Re: New: biology/hmmer

2016-11-09 Thread Senthil Kumar M 

Ping. Can anyone commit this please?

Senthil

On Sun, 6 Nov 2016, Senthil Kumar M wrote:

> Hello ports,
> 
> HMMER is used for searching sequence databases for sequence homologs,
> and for making sequence alignments. It implements methods using
> probabilistic models called profile hidden Markov models (profile
> HMMs).  (http://hmmer.org)
> 
> The latest version 3.1b2 compiles and builds without any additional
> patches/errors on OpenBSD, unlike previous versions (see: `h104'
> on:
> https://raw.githubusercontent.com/EddyRivasLab/hmmer/master/documentation/bugs/BUGTRAX.
> 
> HMMER is an indispensable tool for bioinformatics research and it
> would be neat to have it available on OpenBSD.
> 
> I have tested this on amd64, additional tests, comments are welcome.
> 
> Senthil
> 
> 

hmmer.tar.gz
Description: Binary data

CVS: cvs.openbsd.org: ports

2016-11-09 Thread Alexandr Shadchin 
CVSROOT:/cvs
Module name:ports
Changes by: shadc...@cvs.openbsd.org2016/11/09 23:40:49

Modified files:
devel/py-dateutil: Makefile distinfo 
devel/py-dateutil/pkg: PLIST 

Log message:
Update to py-dateutil 2.6.0

Re: krb5-config --libs

2016-11-09 Thread Jeremie Courreges-Anglas 

(The heimdal krb5-config diff is in.)

Jiri B  writes:

> On Tue, Nov 01, 2016 at 03:52:00PM -0400, Jiri B wrote:
>> With the path and my original path I was able to build curl with
>> gssapi and ssl:
>> 
>> $ curl -V
>> curl 7.50.3 (x86_64-unknown-openbsd6.0) libcurl/7.50.3 LibreSSL/2.0.0 
>> zlib/1.2.3 libidn/1.33 nghttp2/1.16.0
>> Protocols: dict file ftp ftps gopher http https imap imaps pop3 pop3s rtsp 
>> smb smbs smtp smtps telnet tftp
>> Features: IDN IPv6 Largefile GSS-API Kerberos SPNEGO NTLM NTLM_WB SSL libz 
>> HTTP2 UnixSockets
>> 
>> Although I still have some issues to tested in our krb env.
>
> It works! I tried this:

[...]

> Will this go in?

What about something like FLAVOR=full, which would also enable support
for ldap and other features?  I can cook a diff if naddy agrees.

-- 
jca | PGP : 0x1524E7EE / 5135 92C1 AD36 5293 2BDF  DDCC 0DFA 74AE 1524 E7EE

CVS: cvs.openbsd.org: ports

2016-11-09 Thread Alexandr Shadchin 
CVSROOT:/cvs
Module name:ports
Changes by: shadc...@cvs.openbsd.org2016/11/09 23:05:53

Modified files:
devel/py-test-mock: Makefile distinfo 
devel/py-test-mock/pkg: PLIST 

Log message:
Update to py-test-mock 1.4.0

CVS: cvs.openbsd.org: ports

2016-11-09 Thread Jeremie Courreges-Anglas 
CVSROOT:/cvs
Module name:ports
Changes by: j...@cvs.openbsd.org2016/11/09 23:01:45

Modified files:
security/heimdal: Makefile 
Added files:
security/heimdal/patches: patch-tools_krb5-config_in 

Log message:
Tweak krb5-config to fix rpath and search /usr/local/lib for libcom_err

Problem reported by Jiri B.

CVS: cvs.openbsd.org: ports

2016-11-09 Thread Jeremie Courreges-Anglas 
CVSROOT:/cvs
Module name:ports
Changes by: j...@cvs.openbsd.org2016/11/09 22:41:53

Modified files:
games/sdlpop   : Makefile 
games/sdlpop/pkg: PLIST 

Log message:
Install Readme.txt, contains documentation about keybindings.

ok robert@ (maintainer)

CVS: cvs.openbsd.org: ports

2016-11-09 Thread Gleydson Soares 
CVSROOT:/cvs
Module name:ports
Changes by: gsoa...@cvs.openbsd.org 2016/11/09 16:14:31

Modified files:
security/stunnel: Makefile distinfo 
security/stunnel/patches: patch-src_ctx_c patch-src_options_c 
  patch-src_verify_c 
  patch-tools_stunnel_conf-sample_in 
Added files:
security/stunnel/patches: patch-src_common_h 
  patch-src_prototypes_h patch-src_ssl_c 
  patch-src_sthreads_c 

Log message:
update to 5.37
OK benoit@

Re: [new] ympd 0.13

2016-11-09 Thread Landry Breuil 
On Tue, Nov 01, 2016 at 05:27:47PM +0100, Landry Breuil wrote:
> Hi,
> 
> because we all need a new MPD web client, here's one written in C, using
> websockets and bootstrap/js, drops privileges to a separate user and
> listens on a local port - see https://www.ympd.org/. Works fine here, nice 
> ideas.

Also tested working fine on macppc, anyone daring to ok this ?

Landry

Re: net/kea: 1.1.0

2016-11-09 Thread Patrik Lundin 
On Mon, Oct 10, 2016 at 12:28:58AM +0200, Patrik Lundin wrote:
> Hello,
> 
> See below for an update to net/kea from 1.0.0 to 1.1.0.
> 

Ping.

-- 
Patrik Lundin

CVS: cvs.openbsd.org: ports

2016-11-09 Thread Alexandr Shadchin 
CVSROOT:/cvs
Module name:ports
Changes by: shadc...@cvs.openbsd.org2016/11/09 12:21:39

Modified files:
devel/py-country: Makefile distinfo 
devel/py-country/pkg: PLIST 

Log message:
Update to py-country 16.11.8

CVS: cvs.openbsd.org: ports

2016-11-09 Thread Alexandr Shadchin 
CVSROOT:/cvs
Module name:ports
Changes by: shadc...@cvs.openbsd.org2016/11/09 12:02:58

Modified files:
devel/py-xdis  : Makefile distinfo 

Log message:
Update to py-xdis 3.2.3

Re: [UPDATE] print/unpaper

2016-11-09 Thread Jiri B 
On Wed, Nov 09, 2016 at 05:14:01PM +0100, Antoine Jacoutot wrote:
> New diff.

