[R-sig-Debian] [Rd] pcre problems
Michael Rutter
m@rutter @end|ng |rom gm@||@com
Fri Mar 1 16:49:28 CET 2019
On Fri, Mar 1, 2019 at 4:17 AM Martin Maechler
<maechler using stat.math.ethz.ch> wrote:
>
> Dear Robin and Tomas,
>
> By changing the CC, I'm hereby trying to move this to
> R-SIG-Debian (Ubuntu a flavor of Debian) where it belongs ...
>
> Martin
>
> >>>>> robin hankin
> >>>>> on Fri, 1 Mar 2019 21:43:07 +1300 writes:
>
> > Still something wrong. I've uncommented the deb-src lines in
> > sources.list as you suggested (and I thought it couldn't hurt to try
> > --allow-unauthenticated as well) and:
>
> > root using limpet:/etc/apt# apt-get update --allow-unauthenticated
> > Hit:1 http://nz.archive.ubuntu.com/ubuntu bionic InRelease
> > Hit:2 http://repo.steampowered.com/steam precise InRelease
> > Hit:3 http://nz.archive.ubuntu.com/ubuntu bionic-updates InRelease
> > Hit:4 http://nz.archive.ubuntu.com/ubuntu bionic-backports InRelease
> > Ign:5 http://cran.rstudio.com/bin/linux/ubuntu bionic/ InRelease
> > Err:6 http://cran.rstudio.com/bin/linux/ubuntu bionic/ Release
> > 404 Not Found [IP: 13.35.146.80 80]
> > Hit:7 https://cloud.r-project.org/bin/linux/ubuntu cosmic-cran35/
> > InRelease
> > Hit:8 http://ppa.launchpad.net/edd/misc/ubuntu bionic InRelease
> > Hit:9 http://security.ubuntu.com/ubuntu bionic-security InRelease
> > Hit:10 http://ppa.launchpad.net/marutter/c2d4u/ubuntu bionic InRelease
> > Ign:11 http://ppa.launchpad.net/marutter/rdev/ubuntu bionic InRelease
> > Hit:12 http://ppa.launchpad.net/marutter/rrutter3.5/ubuntu bionic InRelease
> > Hit:13 http://ppa.launchpad.net/teejee2008/ppa/ubuntu bionic InRelease
> > Err:14 http://ppa.launchpad.net/marutter/rdev/ubuntu bionic Release
> > 404 Not Found [IP: 91.189.95.83 80]
> > Ign:15 http://dl.google.com/linux/chrome/deb stable InRelease
> > Hit:16 http://dl.google.com/linux/chrome/deb stable Release
> > Reading package lists... Done
> > E: The repository 'http://cran.rstudio.com/bin/linux/ubuntu bionic/
> > Release' does not have a Release file.
> > N: Updating from such a repository can't be done securely, and is
> > therefore disabled by default.
> > N: See apt-secure(8) manpage for repository creation and user
> > configuration details.
> > E: The repository 'http://ppa.launchpad.net/marutter/rdev/ubuntu
> > bionic Release' does not have a Release file.
> > N: Updating from such a repository can't be done securely, and is
> > therefore disabled by default.
> > N: See apt-secure(8) manpage for repository creation and user
> > configuration details.
> > root using limpet:/etc/apt#
Leaving the rest of the email chain below for reference. I see two
issues with the above output and your sources.list file:
1. "http://cran.rstudio.com/bin/linux/ubuntu bionic/" is incorrect.
It should be "http://cran.rstudio.com/bin/linux/ubuntu bionic-cran35/"
2. You are mixing Bionic and Cosmic, which we do not recommend.
Michael
>
> > On Fri, Mar 1, 2019 at 9:19 PM Tomas Kalibera <tomas.kalibera using gmail.com> wrote:
> >>
> >> On 3/1/19 9:03 AM, robin hankin wrote:
> >> > OK thanks Tomas, but I get
> >> >
> >> >
> >> > OK~ sudo apt-get build-dep r-base
> >> > Reading package lists... Done
> >> > E: Unable to find a source package for r-base
> >> > OK~
> >>
> >> It seems you need to enable source code repositories on your system
> >> (and then run apt-get update).
> >> You can enable them in /etc/apt/sources.list, uncomment all lines
> >> starting with deb-src.
> >>
> >> Best
> >> Tomas
> >>
> >> >
> >> >
> >> > hankin.robin using gmail.com
> >> >
> >> >
> >> > On Fri, Mar 1, 2019 at 8:47 PM Tomas Kalibera <tomas.kalibera using gmail.com> wrote:
> >> >> On 3/1/19 7:10 AM, robin hankin wrote:
> >> >>> thanks for this guys.
> >> >>>
> >> >>> I only compiled pcre myself as a last resort, because of the
> >> >>> ./configure failure. But AFAICS apt-get reports correct
> >> >>> installation:
> >> >>>
> >> >>> OK~/Downloads/R-devel sudo apt-get install r-base-dev
> >> >>> Reading package lists... Done
> >> >>> Building dependency tree
> >> >>> Reading state information... Done
> >> >>> r-base-dev is already the newest version (3.5.2-1cosmic).
> >> >>> 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
> >> >>> OK~/Downloads/R-devel
> >> >> I would just run this
> >> >>
> >> >> apt-get build-dep r-base
> >> >>
> >> >> that will install all packages needed to _build_ r-base, so including PCRE.
