R SIG Debian - Dec 2016 - Problems installing tibble (ggplot2) in R running Ubuntu 14.04

Hi,

I am unable to install tibble, a required package for ggplot2 in R. I am 
running R (version 3.3.2 ) in RStudio (version 1.0.44). My OS is ubuntu 
14.04 (64 bits).
I get the same error when running R from the terminal.

Any help would be gretly appreciated.

Kind regards,
Terje

****************
Error messages:
****************
install.packages("tibble")
Installing package into ?/home/terjej/R/x86_64-pc-linux-gnu-library/3.3?
(as ?lib? is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/tibble_1.2.tar.gz'
Content type 'unknown' length 54517 bytes (53 KB)
=================================================downloaded 53 KB

* installing *source* package ?tibble? ...
** package ?tibble? successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG 
-I"/usr/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 
-fstack-protector --param=ssp-buffer-size=4 -Wformat 
-Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o 
RcppExports.o
g++ -I/usr/share/R/include -DNDEBUG 
-I"/usr/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 
-fstack-protector --param=ssp-buffer-size=4 -Wformat 
-Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c matrixToDataFrame.cpp 
-o matrixToDataFrame.o
matrixToDataFrame.cpp: In function ?Rcpp::CharacterVector 
get_names(const Rcpp::Matrix<RTYPE>&, int)?:
matrixToDataFrame.cpp:58:16: error: ?tfm? has not been declared
      names[i] = tfm::format( "V%d", (i+1) ) ;
                 ^
matrixToDataFrame.cpp: In instantiation of ?Rcpp::List 
copy_columns(const Rcpp::Matrix<RTYPE>&) [with int RTYPE = 10; 
Rcpp::List = Rcpp::Vector<19>]?:
matrixToDataFrame.cpp:91:48:   required from here
matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in 
?class Rcpp::Matrix<10>?
      typename Matrix<RTYPE>::ConstColumn column( m.column(j) ) ;
                                          ^
matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in 
?class Rcpp::Matrix<10>?
matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in 
?class Rcpp::Matrix<10>?
matrixToDataFrame.cpp: In instantiation of ?Rcpp::List 
copy_columns(const Rcpp::Matrix<RTYPE>&) [with int RTYPE = 13; 
Rcpp::List = Rcpp::Vector<19>]?:
matrixToDataFrame.cpp:92:48:   required from here
matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in 
?class Rcpp::Matrix<13>?
matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in 
?class Rcpp::Matrix<13>?
matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in 
?class Rcpp::Matrix<13>?
matrixToDataFrame.cpp: In instantiation of ?Rcpp::List 
copy_columns(const Rcpp::Matrix<RTYPE>&) [with int RTYPE = 14; 
Rcpp::List = Rcpp::Vector<19>]?:
matrixToDataFrame.cpp:93:49:   required from here
matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in 
?class Rcpp::Matrix<14>?
matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in 
?class Rcpp::Matrix<14>?
matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in 
?class Rcpp::Matrix<14>?
matrixToDataFrame.cpp: In instantiation of ?Rcpp::List 
copy_columns(const Rcpp::Matrix<RTYPE>&) [with int RTYPE = 15; 
Rcpp::List = Rcpp::Vector<19>]?:
matrixToDataFrame.cpp:94:49:   required from here
matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in 
?class Rcpp::Matrix<15>?
matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in 
?class Rcpp::Matrix<15>?
matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in 
?class Rcpp::Matrix<15>?
matrixToDataFrame.cpp: In instantiation of ?Rcpp::List 
copy_columns(const Rcpp::Matrix<RTYPE>&) [with int RTYPE = 16; 
Rcpp::List = Rcpp::Vector<19>]?:
matrixToDataFrame.cpp:95:48:   required from here
matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in 
?class Rcpp::Matrix<16>?
matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in 
?class Rcpp::Matrix<16>?
matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in 
?class Rcpp::Matrix<16>?
matrixToDataFrame.cpp: In instantiation of ?Rcpp::List 
copy_columns(const Rcpp::Matrix<RTYPE>&) [with int RTYPE = 19; 
Rcpp::List = Rcpp::Vector<19>]?:
matrixToDataFrame.cpp:96:48:   required from here
matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in 
?class Rcpp::Matrix<19>?
matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in 
?class Rcpp::Matrix<19>?
matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in 
?class Rcpp::Matrix<19>?
make: *** [matrixToDataFrame.o] Error 1
ERROR: compilation failed for package ?tibble?
* removing ?/home/terjej/R/x86_64-pc-linux-gnu-library/3.3/tibble?
Warning in install.packages :
   installation of package ?tibble? had non-zero exit status

The downloaded source packages are in
     ?/tmp/RtmpxDCEIv/downloaded_packages?