Nice, thanks!

It's strange I get failure for all F* and G* tests.

j.

~~~
===
   unpaper 6.1: ./test-suite.log
===

# TOTAL: 19
# PASS:  13
# SKIP:  0
# XFAIL: 1
# FAIL:  5
# XPASS: 0
# ERROR: 0

.. contents:: :depth: 2

FAIL: tests/runtestF1.sh


[F1] Merging 2-page layout into single output page (with input and output 
wildcard).
+ rm -f tests/resultsF11.pbm
+ ./unpaper --end-sheet 1 -v --layout double --input-pages 2 
./tests/imgsrcE%03d.png tests/resultsF1%d.pbm
[image2 @ 0x1467617a6800] Encoder did not produce proper pts, making some up.
unpaper 6.1
License GPLv2: GNU GPL version 2.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

---
Processing sheet #1: ./tests/imgsrcE001.png, ./tests/imgsrcE002.png -> 
tests/resultsF11.pbm
input-files for sheet 1: ./tests/imgsrcE001.png, ./tests/imgsrcE002.png
output-file for sheet 1: tests/resultsF11.pbm
sheet size: 7014x2480
...
noise-filter ... deleted 345 clusters.
blur-filter... deleted 0 pixels.
auto-masking (1753,1240): 0,0,3506,2479 (invalid detection, using full page 
size)
auto-masking (5261,1240): 3508,0,7014,2479 (invalid detection, using full page 
size)
gray-filter... deleted 24840220 pixels.
auto-masking (1753,1240): 0,0,3506,2479 (invalid detection, using full page 
size)
auto-masking (5261,1240): 3508,0,7014,2479 (invalid detection, using full page 
size)
detected rotation left: [0,0,3506,2479]: 0.013963
detected rotation right: [0,0,3506,2479]: -0.045379
rotation average: -0.015708  deviation: 0.041961  rotation-scan-deviation 
(maximum): 0.017453  [0,0,3506,2479]
out of deviation range - NO ROTATING
rotate (1753,1240): 0.00
detected rotation left: [3508,0,7014,2479]: 0.013963
detected rotation right: [3508,0,7014,2479]: -0.045379
rotation average: -0.015708  deviation: 0.041961  rotation-scan-deviation 
(maximum): 0.017453  [3508,0,7014,2479]
out of deviation range - NO ROTATING
rotate (5261,1240): 0.00
auto-masking (1753,1240): 0,0,3506,2479 (invalid detection, using full page 
size)
auto-masking (5261,1240): 3508,0,7014,2479 (invalid detection, using full page 
size)
centering mask [0,0,3506,2479] (1753,1240): 0, 0
centering mask [3508,0,7014,2479] (5261,1240): 0, 0 - NO CENTERING (would shift 
area outside visible image)
border detected: (0,110,3507,71) in [0,0,3507,2479]
border detected: (3507,110,1,71) in [3507,0,7013,2479]
aligning mask [0,110,3506,2408] (0,90): 0, -20
aligning mask [3507,110,7012,2408] (3507,90): 0, -20
writing output.
+ [ -f tests/resultsF11.pbm ]
+ md5sum -c -
+ << EOF 
tests/resultsF11.pbm: FAILED
md5sum: WARNING: 1 computed checksum did NOT match

FAIL: tests/runtestF2.sh


[F2] Merging 2-page layout into single output page (with output wildcard only).
+ rm -f tests/resultsF21.pbm
+ ./unpaper -v --layout double --input-pages 2 ./tests/imgsrcE001.png 
./tests/imgsrcE002.png tests/resultsF2%d.pbm
[image2 @ 0x1166a8bba000] Encoder did not produce proper pts, making some up.
unpaper 6.1
License GPLv2: GNU GPL version 2.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

---
Processing sheet #1: ./tests/imgsrcE001.png, ./tests/imgsrcE002.png -> 
tests/resultsF21.pbm
input-files for sheet 1: ./tests/imgsrcE001.png, ./tests/imgsrcE002.png
output-file for sheet 1: tests/resultsF21.pbm
sheet size: 7014x2480
...
noise-filter ... deleted 345 clusters.
blur-filter... deleted 0 pixels.
auto-masking (1753,1240): 0,0,3506,2479 (invalid detection, using full page 
size)
auto-masking (5261,1240): 3508,0,7014,2479 (invalid detection, using full page 
size)
gray-filter... deleted 24840220 pixels.
auto-masking (1753,1240): 0,0,3506,2479 (invalid detection, using full page 
size)
auto-masking (5261,1240): 3508,0,7014,2479 (invalid detection, using full page 
size)
detected rotation left: [0,0,3506,2479]: 0.013963
detected rotation right: [0,0,3506,2479]: -0.045379
rotation average: -0.015708  deviation: 0.041961  rotation-scan-deviation 
(maximum): 0.017453  [0,0,3506,2479]
out of deviation range - NO ROTATING
rotate (1753,1240): 0.00
detected rotation left: [3508,0,7014,2479]: 0.013963
detected rotation right: [3508,0,7014,2479]: -0.045379
rotation average: -0.015708  deviation: 0.041961  rotation-scan-deviation 
(maximum): 0.017453  [3508,0,7014,2479]
out of deviation range - NO ROTATING
rotate (5261,1240): 0.00
auto-masking (1753,1240): 0,0,3506,2479 (invalid detection, using full page 
size)