> >> >>
> >> >> Best
> >> >> Tomas
> >> >>
> >> >>> config.log gives me:
> >> >>>
> >> >>> configure:42208: $? = 0
> >> >>> configure:42208: result: yes
> >> >>> configure:42208: checking for pcre.h
> >> >>> configure:42208: result: yes
> >> >>> configure:42208: checking pcre/pcre.h usability
> >> >>> configure:42208: gcc -c -g -O2 -I/usr/local/include conftest.c >&5
> >> >>> conftest.c:289:10: fatal error: pcre/pcre.h: No such file or directory
> >> >>> #include <pcre/pcre.h>
> >> >>> ^~~~~~~~~~~~~
> >> >>> compilation terminated.
> >> >>> configure:42208: $? = 1
> >> >>> configure: failed program was:
> >> >>> | /* confdefs.h */
> >> >>> | #define PACKAGE_NAME "R"
> >> >>> | #define PACKAGE_TARNAME "R"
> >> >>> | #define PACKAGE_VERSION "3
> >> >>>
> >> >>> and
> >> >>>
> >> >>> HAVE_UNISTD_H
> >> >>> | # include <unistd.h>
> >> >>> | #endif
> >> >>> | #include <pcre/pcre.h>
> >> >>> configure:42208: result: no
> >> >>> configure:42208: checking pcre/pcre.h presence
> >> >>> configure:42208: gcc -E -I/usr/local/include conftest.c
> >> >>> conftest.c:256:10: fatal error: pcre/pcre.h: No such file or directory
> >> >>> #include <pcre/pcre.h>
> >> >>> ^~~~~~~~~~~~~
> >> >>> compilation terminated.
> >> >>> configure:42208: $? = 1
> >> >>> configure: failed program was:
> >> >>> | /* confdefs.h */
> >> >>> | #define PACKAGE_NAME "R"
> >> >>> | #define PACKAGE_TARNAME "R"
> >> >>> | #define PACKAGE_VERSION "3.6.0"
> >> >>> | #define PACKAGE_STRING "R 3.6.0"
> >> >>> | #define PACKAGE_BUGREPOR
> >> >>>
> >> >>>
> >> >>>
> >> >>> hankin.robin using gmail.com
> >> >>>
> >> >>>
> >> >>>
> >> >>>
> >> >>> On Mon, Feb 25, 2019 at 9:39 PM Tomas Kalibera <tomas.kalibera using gmail.com> wrote:
> >> >>>> On 2/25/19 6:25 AM, robin hankin wrote:
> >> >>>>> Hi there, ubuntu 18.04.2, trying to compile R-devel 3.6.0, svn 76155.
> >> >>>>>
> >> >>>>> I am having difficulty compiling R. I think I have pcre installed correctly:
> >> >>>> You can use
> >> >>>>
> >> >>>> apt-get build-dep r-base
> >> >>>>
> >> >>>> to install binary Ubuntu packages needed to build R from source,
> >> >>>> including PCRE, so there should be no need to compile PCRE from source.
> >> >>>> If you need for some special reason to compile PCRE from source, please
> >> >>>> see R Admin Manual, section A.1 on how to configure PCRE. The manual
> >> >>>> also says how to set compilation flags for R to look for headers in
> >> >>>> other directories. Sometimes it helps to search the config.log when
> >> >>>> configure fails. If still in trouble, please report how you built PCRE
> >> >>>> and how you told R where to find it, and the relevant part of
> >> >>>> config.log, to maximize chances people could offer useful advice.
> >> >>>>
> >> >>>> Best,
> >> >>>> Tomas
> >> >>>>
> >> >>>>> OK~/Downloads/R-devel pcretest -C
> >> >>>>> PCRE version 8.41 2017-07-05
> >> >>>>> Compiled with
> >> >>>>> 8-bit support
> >> >>>>> UTF-8 support
> >> >>>>> No Unicode properties support
> >> >>>>> No just-in-time compiler support
> >> >>>>> Newline sequence is LF
> >> >>>>> \R matches all Unicode newlines
> >> >>>>> Internal link size = 2
> >> >>>>> POSIX malloc threshold = 10
> >> >>>>> Parentheses nest limit = 250
> >> >>>>> Default match limit = 10000000
> >> >>>>> Default recursion depth limit = 10000000
> >> >>>>> Match recursion uses stack
> >> >>>>> OK~/Downloads/R-devel
> >> >>>>>
> >> >>>>>
> >> >>>>> But ./configure gives me this:
> >> >>>>>
> >> >>>>> [snip]
> >> >>>>> checking for pcre.h... yes
> >> >>>>> checking pcre/pcre.h usability... no
> >> >>>>> checking pcre/pcre.h presence... no
> >> >>>>> checking for pcre/pcre.h... no
> >> >>>>> checking if PCRE version >= 8.20, < 10.0 and has UTF-8 support... no
> >> >>>>> checking whether PCRE support suffices... configure: error: pcre >=
> >> >>>>> 8.20 library and headers are required
> >> >>>>> OK~/Downloads/R-devel
> >> >>>>>
> >> >>>>> can anyone advise?
> >> >>>>>
> >> >>>>>
> >> >>>>>
> >> >>>>>
> >> >>>>>
> >> >>>>>
> >> >>>>> hankin.robin using gmail.com
> >> >>>>>
> >> >>>>> ______________________________________________
> >> >>>>> R-devel using r-project.org mailing list
> >> >>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>
> >>
>
> > ______________________________________________
> > R-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
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