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
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()
####
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)