auto-masking (5261,1240): 3508,0,7014,2479 (invalid detection, using full page 
size)
centering mask [0,0,3506,2479] (1753,1240): 0, 0
centering mask

Re: openvpn-auth-ldap problem

2016-11-09 Thread Jeremie Courreges-Anglas 
Jeremie Courreges-Anglas  writes:

> "Leclerc, Sebastien"  writes:
>
>>> -Message d'origine-
>>> De : Jeremie Courreges-Anglas [mailto:j...@wxcvbn.org]
>>> Envoyé : 18 octobre 2016 15:29
>>> 
>>> Anyway, is the plugin broken right now, or is that report just about
>>> runtime linker warnings?
>>
>> It is broken, ldap authentication does not work, but is ok with 5.9 amd64.
>
> Does the following patch fix your problem?  Make sure you have the gcc-libs
> package installed before rebuilding and testing.
>
> Here, I can now run ''make test'' successfully, and
>
>   openvpn --config /dev/null --plugin /usr/local/lib/openvpn-auth-ldap.so
>
> doesn't print linker warnings any more.

Rationale: the diff ensures that the plugin is linked against
/usr/lib/libobjc.so.x.y.  x and y will be encoded in the executable's
DT_NEEDED tag, so the correct version will be picked up at runtime even
if /usr/local/lib/libobjc.so sees a version bump.

I think that bumping the major version of /usr/local/lib/libobjc.so
would make sense anyway, as it would reflect the fact that the base and
ports libraries are not compatible.

I'll go ahead with the diff below unless I hear feedback in the next
days.

>
> Index: Makefile
> ===
> RCS file: /cvs/ports/net/openvpn-auth-ldap/Makefile,v
> retrieving revision 1.7
> diff -u -p -r1.7 Makefile
> --- Makefile  1 Oct 2016 11:54:16 -   1.7
> +++ Makefile  1 Nov 2016 17:07:55 -
> @@ -3,7 +3,7 @@
>  COMMENT =LDAP authentication plugin for OpenVPN 2.x
>  
>  VERSION =2.0.3
> -REVISION =   2
> +REVISION =   3
>  DISTNAME =   auth-ldap-${VERSION}
>  PKGNAME =openvpn-${DISTNAME}
>  CATEGORIES = net security
> @@ -22,6 +22,7 @@ MASTER_SITES =  ${MASTER_SITE_GOOGLECODE
>  RUN_DEPENDS =net/openvpn
>  LIB_DEPENDS =databases/openldap
>  BUILD_DEPENDS =  ${RUN_DEPENDS} \
> + devel/check \
>   devel/re2c
>  
>  SEPARATE_BUILD = Yes
> @@ -29,8 +30,11 @@ SEPARATE_BUILD =   Yes
>  CONFIGURE_STYLE =gnu
>  
>  CONFIGURE_ARGS += --prefix=${LOCALBASE} \
> +   --with-check=${LOCALBASE} \
> --with-openldap=${LOCALBASE} \
> --with-openvpn=${LOCALBASE}/include/openvpn
> +
> +TEST_TARGET =test
>  
>  SAMPLES_DIR =${PREFIX}/share/examples/openvpn-auth-ldap
>  
> Index: patches/patch-src_Makefile_in
> ===
> RCS file: patches/patch-src_Makefile_in
> diff -N patches/patch-src_Makefile_in
> --- /dev/null 1 Jan 1970 00:00:00 -
> +++ patches/patch-src_Makefile_in 1 Nov 2016 17:07:55 -
> @@ -0,0 +1,12 @@
> +$OpenBSD$
> +--- src/Makefile.in.orig Fri Sep 15 04:45:57 2006
>  src/Makefile.in  Tue Nov  1 17:52:06 2016
> +@@ -37,7 +37,7 @@ TEST_OBJS= testplugin.o
> + 
> + CFLAGS+=-fPIC $(LDAP_CFLAGS) $(OPENVPN_CFLAGS)
> + OBJCFLAGS+= -fPIC $(LDAP_CFLAGS) $(OPENVPN_CFLAGS)
> +-LIBS+=  $(LDAP_LIBS) $(OBJC_LIBS) $(FLEX_LIBS)
> ++LIBS+=  -L/usr/lib $(LDAP_LIBS) $(OBJC_LIBS) $(FLEX_LIBS)
> + 
> + 
> + INSTALL_LIB=$(INSTALL) -m 755
> Index: patches/patch-tests_Makefile_in
> ===
> RCS file: patches/patch-tests_Makefile_in
> diff -N patches/patch-tests_Makefile_in
> --- /dev/null 1 Jan 1970 00:00:00 -
> +++ patches/patch-tests_Makefile_in   1 Nov 2016 17:07:55 -
> @@ -0,0 +1,12 @@
> +$OpenBSD$
> +--- tests/Makefile.in.orig   Tue Aug  1 05:51:52 2006
>  tests/Makefile.inTue Nov  1 17:52:23 2016
> +@@ -26,7 +26,7 @@ TEST_OBJS= tests.o \
> + CFLAGS+=@CHECK_CFLAGS@ -DTEST_DATA=\"${srcdir}/data\"
> + OBJCFLAGS+= @CHECK_CFLAGS@ -DTEST_DATA=\"${srcdir}/data\"
> + LIBS+=  -lauth-ldap-testing $(OBJC_LIBS) $(LDAP_LIBS) 
> @CHECK_LIBS@
> +-LDFLAGS+=   -L${top_builddir}src $(LIBS)
> ++LDFLAGS+=   -L${top_builddir}/src -L/usr/lib $(LIBS)
> + 
> + # Recompile the tests every time
> + all: tests

-- 
jca | PGP : 0x1524E7EE / 5135 92C1 AD36 5293 2BDF  DDCC 0DFA 74AE 1524 E7EE

Re: [UPDATE] print/unpaper

2016-11-09 Thread Antoine Jacoutot 
> Agreed. And I'm not sure the unpaper.c patch is needed. There's another
> version of the ffmpeg patch at https://github.com/Flameeyes/unpaper/pull/42
> but nothing committed upstream.

That one is definitely better.
It prevents erroring out with:
unpaper: error: unable to open file ./tests/imgsrc001.png: unsupported pixel 
format

> This fixes a bunch of them:
> 
