25 AM
Herald added a subscriber: mat. · View Herald TranscriptApr 15 2018, 5:25 AM
Harbormaster completed remote builds in B16141: Diff 41477.Apr 15 2018, 5:25 AM
jrm added inline comments.Apr 15 2018, 6:17 AM
biology/smithwaterman/Makefile
4 ↗(On Diff #41477)

Since this is not an upstream version, I think we want PORTVERSION here. Have a look at 'Example 5.9. Exotic Case 2' in the PH.

14 ↗(On Diff #41477)

Single block 'USES and USE_x' block?

USES=		gmake
USE_GITHUB=	yes
GH_ACCOUNT=	ekg
GH_TAGNAME=	2610e259611ae4cde8f03c72499d28f03f6d38a7
USE_LDCONFIG=	yes
jwb updated this revision to Diff 41480.Apr 15 2018, 11:43 AM

I was actually following Example 5.13 on the DISTVERSION.

Attribute the blank line to dain bramage.

Thanks.

Harbormaster completed remote builds in B16142: Diff 41480.Apr 15 2018, 11:43 AM
jrm accepted this revision.Apr 15 2018, 11:48 AM
This revision is now accepted and ready to land.Apr 15 2018, 11:48 AM
Closed by commit rP467402: biology/smithwaterman: Smith-waterman-gotoh alignment algorithm (authored by jwb). · Explain WhyApr 15 2018, 5:46 PM
This revision was automatically updated to reflect the committed changes.

Revision Contents
Changeset List

PathSize
head/
biology/
1 line
smithwaterman/
25 lines
3 lines
files/
100 lines
8 lines
12 lines

Diff 41490

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head/biology/Makefile

Show First 20 Lines • Show All 186 Lines • ▼ Show 20 Lines case LINUX_SYS_linux_clock_nanosleep:
putchar(','); putchar(',');
ip++; ip++;
narg--; narg--;
print_mask_arg0(sysdecode_linux_clock_flags, *ip); print_mask_arg0(sysdecode_linux_clock_flags, *ip);
c = ','; c = ',';
ip++; ip++;
narg--; narg--;
break; break;
case LINUX_SYS_linux_clone:
putchar('(');
print_mask_arg(sysdecode_linux_clone_flags, *ip);
ip++;
narg--;
c = ',';
emasteUnsubmitted
Not Done
Inline Actions

FWIW most (but not all) existing cases seem to follow the pattern

		c = ',';
		ip++;
		narg--;

(i.e., setting 'c' first)

emaste: FWIW most (but not all) existing cases seem to follow the pattern ``` c = ','; ip++; narg…
break;
case LINUX_SYS_linux_kill: case LINUX_SYS_linux_kill:
case LINUX_SYS_linux_tkill: case LINUX_SYS_linux_tkill:
case LINUX_SYS_linux_rt_sigqueueinfo: case LINUX_SYS_linux_rt_sigqueueinfo:
print_number(ip, narg, c); print_number(ip, narg, c);
putchar(','); putchar(',');
print_linux_signal(*ip); print_linux_signal(*ip);
ip++; ip++;
narg--; narg--;
▲ Show 20 Lines • Show All 185 Lines • ▼ Show 20 Lines case LINUX32_SYS_linux_clock_nanosleep:
sysdecode_linux_clockid(stdout, *ip); sysdecode_linux_clockid(stdout, *ip);
putchar(','); putchar(',');
ip++; ip++;
narg--; narg--;
print_mask_arg0(sysdecode_linux_clock_flags, *ip); print_mask_arg0(sysdecode_linux_clock_flags, *ip);
c = ','; c = ',';
ip++; ip++;
narg--; narg--;
break;
case LINUX32_SYS_linux_clone:
putchar('(');
print_mask_arg(sysdecode_linux_clone_flags, *ip);
ip++;
narg--;
c = ',';
break; break;
case LINUX32_SYS_linux_kill: case LINUX32_SYS_linux_kill:
case LINUX32_SYS_linux_tkill: case LINUX32_SYS_linux_tkill:
case LINUX32_SYS_linux_rt_sigqueueinfo: case LINUX32_SYS_linux_rt_sigqueueinfo:
print_number(ip, narg, c); print_number(ip, narg, c);
putchar(','); putchar(',');
print_linux_signal(*ip); print_linux_signal(*ip);
ip++; ip++;
▲ Show 20 Lines • Show All 111 Lines • Show Last 20 Lines
View Options

