On Wed, Mar 08, 2017 at 04:34:47PM +0100, Ingo Feinerer wrote:
> Dear useRs,
>
> update math/R 3.3.2 -> 3.3.3
>
> - The zlib configure version test logic changed so adapt.
> - Several R packages (e.g. RCpp) profit from a C++11 compiler, so
> mention CXX1X et al. in the README.
> - make package reports
> LIB_DEPENDS devel/libidn not needed for math/R ?
> I am not sure if this is true or not (or what triggered the change).
>
> OK?
>
> Best regards,
> Ingo
Hi Ingo (and list)
As I mentioned in our private conversation, I've been having some issues
with some R packages and W^X. I've been meaning to look at it more
systematically and do a nice write-up for ports@ but haven't had the
time yet. However, this seemed like a good time to bring the issue to
the list.
What I noticed so far is:
- Some packages need W^X (e.g. rJava and V8) to run. If you end up
needing those packages I *think* R needs to be flagged as WX_NEEDED,
since they run "inside" R. Not sure if its worth it to flag R only
because of optional packages, though.
- If you install those packages on a user library instead of on the
system-wide library, you'll need to mount /home (or wherever your
library is) as wxallowed.
- At compile time, some packages run tests with W^X code in them. This
means "configure" will fail, since it detects that binaries can't be
run (for instance it asks if we're cross-compiling). Since packages
are unpacked and compiled in /tmp, this means that at least during
compilation /tmp also needs to be mounted as wxallowed.
As I told you before, I don't know what the correct approach here would
be, but I believe at least a pkg-readme or a install-message would help.
Let me know if I can help and sorry for the messy reporting.
Cheers
Zé
> Index: Makefile
> ===================================================================
> RCS file: /cvs/ports/math/R/Makefile,v
> retrieving revision 1.89
> diff -u -p -r1.89 Makefile
> --- Makefile 4 Nov 2016 11:35:19 -0000 1.89
> +++ Makefile 8 Mar 2017 15:28:29 -0000
> @@ -1,8 +1,7 @@
> # $OpenBSD: Makefile,v 1.89 2016/11/04 11:35:19 sthen Exp $
>
> COMMENT= powerful math/statistics/graphics language
> -DISTNAME= R-3.3.2
> -REVISION= 0
> +DISTNAME= R-3.3.3
>
> SO_VERSION= 32.0
> .for _lib in R Rblas Rlapack
> Index: distinfo
> ===================================================================
> RCS file: /cvs/ports/math/R/distinfo,v
> retrieving revision 1.32
> diff -u -p -r1.32 distinfo
> --- distinfo 1 Nov 2016 16:55:13 -0000 1.32
> +++ distinfo 8 Mar 2017 15:28:29 -0000
> @@ -1,2 +1,2 @@
> -SHA256 (R-3.3.2.tar.gz) = 0pStIen1dPtIKOuzqUuMs09PMEpBaHqZS+AN1BpOUUw=
> -SIZE (R-3.3.2.tar.gz) = 29440670
> +SHA256 (R-3.3.3.tar.gz) = WrdoBTonUIRhj7ZptPuq3MORWJmKh+hGUyOClZC8/Gw=
> +SIZE (R-3.3.3.tar.gz) = 29804326
> Index: patches/patch-configure
> ===================================================================
> RCS file: /cvs/ports/math/R/patches/patch-configure,v
> retrieving revision 1.29
> diff -u -p -r1.29 patch-configure
> --- patches/patch-configure 1 Nov 2016 16:55:13 -0000 1.29
> +++ patches/patch-configure 8 Mar 2017 15:28:29 -0000
> @@ -1,7 +1,7 @@
> $OpenBSD: patch-configure,v 1.29 2016/11/01 16:55:13 feinerer Exp $
>
> ---- configure.orig Mon Oct 24 13:34:26 2016
> -+++ configure Tue Nov 1 09:06:08 2016
> +--- configure.orig Tue Mar 7 13:02:27 2017
> ++++ configure Tue Mar 7 13:03:01 2017
> @@ -35492,8 +35492,8 @@ fi
>
> fi
> @@ -13,12 +13,12 @@ $OpenBSD: patch-configure,v 1.29 2016/11
> if ${r_cv_header_zlib_h+:} false; then :
> $as_echo_n "(cached) " >&6
> else
> -@@ -35510,7 +35510,7 @@ int main() {
> - #ifdef ZLIB_VERSION
> - /* Work around Debian bug: it uses 1.2.3.4 even though there was no such
> - version on the master site zlib.net */
> -- exit(strncmp(ZLIB_VERSION, "1.2.5", 5) < 0);
> -+ exit(strncmp(ZLIB_VERSION, "1.2.3", 5) < 0);
> - #else
> - exit(1);
> - #endif
> +@@ -35508,7 +35508,7 @@ else
> + #include <zlib.h>
> + int main() {
> + #ifdef ZLIB_VERNUM
> +- if (ZLIB_VERNUM < 0x1250) {
> ++ if (ZLIB_VERNUM < 0x1230) {
> + exit(1);
> + }
> + exit(0);
> Index: pkg/PLIST
> ===================================================================
> RCS file: /cvs/ports/math/R/pkg/PLIST,v
> retrieving revision 1.32
> diff -u -p -r1.32 PLIST
> --- pkg/PLIST 1 Nov 2016 16:55:13 -0000 1.32
> +++ pkg/PLIST 8 Mar 2017 15:28:30 -0000
> @@ -1358,6 +1358,9 @@ lib/R/library/survival/doc/compete.R
> lib/R/library/survival/doc/compete.Rnw
> lib/R/library/survival/doc/compete.pdf
> lib/R/library/survival/doc/index.html
> +lib/R/library/survival/doc/multi.R
> +lib/R/library/survival/doc/multi.Rnw
> +lib/R/library/survival/doc/multi.pdf
> lib/R/library/survival/doc/splines.R
> lib/R/library/survival/doc/splines.Rnw
> lib/R/library/survival/doc/splines.pdf
> Index: pkg/README
> ===================================================================
> RCS file: /cvs/ports/math/R/pkg/README,v
> retrieving revision 1.5
> diff -u -p -r1.5 README
> --- pkg/README 19 Aug 2016 07:02:47 -0000 1.5
> +++ pkg/README 8 Mar 2017 15:28:30 -0000
> @@ -26,3 +26,5 @@ E.g., for using recent compilers (packag
>
> CC=egcc -std=gnu99
> CXX=eg++
> +CXX1X=eg++ -std=c++11
> +CXX1XPICFLAGS=-fpic
>
--