On 12/19/2016 08:27 AM, Terje J?rgensen wrote:
> Hi,
>
> I am unable to install tibble, a required package for ggplot2 in R. I am
> running R (version 3.3.2 ) in RStudio (version 1.0.44). My OS is ubuntu
> 14.04 (64 bits).
> I get the same error when running R from the terminal.
>
> Any help would be gretly appreciated.
>
> Kind regards,
> Terje
Terje,

The simplest thing to do would be to enable the cran2deb4ubuntu PPA 
(https://launchpad.net/~marutter/+archive/ubuntu/c2d4u) and then you can 
just "sudo apt-get install r-cran-tibble" and be good to go.

Since tibble was built on the PPA, the most likely culprit for your 
issue is that the packages used to build tibble are not up to date. Do 
you have the latest version of Rcpp?

Michael
> ****************
> Error messages:
> ****************
> install.packages("tibble")
> Installing package into ?/home/terjej/R/x86_64-pc-linux-gnu-library/3.3?
> (as ?lib? is unspecified)
> trying URL 'https://cran.rstudio.com/src/contrib/tibble_1.2.tar.gz'
> Content type 'unknown' length 54517 bytes (53 KB)
> =================================================> downloaded 53 KB
>
> * installing *source* package ?tibble? ...
> ** package ?tibble? successfully unpacked and MD5 sums checked
> ** libs
> g++ -I/usr/share/R/include -DNDEBUG
> -I"/usr/lib/R/site-library/Rcpp/include"   -fpic  -g -O2
> -fstack-protector --param=ssp-buffer-size=4 -Wformat
> -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o
> RcppExports.o
> g++ -I/usr/share/R/include -DNDEBUG
> -I"/usr/lib/R/site-library/Rcpp/include"   -fpic  -g -O2
> -fstack-protector --param=ssp-buffer-size=4 -Wformat
> -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c matrixToDataFrame.cpp
> -o matrixToDataFrame.o
> matrixToDataFrame.cpp: In function ?Rcpp::CharacterVector
> get_names(const Rcpp::Matrix<RTYPE>&, int)?:
> matrixToDataFrame.cpp:58:16: error: ?tfm? has not been declared
>      names[i] = tfm::format( "V%d", (i+1) ) ;
>                 ^
> matrixToDataFrame.cpp: In instantiation of ?Rcpp::List
> copy_columns(const Rcpp::Matrix<RTYPE>&) [with int RTYPE = 10;
> Rcpp::List = Rcpp::Vector<19>]?:
> matrixToDataFrame.cpp:91:48:   required from here
> matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in
> ?class Rcpp::Matrix<10>?
>      typename Matrix<RTYPE>::ConstColumn column( m.column(j) ) ;
>                                          ^
> matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in
> ?class Rcpp::Matrix<10>?
> matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in
> ?class Rcpp::Matrix<10>?
> matrixToDataFrame.cpp: In instantiation of ?Rcpp::List
> copy_columns(const Rcpp::Matrix<RTYPE>&) [with int RTYPE = 13;
> Rcpp::List = Rcpp::Vector<19>]?:
> matrixToDataFrame.cpp:92:48:   required from here
> matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in
> ?class Rcpp::Matrix<13>?
> matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in
> ?class Rcpp::Matrix<13>?
> matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in
> ?class Rcpp::Matrix<13>?
> matrixToDataFrame.cpp: In instantiation of ?Rcpp::List
> copy_columns(const Rcpp::Matrix<RTYPE>&) [with int RTYPE = 14;
> Rcpp::List = Rcpp::Vector<19>]?:
> matrixToDataFrame.cpp:93:49:   required from here
> matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in
> ?class Rcpp::Matrix<14>?
> matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in
> ?class Rcpp::Matrix<14>?
> matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in
> ?class Rcpp::Matrix<14>?
> matrixToDataFrame.cpp: In instantiation of ?Rcpp::List
> copy_columns(const Rcpp::Matrix<RTYPE>&) [with int RTYPE = 15;
> Rcpp::List = Rcpp::Vector<19>]?:
> matrixToDataFrame.cpp:94:49:   required from here
> matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in
> ?class Rcpp::Matrix<15>?
> matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in
> ?class Rcpp::Matrix<15>?
> matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in
> ?class Rcpp::Matrix<15>?
> matrixToDataFrame.cpp: In instantiation of ?Rcpp::List
> copy_columns(const Rcpp::Matrix<RTYPE>&) [with int RTYPE = 16;
> Rcpp::List = Rcpp::Vector<19>]?:
> matrixToDataFrame.cpp:95:48:   required from here
> matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in
> ?class Rcpp::Matrix<16>?
> matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in
> ?class Rcpp::Matrix<16>?
> matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in
> ?class Rcpp::Matrix<16>?
> matrixToDataFrame.cpp: In instantiation of ?Rcpp::List
> copy_columns(const Rcpp::Matrix<RTYPE>&) [with int RTYPE = 19;
> Rcpp::List = Rcpp::Vector<19>]?:
> matrixToDataFrame.cpp:96:48:   required from here
> matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in
> ?class Rcpp::Matrix<19>?
> matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in
> ?class Rcpp::Matrix<19>?
> matrixToDataFrame.cpp:71:41: error: no type named ?ConstColumn? in
> ?class Rcpp::Matrix<19>?
> make: *** [matrixToDataFrame.o] Error 1
> ERROR: compilation failed for package ?tibble?
> * removing ?/home/terjej/R/x86_64-pc-linux-gnu-library/3.3/tibble?
> Warning in install.packages :
>   installation of package ?tibble? had non-zero exit status
>
> The downloaded source packages are in
>     ?/tmp/RtmpxDCEIv/downloaded_packages?
>
> _______________________________________________
> R-SIG-Debian mailing list
> R-SIG-Debian at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-debian