> TEST_DEPENDS=   sysutils/coreutils
> 
> pre-test:
> ln -fs ${LOCALBASE}/bin/gmd5sum ${WRKDIR}/bin/md5sum

Thanks.

New diff.

Index: Makefile
===
RCS file: /cvs/ports/print/unpaper/Makefile,v
retrieving revision 1.4
diff -u -p -u -p -r1.4 Makefile
--- Makefile10 May 2014 07:42:47 -  1.4
+++ Makefile9 Nov 2016 16:13:32 -
@@ -1,32 +1,34 @@
 # $OpenBSD: Makefile,v 1.4 2014/05/10 07:42:47 ajacoutot Exp $
 
-COMMENT=   post-processing tool for scanned paper sheets
+COMMENT=   post-processing tool for scanned paper sheets
 
-DISTNAME=  unpaper-0.3
+DISTNAME=  unpaper-6.1
 
-CATEGORIES=print graphics
+CATEGORIES=print graphics
 
-HOMEPAGE=  http://unpaper.berlios.de/
+HOMEPAGE=  https://www.flameeyes.eu/projects/unpaper
 
-MAINTAINER=Antoine Jacoutot 
+MAINTAINER=Antoine Jacoutot 
 
 # GPLv2
 PERMIT_PACKAGE_CDROM=  Yes
 
-WANTLIB += c m
+WANTLIB += avcodec avformat avutil c m
 
-MASTER_SITES=  ${MASTER_SITE_SOURCEFORGE:=unpaper/}
+MASTER_SITES=  https://www.flameeyes.eu/files/
+EXTRACT_SUFX=  .tar.xz
 
-NO_TEST=   Yes
+BUILD_DEPENDS= textproc/libxslt # xsltproc
+LIB_DEPENDS=   graphics/ffmpeg
+TEST_DEPENDS=  sysutils/coreutils
 
-do-build:
-   cd ${WRKSRC} && \
-   ${CC} ${CFLAGS} -lm -o unpaper src/unpaper.c
+CONFIGURE_STYLE=   gnu
 
-do-install:
-   ${INSTALL_PROGRAM} ${WRKBUILD}/unpaper ${PREFIX}/bin
-   ${INSTALL_DATA_DIR} ${PREFIX}/share/doc/unpaper
-   ${INSTALL_DATA} ${WRKSRC}/README \
-   ${PREFIX}/share/doc/unpaper
+post-install:
+# useless
+   rm -rf ${PREFIX}/share/doc/unpaper
+
+pre-test:
+   ln -fs ${LOCALBASE}/bin/gmd5sum ${WRKDIR}/bin/md5sum
 
 .include 
Index: distinfo
===
RCS file: /cvs/ports/print/unpaper/distinfo,v
retrieving revision 1.2
diff -u -p -u -p -r1.2 distinfo
--- distinfo18 Jan 2015 03:14:58 -  1.2
+++ distinfo9 Nov 2016 16:13:32 -
@@ -1,2 +1,2 @@
-SHA256 (unpaper-0.3.tar.gz) = NDNmQECUK/djiUbiMn5cZBGcYA/eis6Rj0cQn6+95b4=
-SIZE (unpaper-0.3.tar.gz) = 546488
+SHA256 (unpaper-6.1.tar.xz) = I3yE9dpUSz93CYJ/nxLDfDRs3wKbESj7RjP5uvpcuTA=
+SIZE (unpaper-6.1.tar.xz) = 2655724
Index: patches/patch-file_c
===
RCS file: patches/patch-file_c
diff -N patches/patch-file_c
--- /dev/null   1 Jan 1970 00:00:00 -
+++ patches/patch-file_c9 Nov 2016 16:13:32 -
@@ -0,0 +1,28 @@
+$OpenBSD$
+
+https://github.com/Flameeyes/unpaper/pull/42
+
+--- file.c.origSun Oct 26 23:35:38 2014
 file.c Wed Nov  9 16:53:16 2016
+@@ -93,10 +93,21 @@ void loadImage(const char *filename, AVFrame **image) 
+ if (pkt.stream_index != 0)
+ errOutput("unable to open file %s: invalid stream.", filename);
+ 
++while (!got_frame && pkt.data) {
++
++if (pkt.size <= 0) {
++pkt.data = NULL;
++pkt.size = 0;
++}
++
+ ret = avcodec_decode_video2(avctx, frame, _frame, );
+ if (ret < 0) {
+ av_strerror(ret, errbuff, sizeof(errbuff));
+ errOutput("unable to open file %s: %s", filename, errbuff);
++}
++
++pkt.data += ret;
++pkt.size -= ret;
+ }
+ 
+ switch(frame->format) {
Index: patches/patch-tests_runtestG3_sh
===
RCS file: patches/patch-tests_runtestG3_sh
diff -N patches/patch-tests_runtestG3_sh
--- /dev/null   1 Jan 1970 00:00:00 -
+++ patches/patch-tests_runtestG3_sh9 Nov 2016 16:13:32 -
@@ -0,0 +1,12 @@
+$OpenBSD$
+--- tests/runtestG3.sh.origWed Nov  9 17:01:15 2016
 tests/runtestG3.sh Wed Nov  9 17:01:38 2016
+@@ -8,7 +8,7 @@ set -x
+ rm -f tests/resultsG3.pbm
+ touch tests/resultsG3.pbm
+ 
+-./unpaper -v --no-processing 1 ${srcdir:-.}/tests/imgsrc001.png 
tests/resultsG3.pbm
++./unpaper --overwrite -v --no-processing 1 ${srcdir:-.}/tests/imgsrc001.png 
tests/resultsG3.pbm
+ 
+ [ -s tests/resultsG3.pbm ]
+ 
Index: pkg/PLIST
===
RCS file: /cvs/ports/print/unpaper/pkg/PLIST,v
retrieving revision 1.1.1.1
diff -u -p -u -p -r1.1.1.1 PLIST
--- pkg/PLIST   17 Jul 2010 07:59:37 -  1.1.1.1
+++ pkg/PLIST   9 Nov 2016 16:13:32 -
@@ -1,4 +1,3 @@
 @comment $OpenBSD: PLIST,v 1.1.1.1 2010/07/17 07:59:37 ajacoutot Exp $
 @bin bin/unpaper

CVS: cvs.openbsd.org: ports

2016-11-09 Thread Jeremie Courreges-Anglas 
CVSROOT:/cvs
Module name:ports
Changes by: j...@cvs.openbsd.org2016/11/09 08:59:37

Modified files:
net/samba  : Makefile distinfo 
net/samba/patches: patch-buildtools_wafsamba_samba_autoconf_py 
   patch-lib_replace_wscript 
   patch-python_samba_provision___init___py 
   patch-source3_wscript 
net/samba/pkg  : PLIST-main 

Log message:
Update to samba-4.5.1

Changes:
https://www.samba.org/samba/history/samba-4.5.0.html
