[R] installation of dplyr
Ben Tupper
btupper at bigelow.org
Wed Apr 20 18:10:17 CEST 2016
Increasing memory resolved the issue for me.
Thanks again,
Ben
> On Apr 19, 2016, at 4:10 PM, Hadley Wickham <h.wickham at 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 <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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>> 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
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