Terje,

On 19 December 2016 at 08:43, Michael Rutter wrote:
| The simplest thing to do would be to enable the cran2deb4ubuntu PPA 
| (https://launchpad.net/~marutter/+archive/ubuntu/c2d4u) and then you can 
| just "sudo apt-get install r-cran-tibble" and be good to go.

Seconded.  These binaries are _seriously_ underappreciated.
 
| Since tibble was built on the PPA, the most likely culprit for your 
| issue is that the packages used to build tibble are not up to date. Do 
| you have the latest version of Rcpp?

It is likely something else. 

I just started with a 'plain' Docker container for Ubuntu 14.04, and ran
the
few commands to add CRAN (to get r-base-core and r-base-dev).

I then started R, and asked it to
'install.packages("tibble")'.  Which worked
flawlessly as you would expect.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

On Mon, Dec 19, 2016 at 2:27 PM, Terje J?rgensen <terjej at imr.no>
wrote:
> Hi,
>
> I am unable to install tibble, a required package for ggplot2 in R. I am
> running R (version 3.3.2 ) in RStudio (version 1.0.44). My OS is ubuntu
> 14.04 (64 bits).
I was able to reproduce this problem. What happened is that you
installed "r-cran-rcpp" from the ubuntu repositories, which is a few
years old, and not compatible with the cran version of 'tibble'. You
should either reinstall Rcpp from CRAN, or, install the development
version of 'tibble' which resolves the issue.

On 12 February 2017 at 12:28, Jeroen Ooms wrote:
| On Mon, Dec 19, 2016 at 2:27 PM, Terje J?rgensen <terjej at imr.no>
wrote:
| > Hi,
| >
| > I am unable to install tibble, a required package for ggplot2 in R. I am
| > running R (version 3.3.2 ) in RStudio (version 1.0.44). My OS is ubuntu
| > 14.04 (64 bits).
| 
| I was able to reproduce this problem. What happened is that you
| installed "r-cran-rcpp" from the ubuntu repositories, which is a few
| years old, and not compatible with the cran version of 'tibble'. You
| should either reinstall Rcpp from CRAN, or, install the development
| version of 'tibble' which resolves the issue.

Better still, use the repositories maintained by Michael to get a _wide
variety_ of _current_ packages:

1. Over 3400 packages from CRAN ready to use as binaries:

   root at 092af40cc094:/# apt-cache search r-cran- | wc -l
   3411
   root at 092af40cc094:/# 

2. Obviously a current Rcpp (as well as the distro, here 14.04, one)

   root at 092af40cc094:/# apt-cache policy r-cran-rcpp
   r-cran-rcpp:
     Installed: (none)
     Candidate: 0.12.9-1~ubuntu14.04.1~ppa1
     Version table:
        0.12.9-1~ubuntu14.04.1~ppa1 0
           500 http://ppa.launchpad.net/marutter/c2d4u/ubuntu/ trusty/main amd64
Packages
        0.11.0-1 0
           500 http://archive.ubuntu.com/ubuntu/ trusty/universe amd64 Packages
   root at 092af40cc094:/#

   And if you're beholden to the whateveritscalledtodayverse, it it there
too:

   root at 092af40cc094:/# apt-cache policy r-cran-tibble
   r-cran-tibble:
     Installed: (none)
     Candidate: 1.2-1cran1ppa0trusty0
     Version table:
        1.2-1cran1ppa0trusty0 0
           500 http://ppa.launchpad.net/marutter/c2d4u/ubuntu/ trusty/main amd64
Packages
   root at 092af40cc094:/# 


3. Trivial to use:

   root at 092af40cc094:/# cat /etc/apt/sources.list.d/marutter-*list
   deb http://ppa.launchpad.net/marutter/c2d4u/ubuntu trusty main
   # deb-src http://ppa.launchpad.net/marutter/c2d4u/ubuntu trusty main
   deb http://ppa.launchpad.net/marutter/rrutter/ubuntu trusty main
   # deb-src http://ppa.launchpad.net/marutter/rrutter/ubuntu trusty main
   root at 092af40cc094:/#

4. Factual support for this email brought to you by a convenient Docker
container:

   https://hub.docker.com/r/rocker/r-apt/
   https://github.com/rocker-org/rocker/tree/master/r-apt

   which exists for all relevant flavours.

Cheers, Dirk


-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org