head/biology/smithwaterman/Makefile

Show First 20 Lines • Show All 186 Lines • ▼ Show 20 Lines case LINUX_SYS_linux_clock_nanosleep:
putchar(','); putchar(',');
ip++; ip++;
narg--; narg--;
print_mask_arg0(sysdecode_linux_clock_flags, *ip); print_mask_arg0(sysdecode_linux_clock_flags, *ip);
c = ','; c = ',';
ip++; ip++;
narg--; narg--;
break; break;
case LINUX_SYS_linux_clone:
putchar('(');
print_mask_arg(sysdecode_linux_clone_flags, *ip);
ip++;
narg--;
c = ',';
emasteUnsubmitted
Not Done
Inline Actions

FWIW most (but not all) existing cases seem to follow the pattern

		c = ',';
		ip++;
		narg--;

(i.e., setting 'c' first)

emaste: FWIW most (but not all) existing cases seem to follow the pattern ``` c = ','; ip++; narg…
break;
case LINUX_SYS_linux_kill: case LINUX_SYS_linux_kill:
case LINUX_SYS_linux_tkill: case LINUX_SYS_linux_tkill:
case LINUX_SYS_linux_rt_sigqueueinfo: case LINUX_SYS_linux_rt_sigqueueinfo:
print_number(ip, narg, c); print_number(ip, narg, c);
putchar(','); putchar(',');
print_linux_signal(*ip); print_linux_signal(*ip);
ip++; ip++;
narg--; narg--;
▲ Show 20 Lines • Show All 185 Lines • ▼ Show 20 Lines case LINUX32_SYS_linux_clock_nanosleep:
sysdecode_linux_clockid(stdout, *ip); sysdecode_linux_clockid(stdout, *ip);
putchar(','); putchar(',');
ip++; ip++;
narg--; narg--;
print_mask_arg0(sysdecode_linux_clock_flags, *ip); print_mask_arg0(sysdecode_linux_clock_flags, *ip);
c = ','; c = ',';
ip++; ip++;
narg--; narg--;
break;
case LINUX32_SYS_linux_clone:
putchar('(');
print_mask_arg(sysdecode_linux_clone_flags, *ip);
ip++;
narg--;
c = ',';
break; break;
case LINUX32_SYS_linux_kill: case LINUX32_SYS_linux_kill:
case LINUX32_SYS_linux_tkill: case LINUX32_SYS_linux_tkill:
case LINUX32_SYS_linux_rt_sigqueueinfo: case LINUX32_SYS_linux_rt_sigqueueinfo:
print_number(ip, narg, c); print_number(ip, narg, c);
putchar(','); putchar(',');
print_linux_signal(*ip); print_linux_signal(*ip);
ip++; ip++;
▲ Show 20 Lines • Show All 111 Lines • Show Last 20 Lines
View Options

head/biology/smithwaterman/distinfo

Show First 20 Lines • Show All 186 Lines • ▼ Show 20 Lines case LINUX_SYS_linux_clock_nanosleep:
putchar(','); putchar(',');
ip++; ip++;
narg--; narg--;
print_mask_arg0(sysdecode_linux_clock_flags, *ip); print_mask_arg0(sysdecode_linux_clock_flags, *ip);
c = ','; c = ',';
ip++; ip++;
narg--; narg--;
break; break;
case LINUX_SYS_linux_clone:
putchar('(');
print_mask_arg(sysdecode_linux_clone_flags, *ip);
ip++;
narg--;
c = ',';
emasteUnsubmitted
Not Done
Inline Actions

FWIW most (but not all) existing cases seem to follow the pattern

		c = ',';
		ip++;
		narg--;