https://www.samba.org/samba/history/samba-4.5.1.html

powerpc build test kirby@, ok Ian McWilliam

Re: Update: devel/gmp 6.1.1

2016-11-09 Thread Christian Weisgerber 
On 2016-11-02, Christian Weisgerber  wrote:

> This is a long overdue update of devel/gmp to the latest release
> (6.1.1).

Our old version of devel/mpfr does not build against this and also
requires a straightforward update. (See below.)

The lang/gcc/4.9 Ada bootstraps will also need regenerating.  I
have new bootstraps for amd64 and i386 ready; I lack access to other
architectures.  (Should we add libgmp, libmpfr, and libmpc to the
bootstraps?)

I intend to test these changes in a bulk build, but it may be a few
days before I can squeeze one in.


Index: Makefile
===
RCS file: /cvs/ports/devel/mpfr/Makefile,v
retrieving revision 1.17
diff -u -p -r1.17 Makefile
--- Makefile11 Mar 2016 20:28:24 -  1.17
+++ Makefile9 Nov 2016 15:33:38 -
@@ -2,12 +2,10 @@
 
 COMMENT=   library for multiple-precision floating-point computations
 
-DISTNAME=  mpfr-3.1.0
-PKGNAME=   ${DISTNAME}.3# patch level
-SHARED_LIBS=   mpfr1.1 # 5.0
+DISTNAME=  mpfr-3.1.5
+SHARED_LIBS=   mpfr1.2 # 5.5
 CATEGORIES=devel math
 HOMEPAGE=  http://www.mpfr.org/
-REVISION=  0
 
 MAINTAINER=Christian Weisgerber 
 
@@ -15,13 +13,9 @@ MAINTAINER=  Christian Weisgerber =4.2.0
+LIB_DEPENDS=   devel/gmp
 WANTLIB=   gmp
 
 SEPARATE_BUILD=Yes
Index: distinfo
===
RCS file: /cvs/ports/devel/mpfr/distinfo,v
retrieving revision 1.7
diff -u -p -r1.7 distinfo
--- distinfo18 Jan 2015 03:13:19 -  1.7
+++ distinfo9 Nov 2016 15:33:38 -
@@ -1,8 +1,2 @@
-SHA256 (mpfr-3.1.0/mpfr-3.1.0.tar.gz) = 
VKPLEQ8G9ft+sLwcjxewRQTTKu95QP8VDicLo8tcWME=
-SHA256 (mpfr-3.1.0/patch01) = 8vud3WpLLselgOWqjrJ1od/Rcg9SDhDStJEkb0UTwcU=
-SHA256 (mpfr-3.1.0/patch02) = kgXjxBKt0t2ok0atUv6EUtPmhVlfG5c/b/hGUFxZZ+Y=
-SHA256 (mpfr-3.1.0/patch03) = 8JaEmw9dtDL3DwlF02ZkSUPxHrjJUYX95I8n+qwv9As=
-SIZE (mpfr-3.1.0/mpfr-3.1.0.tar.gz) = 1593567
-SIZE (mpfr-3.1.0/patch01) = 1935
-SIZE (mpfr-3.1.0/patch02) = 4502
-SIZE (mpfr-3.1.0/patch03) = 8260
+SHA256 (mpfr-3.1.5.tar.xz) = AV/egrOXn75fg1AZhtMoMxuo3fAIwf89o8I49JygYrw=
+SIZE (mpfr-3.1.5.tar.xz) = 1126668
-- 
Christian "naddy" Weisgerber  na...@mips.inka.de

Re: [UPDATE] print/unpaper

2016-11-09 Thread Stuart Henderson 
On 2016/11/09 16:12, Antoine Jacoutot wrote:
> On Tue, Nov 08, 2016 at 06:56:45PM -0500, Jiri B wrote:
> > Hi,
> > 
> > an update of unpaper, it needs now libav which is part of ffmpeg.
> > 
> > I tooks diffs from pkgsrc who use ffmpeg and not libav directly.
> > I can't comment those diff but it works for me on amd64.
> 
> I don't like adding random patches without an explanation about what they do.

Agreed. And I'm not sure the unpaper.c patch is needed. There's another
version of the ffmpeg patch at https://github.com/Flameeyes/unpaper/pull/42
but nothing committed upstream.

> > I removed README as it was useless anyway and new doc files are
> > markdown-based so I did not include them.
> > 
> > I'v tried my best ;)
> 
> You are probably missing a bdep on textproc/libxslt for xsltproc.
> HOMEPAGE should be set to https://www.flameeyes.eu/projects/unpaper
> NO_TEST sould be removed and oh by the way, all tests fail so you need to 
> have a look at that.
> 
> It's a good start though ;-)

This fixes a bunch of them:

TEST_DEPENDS=   sysutils/coreutils

pre-test:
ln -fs ${LOCALBASE}/bin/gmd5sum ${WRKDIR}/bin/md5sum

Re: pledge gsm

2016-11-09 Thread Jan Stary 
ping

On Sep 18 10:47:16, s...@spacehopper.org wrote:
> That looks better to me but I am swamped with the sqlite3 move and don't
> have time to test at the moment.
> 
> 
> > On Sep 14 16:50:43, h...@stare.cz wrote:
> > > On Sep 13 17:50:12, danj+o...@chown.me wrote:
> > > > And can you add # uses pledge() just before WANTLIB please?
> > > 
> > > OK.
> > > 
> > > On Sep 13 20:16:57, s...@spacehopper.org wrote:
> > > > On 2016/09/13 13:03, Stuart Henderson wrote:
> > > > > 
> > > > > We also often defer pledge until after option parsing, when we have
> > > > > a better idea of what is actually needed: for toast(/untoast/tcat)
> > > > > this would allow a more accurate pledge because we'll then know
> > > > > whether or not it needs filesystem access.
> > > 
> > > See below for a finer pledge():
> > > 
> > > * initially, restrict to "stdio rpath wpath cpath fattr"
