Date: Wed, 15 Feb 2012 09:31:04 -0800 From: David Wolfskill <david@catwhisker.org> To: freebsd-ports@freebsd.org Subject: math/R vs. devel/pcre Message-ID: <20120215173104.GJ1780@albert.catwhisker.org>
next in thread | raw e-mail | index | archive | help
--k1BdFSKqAqVdu8k/
Content-Type: text/plain; charset=us-ascii
Content-Disposition: inline
Content-Transfer-Encoding: quoted-printable
I had a problem rebuilding math/R this morning after updating
devel/pcre; I'm wondering if there's something obvious (to folks
other than me) that I did incorrectly.
Absent extenuating circumstances, I update the installed ports on
my laptop daily -- after updating FreeBSD itself -- running stable/8
i386.
I use portmaster as my "weapon of choice" for handling the ports.
Per ports/UPDATING, before updating any other ports this morning,
I ran:
portmaster -w devel/pcre
which completed without incident.
I then ran
portmaster -ad --index
to update everything else.
The list of ports to be updated was:
=3D=3D=3D>>> The following actions will be taken if you choose to proceed:
Upgrade p11-kit-0.10 to p11-kit-0.11
Upgrade perl-5.12.4_3 to perl-5.12.4_4
Upgrade apache-2.2.22_4 to apache-2.2.22_5
Upgrade gimp-app-2.6.11_5,1 to gimp-app-2.6.12,1
Upgrade glib-2.28.8_3 to glib-2.28.8_4
Upgrade iso-codes-3.29 to iso-codes-3.32.2
Upgrade goffice-0.8.17 to goffice-0.8.17_1
Upgrade netpbm-10.35.83 to netpbm-10.35.84
Upgrade php5-5.3.10 to php5-5.3.10_1
Upgrade php5-mysql-5.3.10 to php5-mysql-5.3.10_1
Upgrade php5-session-5.3.10 to php5-session-5.3.10_1
Upgrade php5-xml-5.3.10 to php5-xml-5.3.10_1
Upgrade py27-gimp-app-2.6.11 to py27-gimp-app-2.6.12
Upgrade py27-subversion-1.7.2 to py27-subversion-1.7.3
Upgrade subversion-1.7.2 to subversion-1.7.3
Upgrade R-2.14.1 to R-2.14.1_1
Upgrade gimp-2.6.11,2 to gimp-2.6.12,2
Upgrade help2man-1.40.5 to help2man-1.40.6
Upgrade nmap-5.61.t4 to nmap-5.61.t4_1
Upgrade ted-2.21_3 to ted-2.21_4
Upgrade wireshark-1.6.5 to wireshark-1.6.5_1
=3D=3D=3D>>> Proceed? y/n [y]=20
=3D=3D=3D>>> Starting build for ports that need updating <<<=3D=3D=3D
which (as indicated) I accepted.
All went well up to math/R, the build of which ran for a while, then whined:
=2E..
gcc46 -std=3Dgnu99 -I../../src/extra/bzip2 -I../../src/extra -I. -I../=
../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -p=
ipe -Wl,-rpath=3D/usr/local/lib/gcc46 -fno-strict-aliasing -c version.c -o =
version.o
gcc46 -std=3Dgnu99 -I../../src/extra/bzip2 -I../../src/extra -I. -I../=
../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -p=
ipe -Wl,-rpath=3D/usr/local/lib/gcc46 -fno-strict-aliasing -c vfonts.c -o v=
fonts.o
gfortran46 -fopenmp -fpic -O -Wl,-rpath=3D/usr/local/lib/gcc46 -c xxxpr.f=
-o xxxpr.o
gcc46 -std=3Dgnu99 -fpic -shared -fopenmp -Wl,-rpath=3D/usr/local/lib/gcc46=
-o libR.so CConverters.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o ag=
rep.o apply.o arithmetic.o array.o attrib.o base.o bind.o builtin.o charact=
er.o coerce.o colors.o complex.o connections.o context.o cov.o cum.o dcf.o =
datetime.o debug.o deparse.o deriv.o devices.o dotcode.o dounzip.o dstruct.=
o duplicate.o engine.o envir.o errors.o eval.o format.o fourier.o gevents.o=
gram.o gram-ex.o gramLatex.o gramRd.o graphics.o grep.o identical.o inline=
d.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.=
o main.o mapply.o match.o memory.o model.o names.o objects.o optim.o optimi=
ze.o options.o par.o paste.o platform.o plot.o plot3d.o plotmath.o print.o =
printarray.o printvector.o printutils.o qsort.o random.o raw.o registration=
.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o size.o sort.o sour=
ce.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o=
sysutils.o unique.o util.o version.o vfonts.o xxxpr.o ../unix/Rembedded.o =
../unix/libunix.a ../appl/libappl.a ../nmath/libnmath.a ../extra/bzip2/lib=
bz2.a ../extra/tre/libtre.a -L../../lib -lRblas -lgfortran -lm -lquadma=
th /usr/local/lib/libintl.so -L/usr/local/lib /usr/local/lib/libiconv.so -=
Wl,-rpath -Wl,/usr/local/lib -lreadline -lpcre -llzma -lz -lm -liconv -licu=
uc -licui18n
mkdir /common/ports/math/R/work/R-2.14.1/bin/exec
gcc46 -std=3Dgnu99 -I../../src/extra/bzip2 -I../../src/extra -I. -I../=
../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -p=
ipe -Wl,-rpath=3D/usr/local/lib/gcc46 -fno-strict-aliasing -c Rmain.c -o Rm=
ain.o
gcc46 -std=3Dgnu99 -export-dynamic -fopenmp -Wl,-rpath=3D/usr/local/lib/gcc=
46 -o R.bin Rmain.o -L../../lib -lR -lRblas
=2E./../lib/libR.so: undefined reference to `_pcre_valid_utf8'
collect2: ld returned 1 exit status
*** Error code 1
Stop in /common/ports/math/R/work/R-2.14.1/src/main.