(i.e., setting 'c' first)

emaste: FWIW most (but not all) existing cases seem to follow the pattern ``` c = ','; ip++; narg…
break;
case LINUX_SYS_linux_kill: case LINUX_SYS_linux_kill:
case LINUX_SYS_linux_tkill: case LINUX_SYS_linux_tkill:
case LINUX_SYS_linux_rt_sigqueueinfo: case LINUX_SYS_linux_rt_sigqueueinfo:
print_number(ip, narg, c); print_number(ip, narg, c);
putchar(','); putchar(',');
print_linux_signal(*ip); print_linux_signal(*ip);
ip++; ip++;
narg--; narg--;
▲ Show 20 Lines • Show All 185 Lines • ▼ Show 20 Lines case LINUX32_SYS_linux_clock_nanosleep:
sysdecode_linux_clockid(stdout, *ip); sysdecode_linux_clockid(stdout, *ip);
putchar(','); putchar(',');
ip++; ip++;
narg--; narg--;
print_mask_arg0(sysdecode_linux_clock_flags, *ip); print_mask_arg0(sysdecode_linux_clock_flags, *ip);
c = ','; c = ',';
ip++; ip++;
narg--; narg--;
break;
case LINUX32_SYS_linux_clone:
putchar('(');
print_mask_arg(sysdecode_linux_clone_flags, *ip);
ip++;
narg--;
c = ',';
break; break;
case LINUX32_SYS_linux_kill: case LINUX32_SYS_linux_kill:
case LINUX32_SYS_linux_tkill: case LINUX32_SYS_linux_tkill:
case LINUX32_SYS_linux_rt_sigqueueinfo: case LINUX32_SYS_linux_rt_sigqueueinfo:
print_number(ip, narg, c); print_number(ip, narg, c);
putchar(','); putchar(',');
print_linux_signal(*ip); print_linux_signal(*ip);
ip++; ip++;
▲ Show 20 Lines • Show All 111 Lines • Show Last 20 Lines
View Options

head/biology/smithwaterman/files/Makefile

Show First 20 Lines • Show All 186 Lines • ▼ Show 20 Lines case LINUX_SYS_linux_clock_nanosleep:
putchar(','); putchar(',');
ip++; ip++;
narg--; narg--;
print_mask_arg0(sysdecode_linux_clock_flags, *ip); print_mask_arg0(sysdecode_linux_clock_flags, *ip);
c = ','; c = ',';
ip++; ip++;
narg--; narg--;
break; break;
case LINUX_SYS_linux_clone:
putchar('(');
print_mask_arg(sysdecode_linux_clone_flags, *ip);
ip++;
narg--;
c = ',';
emasteUnsubmitted
Not Done
Inline Actions

FWIW most (but not all) existing cases seem to follow the pattern

		c = ',';
		ip++;
		narg--;

(i.e., setting 'c' first)

emaste: FWIW most (but not all) existing cases seem to follow the pattern ``` c = ','; ip++; narg…
break;
case LINUX_SYS_linux_kill: case LINUX_SYS_linux_kill:
case LINUX_SYS_linux_tkill: case LINUX_SYS_linux_tkill:
case LINUX_SYS_linux_rt_sigqueueinfo: case LINUX_SYS_linux_rt_sigqueueinfo:
print_number(ip, narg, c); print_number(ip, narg, c);
putchar(','); putchar(',');
print_linux_signal(*ip); print_linux_signal(*ip);
ip++; ip++;
narg--; narg--;
▲ Show 20 Lines • Show All 185 Lines • ▼ Show 20 Lines case LINUX32_SYS_linux_clock_nanosleep:
sysdecode_linux_clockid(stdout, *ip); sysdecode_linux_clockid(stdout, *ip);
putchar(','); putchar(',');
ip++; ip++;
narg--; narg--;
print_mask_arg0(sysdecode_linux_clock_flags, *ip); print_mask_arg0(sysdecode_linux_clock_flags, *ip);
c = ','; c = ',';
ip++; ip++;
narg--; narg--;
break;
case LINUX32_SYS_linux_clone:
putchar('(');
print_mask_arg(sysdecode_linux_clone_flags, *ip);
ip++;
narg--;
c = ',';
break; break;
case LINUX32_SYS_linux_kill: case LINUX32_SYS_linux_kill:
case LINUX32_SYS_linux_tkill: case LINUX32_SYS_linux_tkill:
case LINUX32_SYS_linux_rt_sigqueueinfo: case LINUX32_SYS_linux_rt_sigqueueinfo:
print_number(ip, narg, c); print_number(ip, narg, c);
putchar(','); putchar(',');
print_linux_signal(*ip); print_linux_signal(*ip);
ip++; ip++;
▲ Show 20 Lines • Show All 111 Lines • Show Last 20 Lines
View Options

head/biology/smithwaterman/pkg-descr

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head/biology/smithwaterman/pkg-plist

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