> > > * if we are tcat(1), restrict to "stdio rpath"
> > > * if we are just a filter, restrict to "stdio"
> > > 
> > > The "fattr" is for preserving mtime.
> > > 
> > > The following works with these restrictions:
> > > 
> > >  $ toast file
> > >  $ tcat file.gsm > file
> > >  $ untoast file.gsm
> > >  $ toast < file > file.gsm
> > >  $ untoast < file.gsm > file
> > > 
> > >   Jan
> > > 
> > > 
> > > Index: Makefile
> > > ===
> > > RCS file: /cvs/ports/audio/gsm/Makefile,v
> > > retrieving revision 1.45
> > > diff -u -p -r1.45 Makefile
> > > --- Makefile  13 Sep 2016 11:33:28 -  1.45
> > > +++ Makefile  14 Sep 2016 14:48:53 -
> > > @@ -3,6 +3,7 @@
> > >  COMMENT= GSM audio codec library and converter
> > >  
> > >  DISTNAME=gsm-1.0.15
> > > +REVISION=0
> > >  WRKDIST= ${WRKDIR}/gsm-1.0-pl15
> > >  
> > >  SHARED_LIBS= gsm 1.0
> > > @@ -16,6 +17,7 @@ MAINTAINER= Stuart Henderson  > >  # ISC-like
> > >  PERMIT_PACKAGE_CDROM=Yes
> > >  
> > > +# uses pledge(2)
> > >  WANTLIB += c
> > >  
> > >  MASTER_SITES=${HOMEPAGE}
> > > Index: patches/patch-src_toast_c
> > > ===
> > > RCS file: patches/patch-src_toast_c
> > > diff -N patches/patch-src_toast_c
> > > --- /dev/null 1 Jan 1970 00:00:00 -
> > > +++ patches/patch-src_toast_c 14 Sep 2016 14:48:53 -
> > > @@ -0,0 +1,47 @@
> > > +$OpenBSD$
> > > +--- src/toast.c.orig Wed Apr 26 21:14:26 2006
> > >  src/toast.c  Wed Sep 14 14:14:29 2016
> > > +@@ -129,9 +129,22 @@ static void parse_argv0 P1((av0), char * av0 )
> > > +  *  and decode as well.
> > > +  */
> > > + 
> > > +-if (!strncmp(av0, "un", 2)) f_decode = 1;
> > > ++if (pledge("stdio rpath wpath cpath fattr", NULL) == -1) {
> > > ++perror("pledge");
> > > ++exit(1);
> > > ++}
> > > ++
> > > ++if (!strncmp(av0, "un", 2)) {
> > > ++f_decode = 1;
> > > ++}
> > > + if (  (l = strlen(av0)) >= 3 /* strlen("cat") */
> > > +-   && !strcmp( av0 + l - 3, "cat" )) f_cat = f_decode = 1;
> > > ++   && !strcmp( av0 + l - 3, "cat" )) {
> > > ++if (pledge("stdio rpath", NULL) == -1) {
> > > ++perror("pledge");
> > > ++exit(1);
> > > ++}
> > > ++f_cat = f_decode = 1;
> > > ++}
> > > + }
> > > + 
> > > + 
> > > +@@ -793,8 +806,16 @@ int main P2((ac, av), int ac, char **av)
> > > + 
> > > + catch_signals(onintr);
> > > + 
> > > +-if (ac <= 0) process( (char *)0 );
> > > +-else while (ac--) process( *av++ );
> > > ++if (ac <= 0) {
> > > ++if (pledge("stdio", NULL) == -1) {
> > > ++perror("pledge");
> > > ++exit(1);
> > > ++}
> > > ++process( (char *)0 );
> > > ++} else {
> > > ++while (ac--)
> > > ++process( *av++ );
> > > ++}
> > > + 
> > > + exit(0);
> > > + }
> >

Re: [UPDATE] print/unpaper

2016-11-09 Thread Antoine Jacoutot 
On Tue, Nov 08, 2016 at 06:56:45PM -0500, Jiri B wrote:
> Hi,
> 
> an update of unpaper, it needs now libav which is part of ffmpeg.
> 
> I tooks diffs from pkgsrc who use ffmpeg and not libav directly.
> I can't comment those diff but it works for me on amd64.

I don't like adding random patches without an explanation about what they do.

> I removed README as it was useless anyway and new doc files are
> markdown-based so I did not include them.
> 
> I'v tried my best ;)

You are probably missing a bdep on textproc/libxslt for xsltproc.
HOMEPAGE should be set to https://www.flameeyes.eu/projects/unpaper
NO_TEST sould be removed and oh by the way, all tests fail so you need to have 
a look at that.

It's a good start though ;-)

> Index: Makefile
> ===
> RCS file: /cvs/ports/print/unpaper/Makefile,v
> retrieving revision 1.4
> diff -u -p -r1.4 Makefile
> --- Makefile  10 May 2014 07:42:47 -  1.4
> +++ Makefile  8 Nov 2016 23:52:18 -
> @@ -2,31 +2,29 @@
>  
>  COMMENT= post-processing tool for scanned paper sheets
>  
> -DISTNAME=unpaper-0.3
> +DISTNAME=unpaper-6.1
>  
>  CATEGORIES=  print graphics
>  
> -HOMEPAGE=http://unpaper.berlios.de/
> +HOMEPAGE=https://github.com/Flameeyes/unpaper
>  
>  MAINTAINER=  Antoine Jacoutot 
>  
>  # GPLv2
>  PERMIT_PACKAGE_CDROM=Yes
>  
> -WANTLIB += c m
> +WANTLIB += avcodec avformat avutil c m
>  
> -MASTER_SITES=${MASTER_SITE_SOURCEFORGE:=unpaper/}
> +MASTER_SITES=https://www.flameeyes.eu/files/
>  
>  NO_TEST= Yes
> +EXTRACT_SUFX=.tar.xz
>  
> -do-build:
> - cd ${WRKSRC} && \
> - ${CC} ${CFLAGS} -lm -o unpaper src/unpaper.c
> +CONFIGURE_STYLE= gnu
> +LIB_DEPENDS= graphics/ffmpeg
>  
>  do-install:
>   ${INSTALL_PROGRAM} ${WRKBUILD}/unpaper ${PREFIX}/bin