*** Error code 1
Stop in /common/ports/math/R/work/R-2.14.1/src/main.
*** Error code 1
Stop in /common/ports/math/R/work/R-2.14.1/src.
*** Error code 1
Stop in /common/ports/math/R/work/R-2.14.1.
*** Error code 1
Stop in /common/ports/math/R.
*** Error code 1
Stop in /common/ports/math/R.
=3D=3D=3D>>> make failed for math/R
=3D=3D=3D>>> Aborting update
=3D=3D=3D>>> Update for math/R failed
=3D=3D=3D>>> Aborting update
Terminated
[End of log excerpt]
Since I was fairly sure that the remaining ports had no dependency
on math/R, I updated them, then re-tried math/R; symptoms were the
same.
Here's what I have for config options for math/R:
d134(8.2-S)[24] dirs
/usr/ports/math/R=20
d134(8.2-S)[25] make showconfig
=3D=3D=3D> The following configuration options are available for R-2.14.1_1:
ATLAS=3Doff "Use ATLAS instead of BLAS/LAPACK"
ICU=3Don "Use ICU for collation in multibyte locales"
NLS=3Don "Build with NLS support"
PCRE_PORT=3Don "Use PCRE port instead of bundled source"
THREADS=3Don "Build a multithreaded R"
GHOSTSCRIPT=3Don "Enable the [dev2]bitmap() graphics devices"
JPEG=3Don "Enable the jpeg() graphics device"
LETTER_PAPER=3Don "Use US Letter paper"
LIBR=3Don "Install libR and a dynamically-linked R"
PANGOCAIRO=3Don "Enable cairo and pango in graphics devices"
PNG=3Don "Enable the png() graphics device"
TCLTK=3Don "Use Tcl/Tk (for the tcltk package)"
X11=3Don "Enable the X11() graphics device"
INFO_MANUALS=3Don "Install GNU info manuals"
PDF_MANUALS=3Doff "Install PDF manuals (requires TeX)"
=3D=3D=3D> Use 'make config' to modify these settings
d134(8.2-S)[26]=20
Here's "uname -a" output as of the time I was doing the above:
FreeBSD g1-227.catwhisker.org 8.2-STABLE FreeBSD 8.2-STABLE #326 231755M: W=
ed Feb 15 03:52:51 PST 2012 root@g1-227.catwhisker.org:/common/S1/obj/u=
sr/src/sys/CANARY i386
The above work was done within script(1), so I have a typescript
available, if folks would find that useful.
Clues welcome; thanks in advance.
Peace,
david
--=20
David H. Wolfskill david@catwhisker.org
Depriving a girl or boy of an opportunity for education is evil.
See http://www.catwhisker.org/~david/publickey.gpg for my public key.
--k1BdFSKqAqVdu8k/
Content-Type: application/pgp-signature
Content-Disposition: inline
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v2.0.18 (FreeBSD)
iEYEARECAAYFAk8769cACgkQmprOCmdXAD0m8QCfc/9OMLXHn5Fr3fVZdc4HeRsS
KugAnixWnrOqYBikyFOKJZBI0vyP/3HM
=TnK5
-----END PGP SIGNATURE-----
--k1BdFSKqAqVdu8k/--
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?20120215173104.GJ1780>