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 <btup...@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@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@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) >> > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- http://hadley.nz ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.