> - ${INSTALL_DATA_DIR} ${PREFIX}/share/doc/unpaper
> - ${INSTALL_DATA} ${WRKSRC}/README \
> - ${PREFIX}/share/doc/unpaper
> + ${INSTALL_MAN} ${WRKBUILD}/unpaper.1 ${PREFIX}/man/man1/unpaper.1
>  
>  .include 
> Index: distinfo
> ===
> RCS file: /cvs/ports/print/unpaper/distinfo,v
> retrieving revision 1.2
> diff -u -p -r1.2 distinfo
> --- distinfo  18 Jan 2015 03:14:58 -  1.2
> +++ distinfo  8 Nov 2016 23:52:18 -
> @@ -1,2 +1,2 @@
> -SHA256 (unpaper-0.3.tar.gz) = NDNmQECUK/djiUbiMn5cZBGcYA/eis6Rj0cQn6+95b4=
> -SIZE (unpaper-0.3.tar.gz) = 546488
> +SHA256 (unpaper-6.1.tar.xz) = I3yE9dpUSz93CYJ/nxLDfDRs3wKbESj7RjP5uvpcuTA=
> +SIZE (unpaper-6.1.tar.xz) = 2655724
> Index: patches/patch-file_c
> ===
> RCS file: patches/patch-file_c
> diff -N patches/patch-file_c
> --- /dev/null 1 Jan 1970 00:00:00 -
> +++ patches/patch-file_c  8 Nov 2016 23:52:18 -
> @@ -0,0 +1,92 @@
> +$OpenBSD$
> +
> +From pkgsrc-wip
> +
> +--- file.c.orig  Sun Oct 26 23:35:38 2014
>  file.c   Tue Nov  8 20:13:38 2016
> +@@ -105,7 +105,7 @@ void loadImage(const char *filename, AVFrame **image) 
> + case AV_PIX_FMT_RGB24:
> + case AV_PIX_FMT_MONOBLACK:
> + case AV_PIX_FMT_MONOWHITE:
> +-*image = frame;
> ++*image = av_frame_clone(frame);
> + break;
> + 
> + case AV_PIX_FMT_PAL8:
> +@@ -123,6 +123,10 @@ void loadImage(const char *filename, AVFrame **image) 
> + default:
> + errOutput("unable to open file %s: unsupported pixel format", 
> filename);
> + }
> ++
> ++avcodec_close(avctx);
> ++av_free(avctx);
> ++avformat_close_input();
> + }
> + 
> + 
> +@@ -134,13 +138,14 @@ void loadImage(const char *filename, AVFrame **image) 
> +  * @param type filetype of the image to save
> +  * @return true on success, false on failure
> +  */
> +-void saveImage(char *filename, AVFrame *image, int outputPixFmt) {
> ++void saveImage(char *filename, AVFrame *input, int outputPixFmt) {
> + AVOutputFormat *fmt = NULL;
> + enum AVCodecID output_codec = -1;
> + AVCodec *codec;
> + AVFormatContext *out_ctx;
> + AVCodecContext *codec_ctx;
> + AVStream *video_st;
> ++AVFrame *output = input;
> + int ret;
> + char errbuff[1024];
> + 
> +@@ -174,13 +179,11 @@ void saveImage(char *filename, AVFrame *image, int out
> + break;
> + }
> + 
> +-if ( image->format != outputPixFmt ) {
> +-AVFrame *output;
> +-initImage(, image->width, image->height,
> ++if ( input->format != outputPixFmt ) {
> ++initImage(, input->width, input->height,
> +   outputPixFmt, -1);
> +-copyImageArea(0, 0, image->width, image->height,
> +-  image, 0, 0, output);
> +-image = output;
> ++copyImageArea(0, 0, input->width, input->height,
> ++  input, 0, 0, output);
> + }
> + 
> + codec =

Re: pledge iogen

2016-11-09 Thread Jan Stary 
ping

On Sep 14 19:07:48, h...@stare.cz wrote:
> On Sep 14 16:54:52, h...@stare.cz wrote:
> > Below please find a patch to pledge sysutils/iogen.
> > The "stdio rpath wpath cpath" seems obvious,
> > and the "proc" is for killing. I don't know
> > if the pledge() could somehow be refined.
> 
> The actual diff below.
> 
> ("wpat" was where I was testing with a failing pledge()
> to see if the err() is suitable.)
> 
>   Jan
> 
> 
> Index: Makefile
> ===
> RCS file: /cvs/ports/sysutils/iogen/Makefile,v
> retrieving revision 1.25
> diff -u -p -r1.25 Makefile
> --- Makefile  11 Mar 2016 19:43:45 -  1.25
> +++ Makefile  14 Sep 2016 14:53:29 -
> @@ -3,7 +3,7 @@
>  COMMENT= i/o generator
>  
>  V=   3.1
> -REVISION=2
> +REVISION=3
>  GH_TAGNAME=  IOGEN_${V:S/./_/g}
>  GH_ACCOUNT=  conformal
>  GH_PROJECT=  iogen
> Index: patches/patch-iogen_c
> ===
> RCS file: patches/patch-iogen_c
> diff -N patches/patch-iogen_c
> --- /dev/null 1 Jan 1970 00:00:00 -
> +++ patches/patch-iogen_c 14 Sep 2016 14:53:29 -
> @@ -0,0 +1,13 @@
> +$OpenBSD$
> +--- iogen.c.orig Fri May 18 16:48:16 2007
>  iogen.c  Wed Sep 14 15:42:25 2016
> +@@ -805,6 +805,9 @@ main(int argc, char *argv[])
> + }
> + }
> + 
> ++if (pledge("stdio rpath wpath cpath proc", NULL) == -1)
> ++err(1, "pledge");
> ++
> + err_log(0, "%s test run commences with %u proc(s)",
> + VERSION, nr_proc);
> + err_log(0,

CVS: cvs.openbsd.org: ports

2016-11-09 Thread Jeremie Courreges-Anglas 
CVSROOT:/cvs
Module name:ports
Changes by: j...@cvs.openbsd.org2016/11/09 07:53:00

Modified files:
graphics/imlib2: Makefile distinfo 
graphics/imlib2/pkg: PLIST 
Removed files:
