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pcre problems

robin hankin-3
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:

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?






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Re: pcre problems

Tomas Kalibera
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?
>
>
>
>
>
>
> [hidden email]
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

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Re: pcre problems

Dirk Eddelbuettel
In reply to this post by robin hankin-3

On 25 February 2019 at 18:25, 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:
|
| 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

That is a front-end tool. I don't even have it installed :)
 
| 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?

Ensure you have the corresponding -dev package. My system is now at the
current Ubuntu 18.10, not the Ubuntu LTS 18.04 you have -- but I have been
building R-devel on it about once every week or other week for years:

edd@rob:~$ COLUMNS=100 dpkg -l libpcre*dev | cut -c-100
Desired=Unknown/Install/Remove/Purge/Hold
| Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
||/ Name                Version        Architecture   Description
+++-===================-==============-==============-===========================================
ii  libpcre3-dev:amd64  2:8.39-11      amd64          Old Perl 5 Compatible Regular Expression Li
edd@rob:~$


Dirk

--
http://dirk.eddelbuettel.com | @eddelbuettel | [hidden email]

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Re: pcre problems

robin hankin-3
In reply to this post by Tomas Kalibera
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

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



[hidden email]




On Mon, Feb 25, 2019 at 9:39 PM Tomas Kalibera <[hidden email]> 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?
> >
> >
> >
> >
> >
> >
> > [hidden email]
> >
> > ______________________________________________
> > [hidden email] mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
>

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Re: pcre problems

Tomas Kalibera
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
>
>
>
> [hidden email]
>
>
>
>
> On Mon, Feb 25, 2019 at 9:39 PM Tomas Kalibera <[hidden email]> 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?
>>>
>>>
>>>
>>>
>>>
>>>
>>> [hidden email]
>>>
>>> ______________________________________________
>>> [hidden email] mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>

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Re: pcre problems

robin hankin-3
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~


[hidden email]


On Fri, Mar 1, 2019 at 8:47 PM Tomas Kalibera <[hidden email]> 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
> >
> >
> >
> > [hidden email]
> >
> >
> >
> >
> > On Mon, Feb 25, 2019 at 9:39 PM Tomas Kalibera <[hidden email]> 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?
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> [hidden email]
> >>>
> >>> ______________________________________________
> >>> [hidden email] mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>
>

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Re: pcre problems

Tomas Kalibera
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 codeĀ  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

>
>
> [hidden email]
>
>
> On Fri, Mar 1, 2019 at 8:47 PM Tomas Kalibera <[hidden email]> 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
>>>
>>>
>>>
>>> [hidden email]
>>>
>>>
>>>
>>>
>>> On Mon, Feb 25, 2019 at 9:39 PM Tomas Kalibera <[hidden email]> 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?
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> [hidden email]
>>>>>
>>>>> ______________________________________________
>>>>> [hidden email] mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel

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Re: pcre problems

robin hankin-3
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@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@limpet:/etc/apt#



[hidden email]



[hidden email]




On Fri, Mar 1, 2019 at 9:19 PM Tomas Kalibera <[hidden email]> 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
>
> >
> >
> > [hidden email]
> >
> >
> > On Fri, Mar 1, 2019 at 8:47 PM Tomas Kalibera <[hidden email]> 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
> >>>
> >>>
> >>>
> >>> [hidden email]
> >>>
> >>>
> >>>
> >>>
> >>> On Mon, Feb 25, 2019 at 9:39 PM Tomas Kalibera <[hidden email]> 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?
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> [hidden email]
> >>>>>
> >>>>> ______________________________________________
> >>>>> [hidden email] mailing list
> >>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>

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Re: pcre problems

Tomas Kalibera
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@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@limpet:/etc/apt#
>
>
>
> [hidden email]
>
>
>
> [hidden email]
>
>
>
>
> On Fri, Mar 1, 2019 at 9:19 PM Tomas Kalibera <[hidden email]> 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
>>
>>>
>>> [hidden email]
>>>
>>>
>>> On Fri, Mar 1, 2019 at 8:47 PM Tomas Kalibera <[hidden email]> 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
>>>>>
>>>>>
>>>>>
>>>>> [hidden email]
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Feb 25, 2019 at 9:39 PM Tomas Kalibera <[hidden email]> 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?
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> [hidden email]
>>>>>>>
>>>>>>> ______________________________________________
>>>>>>> [hidden email] mailing list
>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel