Re: [R-sig-Fedora] No rule to make target all.R, needed by compiler.rdb building R 3.4.1 from source, Scientific Linux release 6.9 (Carbon)

2017-08-23 Thread Tom Callaway 
No, not R's configure, PCRE's configure. The PCRE library that you've built
is missing some functionality.

~tom

On Aug 23, 2017 7:53 PM, "Jaime Alvarez Benayas" <
jalvarezbenay...@sheffield.ac.uk> wrote:

> Hello,
>
> Thanks again. I have checked the configure step, the only messages I get
> containing pcre are:
>
> checking for pcre_fullinfo in -lpcre... yes
> checking pcre.h usability... yes
> checking pcre.h presence... yes
> 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... yes
> checking if PCRE version >= 8.32... yes
> checking whether PCRE support suffices... yes
>
>
> The final status from the command:
>
> R is now configured for x86_64-pc-linux-gnu
>
>   Source directory:  .
>   Installation directory:/fastdata/mbp15ja/R-3.4.1
>
>   C compiler:gcc  -I/usr/local/packages6/
> compilers/gcc/5.4.0/include
>   Fortran 77 compiler:   gfortran  -g -O2
>
>   Default C++ compiler:  g++   -g -O2
>   C++98 compiler:g++  -g -O2
>   C++11 compiler:g++ -std=gnu++11 -g -O2
>   C++14 compiler:g++ -std=gnu++14 -g -O2
>   C++17 compiler:
>   Fortran 90/95 compiler:gfortran -g -O2
>   Obj-C compiler:
>
>   Interfaces supported:  X11, tcltk
>   External libraries:readline, curl
>   Additional capabilities:   PNG, JPEG, NLS, cairo
>   Options enabled:   shared R library, shared BLAS, R profiling
>
>   Capabilities skipped:  TIFF, ICU
>   Options not enabled:   memory profiling
>
>   Recommended packages:  yes
>
>
>
> I haven't seen the JIT message but will give a try at the glibc-devel:
>
>
> Here is the whole log from the configure command
> https://www.dropbox.com/s/m4g2w1hrr2uqldr/configure%20result%20R.txt?dl=0
>
>
>
> -Original Message-
> From: Tom Callaway [mailto:tcall...@redhat.com]
> Sent: miércoles, 23 de agosto de 2017 21:48
> To: Jaime Alvarez Benayas ;
> r-sig-fedora@r-project.org
> Subject: Re: [R-sig-Fedora] No rule to make target all.R, needed by
> compiler.rdb building R 3.4.1 from source, Scientific Linux release 6.9
> (Carbon)
>
>
>
> On 08/23/2017 03:58 PM, Jaime Alvarez Benayas wrote:
> > ../../lib/libR.so: undefined reference to `pcre_assign_jit_stack'
> > ../../lib/libR.so: undefined reference to `pcre_jit_stack_alloc'
> > ../../lib/libR.so: undefined reference to `pcre_free_study'
>
> This is the error. Your PCRE is being built with SUPPORT_JIT undefined.
>
> You should see some warning during the configure phase for PCRE that says
> "JIT support requires pthreads" or something like that. You should get that
> from glibc-devel.
>
> ~tom
>
>
>

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Re: [R-sig-Fedora] No rule to make target all.R, needed by compiler.rdb building R 3.4.1 from source, Scientific Linux release 6.9 (Carbon)

2017-08-23 Thread Jaime Alvarez Benayas 
Hello,

Thanks again. I have checked the configure step, the only messages I get 
containing pcre are:

checking for pcre_fullinfo in -lpcre... yes
checking pcre.h usability... yes
checking pcre.h presence... yes
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... yes
checking if PCRE version >= 8.32... yes
checking whether PCRE support suffices... yes


The final status from the command:

R is now configured for x86_64-pc-linux-gnu

  Source directory:  .
  Installation directory:/fastdata/mbp15ja/R-3.4.1

  C compiler:gcc  
-I/usr/local/packages6/compilers/gcc/5.4.0/include
  Fortran 77 compiler:   gfortran  -g -O2

  Default C++ compiler:  g++   -g -O2
  C++98 compiler:g++  -g -O2
  C++11 compiler:g++ -std=gnu++11 -g -O2
  C++14 compiler:g++ -std=gnu++14 -g -O2
  C++17 compiler:
  Fortran 90/95 compiler:gfortran -g -O2
  Obj-C compiler:

  Interfaces supported:  X11, tcltk
  External libraries:readline, curl
  Additional capabilities:   PNG, JPEG, NLS, cairo
  Options enabled:   shared R library, shared BLAS, R profiling

  Capabilities skipped:  TIFF, ICU
  Options not enabled:   memory profiling

  Recommended packages:  yes



I haven't seen the JIT message but will give a try at the glibc-devel:


Here is the whole log from the configure command
https://www.dropbox.com/s/m4g2w1hrr2uqldr/configure%20result%20R.txt?dl=0



-Original Message-
From: Tom Callaway [mailto:tcall...@redhat.com] 
Sent: miércoles, 23 de agosto de 2017 21:48
To: Jaime Alvarez Benayas ; 
r-sig-fedora@r-project.org
Subject: Re: [R-sig-Fedora] No rule to make target all.R, needed by 
compiler.rdb building R 3.4.1 from source, Scientific Linux release 6.9 (Carbon)



On 08/23/2017 03:58 PM, Jaime Alvarez Benayas wrote:
> ../../lib/libR.so: undefined reference to `pcre_assign_jit_stack'
> ../../lib/libR.so: undefined reference to `pcre_jit_stack_alloc'
> ../../lib/libR.so: undefined reference to `pcre_free_study'

This is the error. Your PCRE is being built with SUPPORT_JIT undefined.

You should see some warning during the configure phase for PCRE that says "JIT 
support requires pthreads" or something like that. You should get that from 
glibc-devel.

~tom

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Re: [R-sig-Fedora] No rule to make target all.R, needed by compiler.rdb building R 3.4.1 from source, Scientific Linux release 6.9 (Carbon)

2017-08-23 Thread Tom Callaway 


On 08/23/2017 03:58 PM, Jaime Alvarez Benayas wrote:
> ../../lib/libR.so: undefined reference to `pcre_assign_jit_stack'
> ../../lib/libR.so: undefined reference to `pcre_jit_stack_alloc'
> ../../lib/libR.so: undefined reference to `pcre_free_study'

This is the error. Your PCRE is being built with SUPPORT_JIT undefined.

You should see some warning during the configure phase for PCRE that
says "JIT support requires pthreads" or something like that. You should
get that from glibc-devel.

~tom

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Re: [R-sig-Fedora] No rule to make target all.R, needed by compiler.rdb building R 3.4.1 from source, Scientific Linux release 6.9 (Carbon)

2017-08-23 Thread Tom Callaway 


On 08/18/2017 01:12 PM, Jaime Alvarez Benayas wrote:
> Hello,
> 
> I am trying to build R from source on Scientific Linux release 6.9
> (Carbon), Linux version 2.6.32-696.3.2.el6.x86_64 (Red Hat 4.4.7-18).

Okay, so the versions of zlib, bzip2, xz, curl, and pcre are too old on
Scientific Linux 6.9 (unless they've updated all of them when I wasn't
looking). That said, I don't think your problem is there.

Why are you calling make -n instead of just make?

~tom

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Re: [R-sig-Fedora] No rule to make target all.R, needed by compiler.rdb building R 3.4.1 from source, Scientific Linux release 6.9 (Carbon)

2017-08-23 Thread Jaime Alvarez Benayas 
Hello,

I am installing R in an environment where I am not admin...

Thanks

-Original Message-
From: Tom Callaway [mailto:tcall...@redhat.com] 
Sent: miércoles, 23 de agosto de 2017 19:42
To: Jaime Alvarez Benayas ; 
r-sig-fedora@r-project.org
Subject: Re: [R-sig-Fedora] No rule to make target all.R, needed by 
compiler.rdb building R 3.4.1 from source, Scientific Linux release 6.9 (Carbon)



On 08/18/2017 01:12 PM, Jaime Alvarez Benayas wrote:
> Hello,
> 
> I am trying to build R from source on Scientific Linux release 6.9 
> (Carbon), Linux version 2.6.32-696.3.2.el6.x86_64 (Red Hat 4.4.7-18).

Before debugging this too far, is there a reason you're building from source as 
opposed to using the R prebuilt packages in EPEL?

~tom

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Re: [R-sig-Fedora] No rule to make target all.R, needed by compiler.rdb building R 3.4.1 from source, Scientific Linux release 6.9 (Carbon)

2017-08-23 Thread Tom Callaway 


On 08/18/2017 01:12 PM, Jaime Alvarez Benayas wrote:
> Hello,
> 
> I am trying to build R from source on Scientific Linux release 6.9
> (Carbon), Linux version 2.6.32-696.3.2.el6.x86_64 (Red Hat 4.4.7-18).

Before debugging this too far, is there a reason you're building from
source as opposed to using the R prebuilt packages in EPEL?

~tom

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Re: [R-sig-Fedora] Error "translateCharUTF8' must be called on a CHARSXP Execution halted"

2017-08-23 Thread Martyn Plummer 
It is difficult to debug this without a reproducible example. 

Do you have, in the file system that you are trying to list, files with
names that are not utf8-encoded?

Martyn

On Wed, 2017-08-23 at 13:12 +0200, Johannes Lips wrote:
> On 23.08.2017 12:02, Braun, Stefan wrote:
> > Dear list,
> > 
> > I installed R 3.3.2 on a Red Hat Linux Enterprise 7.3 machine by
> > adding the EPEL-repository and then installing it via yum.
> > R starts up and seems to be doing fine at first sight. However,
> > when I try to list the files in a directory with the command
> > 
> > files <- list.files(path="/home/username/directory_name/",
> > pattern="*.Rda",, full.names=T, recursive=FALSE)
> > 
> > I get the error
> > 
> > translateCharUTF8' must be called on a CHARSXP
> > Execution halted
> > 
> > On my local windows machine the command works fine.
> > Googling this nothing really comes up except that the installation
> > might be broken. (See http://r.789695.n4.nabble.com/list-files-erro
> > r-message-translateCharUTF8-must-be-called-on-a-CHARSXP-
> > td3250302.html)
> > 
> > The strange thing is, that if I copy and paste the command into R
> > and execute it, it does not work, but if I copy and paste it into R
> > and change that command in a way that should not change its result
> > but only add spaces or something like that it might run. E.g.
> > changing it to
> > 
> > files <- list.files(path = "/home/username/directory_name/",
> > pattern = "*.Rda",, full.names = T, recursive = FALSE)
> > 
> > might work, might not work and return the same error, or might
> > execute but when I then type "files" that might return
> > 
> > [1]Error: 'getCharCE' must be called on a CHARSXP
> > 
> > The sessionInfo commmand gives me:
> > sessionInfo()
> > R version 3.3.2 (2016-10-31)
> > Platform: x86_64-redhat-linux-gnu (64-bit)
> > Running under: Red Hat Enterprise Linux Server 7.3 (Maipo)
> > 
> > locale:
> > [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
> > [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
> > [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
> > [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
> > [9] LC_ADDRESS=C   LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> > 
> > attached base packages:
> > [1] stats graphics  grDevices
> > utils datasets  methods   base
> > 
> > uname -mrs gives me:
> > Linux 3.10.0-514.el7.x86_64 x86_64
> > 
> > Any help would be greatly appreciated.
> > 
> > Best regards,
> > Stefan Braun
> 
> Just for the record, there's the stackoverflow question
> https://stackoverflow.com/questions/45835818/translatecharutf8-must-b
> e-called-on-a-charsxp-execution-halted
> Cheers
> Johannes
> > 
> > [[alternative HTML version deleted]]
> > 
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Re: [R-sig-Fedora] Error "translateCharUTF8' must be called on a CHARSXP Execution halted"