graphics/imlib2/patches: patch-src_lib_ellipse_c 
 patch-src_lib_font_load_c 
 patch-src_lib_image_h 
 patch-src_lib_updates_c 
 patch-src_modules_filters_Makefile_in 
 patch-src_modules_loaders_Makefile_in 
 patch-src_modules_loaders_loader_gif_c 

Log message:
Update to imlib2-1.4.9

Drop patches:
- gcc 2.95
- .a modules support
- CVEs fixed upstream

CVS: cvs.openbsd.org: ports

2016-11-09 Thread Jeremie Courreges-Anglas 
CVSROOT:/cvs
Module name:ports
Changes by: j...@cvs.openbsd.org2016/11/09 07:45:56

Modified files:
devel/py-cparser: Makefile distinfo 
devel/py-cparser/pkg: PLIST 

Log message:
Update to pycparser-2.17

CVS: cvs.openbsd.org: ports

2016-11-09 Thread Gonzalo L . Rodriguez 
CVSROOT:/cvs
Module name:ports
Changes by: gonz...@cvs.openbsd.org 2016/11/09 06:50:22

Modified files:
security/lynis : Makefile distinfo 
security/lynis/pkg: PLIST 

Log message:
Update for Lynis to 2.4.0:

https://www.cisofy.com/changelog/lynis/2.4.0/

OK benoit@

CVS: cvs.openbsd.org: ports

2016-11-09 Thread Stuart Henderson 
CVSROOT:/cvs
Module name:ports
Changes by: st...@cvs.openbsd.org   2016/11/09 06:25:12

Modified files:
comms/fldigi   : Makefile distinfo 

Log message:
update to fldigi-3.23.15, including a fix for libsamplerate change

CVS: cvs.openbsd.org: ports

2016-11-09 Thread Antoine Jacoutot 
CVSROOT:/cvs
Module name:ports
Changes by: ajacou...@cvs.openbsd.org   2016/11/09 06:21:25

Modified files:
sysutils/ruby-puppet/4: Makefile 
sysutils/ruby-puppet/4/pkg: PLIST 

Log message:
VARBASE -> LOCALSTATEDIR.
Don't hardcode /var.
Create the complete hierarchy of @sampled files to allow proper cleanup at
deinstall time.

ok sebastia@ (maintainer)

CVS: cvs.openbsd.org: ports

2016-11-09 Thread Stuart Henderson 
CVSROOT:/cvs
Module name:ports
Changes by: st...@cvs.openbsd.org   2016/11/09 04:58:20

Modified files:
games/chocolate-doom: Makefile 
Added files:
games/chocolate-doom/patches: patch-src_i_sdlsound_c 

Log message:
add upstream patch to unbreak chocolate-doom following libsamplerate update

>From 15b8e6e1e47e4f733f862c16a5c18a3485bd22d4 Mon Sep 17 00:00:00 2001
From: Fabian Greffrath 
Date: Mon, 24 Oct 2016 15:30:18 +0200
Subject: [PATCH] i_sdlsound.c: fix compilation with libsamplerate 0.1.9

CVS: cvs.openbsd.org: ports

2016-11-09 Thread Stuart Henderson 
CVSROOT:/cvs
Module name:ports
Changes by: st...@cvs.openbsd.org   2016/11/09 04:46:28

Modified files:
security/py-cryptography: Makefile distinfo 
security/py-cryptography_vectors: Makefile distinfo 

Log message:
update to py-cryptography 1.5.3

CVS: cvs.openbsd.org: ports

2016-11-09 Thread Antoine Jacoutot 
CVSROOT:/cvs
Module name:ports
Changes by: ajacou...@cvs.openbsd.org   2016/11/09 04:18:37

Modified files:
x11/gnome/mono-gnome: Makefile 
Added files:
x11/gnome/mono-gnome/patches: patch-gconf_GConf_ClientBase_cs 
  patch-gconf_GConf_Client_cs 
  
patch-gconf_GConf_gconf-sharp_dll_config_in 
  patch-gnome_CanvasPathDef_custom 

Log message:
Fix build with mono-gtk2 >=2.12.42.
Fix GConf initialization.

CVS: cvs.openbsd.org: ports

2016-11-09 Thread Antoine Jacoutot 
CVSROOT:/cvs
Module name:ports
Changes by: ajacou...@cvs.openbsd.org   2016/11/09 04:17:02

Modified files:
lang/mono  : Makefile distinfo 

Log message:
Update to mono-4.6.2.6.

ok robert@ (maintainer)

CVS: cvs.openbsd.org: ports

2016-11-09 Thread Kirill Bychkov 
CVSROOT:/cvs
Module name:ports
Changes by: ki...@cvs.openbsd.org   2016/11/09 03:28:19

Modified files:
www/goaccess   : Makefile distinfo 

Log message:
update to goaccess-1.1

[NEW] textproc/lua-lunamark

2016-11-09 Thread Frederic Cambus 
Hi ports@,

Here is a new port: textproc/lua-lunamark

I originally wanted to also ship the bundled tools but they depend on
the 'alt_getopt' module which doesn't work with Lua 5.3 and add a
dependency not otherwise useful for other ports. Same for tests, they
rely on those bundled tools and yet another module. So only packaging
the module, at least for now.

Comments? OK?

>From DESCR:

Lunamark is a Lua module for converting Markdown to other textual formats.
Currently HTML, dzslides, Docbook, ConTeXt, LaTeX, and Groff man are the
supported output formats. The markdown parser is written using a PEG
grammar and can also be modified by the user.

The API is described at http://jgm.github.io/lunamark/doc/


lua-lunamark.tar.gz
Description: application/tar-gz