Re: [R] installation of dplyr

2016-04-20 Thread Ben Tupper 
Increasing memory resolved the issue for me.

Thanks again,
Ben

> On Apr 19, 2016, at 4:10 PM, Hadley Wickham  wrote:
> 
> You normally see these errors when compiling on a vm that has very
> little memory.
> Hadley
> 
> On Tue, Apr 19, 2016 at 2:47 PM, Ben Tupper  wrote:
>> Hello,
>> 
>> I am getting a fresh CentOS 6.7 machine set up with all of the goodies for R 
>> 3.2.3, including dplyr package. I am unable to successfully install it.  
>> Below I show the failed installation using utils::install.packages() and 
>> then again using devtools::install_github().  Each yields an error similar 
>> to the other but not quite exactly the same - the error messages sail right 
>> over my head.
>> 
>> I can contact the package author if that would be better, but thought it 
>> best to start here.
>> 
>> Thanks!
>> Ben
>> 
>> Ben Tupper
>> Bigelow Laboratory for Ocean Sciences
>> 60 Bigelow Drive, P.O. Box 380
>> East Boothbay, Maine 04544
>> http://www.bigelow.org
>> 
>>> sessionInfo()
>> R version 3.2.3 (2015-12-10)
>> Platform: x86_64-redhat-linux-gnu (64-bit)
>> Running under: CentOS release 6.7 (Final)
>> 
>> 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
>> 
>> 
>> 
>> 
>> #   utils::install.packages()
>> 
>> 
>>> install.packages("dplyr", repo = "http://cran.r-project.org;)
>> Installing package into ‘/usr/lib64/R/library’
>> (as ‘lib’ is unspecified)
>> trying URL 'http://cran.r-project.org/src/contrib/dplyr_0.4.3.tar.gz'
>> Content type 'application/x-gzip' length 655997 bytes (640 KB)
>> ==
>> downloaded 640 KB
>> 
>> * installing *source* package ‘dplyr’ ...
>> ** package ‘dplyr’ successfully unpacked and MD5 sums checked
>> ** libs
>> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
>> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
>> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
>> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c RcppExports.cpp -o 
>> RcppExports.o
>> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
>> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
>> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
>> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c address.cpp -o address.o
>> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
>> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
>> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
>> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c api.cpp -o api.o
>> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
>> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
>> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
>> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c arrange.cpp -o arrange.o
>> In file included from ../inst/include/dplyr.h:131,
>> from arrange.cpp:1:
>> ../inst/include/dplyr/DataFrameSubsetVisitors.h: In constructor 
>> ‘dplyr::DataFrameSubsetVisitors::DataFrameSubsetVisitors(const 
>> Rcpp::DataFrame&, const Rcpp::CharacterVector&)’:
>> ../inst/include/dplyr/DataFrameSubsetVisitors.h:40: warning: ‘column’ may be 
>> used uninitialized in this function
>> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
>> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
>> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
>> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c between.cpp -o between.o
>> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
>> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
>> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
>> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c bind.cpp -o bind.o
>> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
>> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
>> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
>> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c combine_variables.cpp -o 
>> combine_variables.o
>> g++ -m64 -I/usr/include/R

Re: [R] installation of dplyr

2016-04-19 Thread Ben Tupper 
Hi,

OK - that can be fixed by our IT whizzes.  

Thanks,
Ben

P.S.  Thanks for dplyr!

> On Apr 19, 2016, at 4:10 PM, Hadley Wickham  wrote:
> 
> You normally see these errors when compiling on a vm that has very
> little memory.
> Hadley
> 
> On Tue, Apr 19, 2016 at 2:47 PM, Ben Tupper  wrote:
>> Hello,
>> 
>> I am getting a fresh CentOS 6.7 machine set up with all of the goodies for R 
>> 3.2.3, including dplyr package. I am unable to successfully install it.  
>> Below I show the failed installation using utils::install.packages() and 
>> then again using devtools::install_github().  Each yields an error similar 
>> to the other but not quite exactly the same - the error messages sail right 
>> over my head.
>> 
>> I can contact the package author if that would be better, but thought it 
>> best to start here.
>> 
>> Thanks!
>> Ben
>> 
>> Ben Tupper
>> Bigelow Laboratory for Ocean Sciences
>> 60 Bigelow Drive, P.O. Box 380
>> East Boothbay, Maine 04544
>> http://www.bigelow.org
>> 
>>> sessionInfo()
>> R version 3.2.3 (2015-12-10)
>> Platform: x86_64-redhat-linux-gnu (64-bit)
>> Running under: CentOS release 6.7 (Final)
>> 
>> 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
>> 
>> 
>> 
>> 
>> #   utils::install.packages()
>> 
>> 
>>> install.packages("dplyr", repo = "http://cran.r-project.org;)
>> Installing package into ‘/usr/lib64/R/library’
>> (as ‘lib’ is unspecified)
>> trying URL 'http://cran.r-project.org/src/contrib/dplyr_0.4.3.tar.gz'
>> Content type 'application/x-gzip' length 655997 bytes (640 KB)
>> ==
>> downloaded 640 KB
>> 
>> * installing *source* package ‘dplyr’ ...
>> ** package ‘dplyr’ successfully unpacked and MD5 sums checked
>> ** libs
>> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
>> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
>> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
>> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c RcppExports.cpp -o 
>> RcppExports.o
>> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
>> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
>> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
>> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c address.cpp -o address.o
>> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
>> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
>> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
>> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c api.cpp -o api.o
>> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
>> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
>> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
>> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c arrange.cpp -o arrange.o
>> In file included from ../inst/include/dplyr.h:131,
>> from arrange.cpp:1:
>> ../inst/include/dplyr/DataFrameSubsetVisitors.h: In constructor 
>> ‘dplyr::DataFrameSubsetVisitors::DataFrameSubsetVisitors(const 
>> Rcpp::DataFrame&, const Rcpp::CharacterVector&)’:
>> ../inst/include/dplyr/DataFrameSubsetVisitors.h:40: warning: ‘column’ may be 
>> used uninitialized in this function
>> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
>> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
>> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
>> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c between.cpp -o between.o
>> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
>> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
>> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
>> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c bind.cpp -o bind.o
>> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
>> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
>> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
>> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c combine_variables.cpp -o 
>> combine_variables.o
>> g++

Re: [R] installation of dplyr

2016-04-19 Thread Hadley Wickham 
You normally see these errors when compiling on a vm that has very
little memory.
Hadley

On Tue, Apr 19, 2016 at 2:47 PM, Ben Tupper  wrote:
> Hello,
>
> I am getting a fresh CentOS 6.7 machine set up with all of the goodies for R 
> 3.2.3, including dplyr package. I am unable to successfully install it.  
> Below I show the failed installation using utils::install.packages() and then 
> again using devtools::install_github().  Each yields an error similar to the 
> other but not quite exactly the same - the error messages sail right over my 
> head.
>
> I can contact the package author if that would be better, but thought it best 
> to start here.
>
> Thanks!
> Ben
>
> Ben Tupper
> Bigelow Laboratory for Ocean Sciences
> 60 Bigelow Drive, P.O. Box 380
> East Boothbay, Maine 04544
> http://www.bigelow.org
>
>> sessionInfo()
> R version 3.2.3 (2015-12-10)
> Platform: x86_64-redhat-linux-gnu (64-bit)
> Running under: CentOS release 6.7 (Final)
>
> 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
>
>
>
> 
> #   utils::install.packages()
> 
>
>> install.packages("dplyr", repo = "http://cran.r-project.org;)
> Installing package into ‘/usr/lib64/R/library’
> (as ‘lib’ is unspecified)
> trying URL 'http://cran.r-project.org/src/contrib/dplyr_0.4.3.tar.gz'
> Content type 'application/x-gzip' length 655997 bytes (640 KB)
> ==
> downloaded 640 KB
>
> * installing *source* package ‘dplyr’ ...
> ** package ‘dplyr’ successfully unpacked and MD5 sums checked
> ** libs
> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c RcppExports.cpp -o 
> RcppExports.o
> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c address.cpp -o address.o
> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c api.cpp -o api.o
> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c arrange.cpp -o arrange.o
> In file included from ../inst/include/dplyr.h:131,
>  from arrange.cpp:1:
> ../inst/include/dplyr/DataFrameSubsetVisitors.h: In constructor 
> ‘dplyr::DataFrameSubsetVisitors::DataFrameSubsetVisitors(const 
> Rcpp::DataFrame&, const Rcpp::CharacterVector&)’:
> ../inst/include/dplyr/DataFrameSubsetVisitors.h:40: warning: ‘column’ may be 
> used uninitialized in this function
> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c between.cpp -o between.o
> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c bind.cpp -o bind.o
> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c combine_variables.cpp -o 
> combine_variables.o
> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
> --param=ssp-buffer-size=4