From tom@@@k@||ber@ @end|ng |rom gm@||@com  Fri Mar  1 09:58:16 2019
From: tom@@@k@||ber@ @end|ng |rom gm@||@com (Tomas Kalibera)
Date: Fri, 1 Mar 2019 09:58:16 +0100
Subject: [Rd] pcre problems
In-Reply-To: <CAHHjBM71_c8Gi+OcJVnhxO8JLNceGY5fgNoWVT9dtxEm_gCDVQ@mail.gmail.com>
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Message-ID: <528fb3dd-7e91-b1a0-e372-ffd86cf9129d@gmail.com>

On 3/1/19 9:43 AM, robin hankin wrote:
> 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:

So you can try commenting again the sources that are failing, R should 
be in universe (and --allow-unauthenticated should not be necessary for 
that).

If you still have problems please take it offline, these are already 
Ubuntu/Debain topics, not R (you can also try ubuntu-users). Some 
documentation is here: 
https://help.ubuntu.com/community/Repositories/CommandLine

Best
Tomas

>
> root at 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 at limpet:/etc/apt#
>
>
>
> hankin.robin at gmail.com
>
>
>
> hankin.robin at gmail.com
>
>
>
>
> On Fri, Mar 1, 2019 at 9:19 PM Tomas Kalibera <tomas.kalibera at 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 at gmail.com
>>>
>>>
>>> On Fri, Mar 1, 2019 at 8:47 PM Tomas Kalibera <tomas.kalibera at 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 at gmail.com
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Feb 25, 2019 at 9:39 PM Tomas Kalibera <tomas.kalibera at 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 at gmail.com
>>>>>>>
>>>>>>> ______________________________________________
>>>>>>> R-devel at r-project.org mailing list
>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>



[Rd] pcre problems
Tomas Kalibera