[R] installation of dplyr
Hadley Wickham
h.wickham at gmail.com
Tue Apr 19 22:10:20 CEST 2016
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 <btupper at bigelow.org> 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-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8 LC_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 -m64 -mtune=generic -c distinct.cpp -o distinct.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 dplyr.cpp -o dplyr.o
> dplyr.cpp: In function ‘dplyr::Result* ntile_prototype(SEXPREC*, const dplyr::LazySubsets&, int)’:
> dplyr.cpp:242: warning: ‘number_tiles’ may be used uninitialized in this function
> {standard input}: Assembler messages:
> {standard input}:509159: Warning: end of file not at end of a line; newline inserted
> {standard input}:509591: Error: open CFI at the end of file; missing .cfi_endproc directive
> g++: Internal error: Killed (program cc1plus)
> Please submit a full bug report.
> See <http://bugzilla.redhat.com/bugzilla> for instructions.
> make: *** [dplyr.o] Error 1
> ERROR: compilation failed for package ‘dplyr’
> * removing ‘/usr/lib64/R/library/dplyr’
>
> The downloaded source packages are in
> ‘/tmp/RtmpkdCODF/downloaded_packages’
> Updating HTML index of packages in '.Library'
> Making 'packages.html' ... done
> Warning message:
> In install.packages("dplyr", repo = "http://cran.r-project.org") :
> installation of package ‘dplyr’ had non-zero exit status
>
>
>
> ####
> # devtools::install_github()
> ####
>
>
>> library(devtools)
>> install_github("hadley/dplyr", lib = '/usr/lib64/R/library')
> Using GitHub PAT from envvar GITHUB_PAT
> Downloading GitHub repo hadley/dplyr at master
> from URL https://api.github.com/repos/hadley/dplyr/zipball/master
> Installing dplyr
> Using GitHub PAT from envvar GITHUB_PAT
> Downloading GitHub repo hadley/testthat at master
> from URL https://api.github.com/repos/hadley/testthat/zipball/master
> Installing testthat
> '/usr/lib64/R/bin/R' --no-site-file --no-environ --no-save --no-restore \
> --quiet CMD INSTALL \
> '/tmp/RtmpkdCODF/devtools45c22638b2f2/hadley-testthat-52d5494' \
> --library='/usr/lib64/R/library' --install-tests
>
> * installing *source* package ‘testthat’ ...
> ** libs
> gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c label.c -o label.o
> gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c reassign.c -o reassign.o
> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c test-catch.cpp -o test-catch.o
> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c test-example.cpp -o test-example.o
> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c test-runner.cpp -o test-runner.o
> g++ -m64 -shared -L/usr/lib64/R/lib -L/usr/local/lib64 -o testthat.so label.o reassign.o test-catch.o test-example.o test-runner.o -L/usr/lib64/R/lib -lR
> installing to /usr/lib64/R/library/testthat/libs
> ** R
> ** inst
> ** tests
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> converting help for package ‘testthat’
> finding HTML links ... done
> CheckReporter html
> FailReporter html
> ListReporter html
> MinimalReporter html
> MultiReporter html
> Reporter html
> RstudioReporter html
> SilentReporter html
> StopReporter html
> SummaryReporter html
> TapReporter html
> TeamcityReporter html
> auto_test html
> auto_test_package html
> compare html
> compare_state html
> comparison-expectations html
> context html
> describe html
> dir_state html
> equality-expectations html
> evaluate_promise html
> expect_cpp_tests_pass html
> expect_equal_to_reference html
> expect_length html
> expect_match html
> expect_named html
> expect_success html
> expect_that html
> expectation html
> fail html
> find_reporter html
> find_test_scripts html
> inheritance-expectations html
> logical-expectations html
> make_expectation html
> not html
> oldskool html
> output-expectations html
> reexports html
> Rd warning: /tmp/RtmpkdCODF/devtools45c22638b2f2/hadley-testthat-52d5494/man/reexports.Rd:13: missing file link ‘%>%’
> reporter-accessors html
> safe_digest html
> skip html
> source_file html
> takes_less_than html
> test_dir html
> test_env html
> test_examples html
> test_file html
> test_package html
> test_path html
> test_that html
> testthat html
> testthat_results html
> try_again html
> use_catch html
> watch html
> with_mock html
> ** building package indices
> ** testing if installed package can be loaded
> * DONE (testthat)
> Making 'packages.html' ... done
> Using GitHub PAT from envvar GITHUB_PAT
> Skipping install for github remote, the SHA1 (cb38672f) has not changed since last install.
> Use `force = TRUE` to force installation
> Skipping 2 packages ahead of CRAN: lazyeval, tibble
> '/usr/lib64/R/bin/R' --no-site-file --no-environ --no-save --no-restore \
> --quiet CMD INSTALL \
> '/tmp/RtmpkdCODF/devtools45c2fff716f/hadley-dplyr-afb9ac7' \
> --library='/usr/lib64/R/library' --install-tests
>
> * installing *source* package ‘dplyr’ ...
> ** 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" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -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" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -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" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -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" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -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:141,
> 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:41: 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" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -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" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -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" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -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" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c distinct.cpp -o distinct.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" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c dplyr.cpp -o dplyr.o
> dplyr.cpp: In function ‘dplyr::Result* ntile_prototype(SEXPREC*, const dplyr::LazySubsets&, int)’:
> dplyr.cpp:213: warning: ‘number_tiles’ may be used uninitialized in this function
> In file included from ../inst/include/dplyr.h:141,
> from dplyr.cpp:1:
> ../inst/include/dplyr/DataFrameSubsetVisitors.h: In constructor ‘dplyr::DataFrameSubsetVisitors::DataFrameSubsetVisitors(const Rcpp::DataFrame&, const Rcpp::CharacterVector&)’:
> ../inst/include/dplyr/DataFrameSubsetVisitors.h:41: warning: ‘column’ may be used uninitialized in this function
> {standard input}: Assembler messages:
> {standard input}:812569: Warning: end of file not at end of a line; newline inserted
> g++: Internal error: Killed (program cc1plus)
> Please submit a full bug report.
> See <http://bugzilla.redhat.com/bugzilla> for instructions.
> make: *** [dplyr.o] Error 1
> ERROR: compilation failed for package ‘dplyr’
> * removing ‘/usr/lib64/R/library/dplyr’
> Error: Command failed (1)
>>
>
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