Increasing memory resolved the issue for me. Thanks again, Ben
> On Apr 19, 2016, at 4:10 PM, Hadley Wickham <h.wick...@gmail.com> 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 <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 Ben Tupper Bigelow Laboratory for Ocean Sciences 60 Bigelow Drive, P.O. Box 380 East Boothbay, Maine 04544 http://www.bigelow.org ______________________________________________ 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.