2017-08-23 Thread Johannes Lips 

On 23.08.2017 12:02, Braun, Stefan wrote:

Dear list,

I installed R 3.3.2 on a Red Hat Linux Enterprise 7.3 machine by adding the 
EPEL-repository and then installing it via yum.
R starts up and seems to be doing fine at first sight. However, when I try to 
list the files in a directory with the command

files <- list.files(path="/home/username/directory_name/", pattern="*.Rda",, 
full.names=T, recursive=FALSE)

I get the error

translateCharUTF8' must be called on a CHARSXP
Execution halted

On my local windows machine the command works fine.
Googling this nothing really comes up except that the installation might be 
broken. (See 
http://r.789695.n4.nabble.com/list-files-error-message-translateCharUTF8-must-be-called-on-a-CHARSXP-td3250302.html)

The strange thing is, that if I copy and paste the command into R and execute 
it, it does not work, but if I copy and paste it into R and change that command 
in a way that should not change its result but only add spaces or something 
like that it might run. E.g. changing it to

files <- list.files(path = "/home/username/directory_name/", pattern = 
"*.Rda",, full.names = T, recursive = FALSE)

might work, might not work and return the same error, or might execute but when I then 
type "files" that might return

[1]Error: 'getCharCE' must be called on a CHARSXP

The sessionInfo commmand gives me:
sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.3 (Maipo)

locale:
[1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8   LC_NAME=C
[9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

uname -mrs gives me:
Linux 3.10.0-514.el7.x86_64 x86_64

Any help would be greatly appreciated.

Best regards,
Stefan Braun

Just for the record, there's the stackoverflow question
https://stackoverflow.com/questions/45835818/translatecharutf8-must-be-called-on-a-charsxp-execution-halted
Cheers
Johannes


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[R-sig-Fedora] Error "translateCharUTF8' must be called on a CHARSXP Execution halted"

2017-08-23 Thread Braun, Stefan 
Dear list,

I installed R 3.3.2 on a Red Hat Linux Enterprise 7.3 machine by adding the 
EPEL-repository and then installing it via yum.
R starts up and seems to be doing fine at first sight. However, when I try to 
list the files in a directory with the command

files <- list.files(path="/home/username/directory_name/", pattern="*.Rda",, 
full.names=T, recursive=FALSE)

I get the error

translateCharUTF8' must be called on a CHARSXP
Execution halted

On my local windows machine the command works fine.
Googling this nothing really comes up except that the installation might be 
broken. (See 
http://r.789695.n4.nabble.com/list-files-error-message-translateCharUTF8-must-be-called-on-a-CHARSXP-td3250302.html)

The strange thing is, that if I copy and paste the command into R and execute 
it, it does not work, but if I copy and paste it into R and change that command 
in a way that should not change its result but only add spaces or something 
like that it might run. E.g. changing it to

files <- list.files(path = "/home/username/directory_name/", pattern = 
"*.Rda",, full.names = T, recursive = FALSE)

might work, might not work and return the same error, or might execute but when 
I then type "files" that might return

[1]Error: 'getCharCE' must be called on a CHARSXP

The sessionInfo commmand gives me:
sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.3 (Maipo)

locale:
[1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8   LC_NAME=C
[9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

uname -mrs gives me:
Linux 3.10.0-514.el7.x86_64 x86_64

Any help would be greatly appreciated.

Best regards,
Stefan Braun

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