I am using this site for reference:
http://r4ds.had.co.nz/introduction.html
but I am unable to install the tidyverse package. Using dependencies = TRUE did not help. What else can I do?
installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lcurl
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
* deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
* rpm: libcurl-devel (Fedora, CentOS, RHEL)
* csw: libcurl_dev (Solaris)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘curl’
* removing ‘/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/curl’
Warning in install.packages :
installation of package ‘curl’ had non-zero exit status
* installing *source* package ‘openssl’ ...
** package ‘openssl’ successfully unpacked and MD5 sums checked
Using PKG_CFLAGS=
Using PKG_LIBS=-lssl -lcrypto
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because openssl was not found. Try installing:
* deb: libssl-dev (Debian, Ubuntu, etc)
* rpm: openssl-devel (Fedora, CentOS, RHEL)
* csw: libssl_dev (Solaris)
* brew: openssl#1.1 (Mac OSX)
If openssl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘openssl’
* removing ‘/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/openssl’
Warning in install.packages :
installation of package ‘openssl’ had non-zero exit status
* installing *source* package ‘evaluate’ ...
** package ‘evaluate’ successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (evaluate)
* installing *source* package ‘highr’ ...
** package ‘highr’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (highr)
* installing *source* package ‘markdown’ ...
** package ‘markdown’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rbase64.c -o Rbase64.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rmarkdown.c -o Rmarkdown.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c autolink.c -o autolink.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c buffer.c -o buffer.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c houdini_href_e.c -o houdini_href_e.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c houdini_html_e.c -o houdini_html_e.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c html.c -o html.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c html_smartypants.c -o html_smartypants.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c markdown.c -o markdown.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stack.c -o stack.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o markdown.so Rbase64.o Rinit.o Rmarkdown.o autolink.o buffer.o houdini_href_e.o houdini_html_e.o html.o html_smartypants.o markdown.o stack.o -L/usr/lib/R/lib -lR
installing to /home/akriti/R/x86_64-pc-linux-gnu-library/3.2/markdown/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (markdown)
* installing *source* package ‘yaml’ ...
** package ‘yaml’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c api.c -o api.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dumper.c -o dumper.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c emitter.c -o emitter.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c implicit.c -o implicit.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c loader.c -o loader.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c parser.c -o parser.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c r-ext.c -o r-ext.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c reader.c -o reader.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c scanner.c -o scanner.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c writer.c -o writer.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o yaml.so api.o dumper.o emitter.o implicit.o loader.o parser.o r-ext.o reader.o scanner.o writer.o -L/usr/lib/R/lib -lR
installing to /home/akriti/R/x86_64-pc-linux-gnu-library/3.2/yaml/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (yaml)
* installing *source* package ‘htmltools’ ...
** package ‘htmltools’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -I"/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -I/usr/share/R/include -DNDEBUG -I"/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c template.cpp -o template.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o htmltools.so RcppExports.o template.o -L/usr/lib/R/lib -lR
installing to /home/akriti/R/x86_64-pc-linux-gnu-library/3.2/htmltools/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (htmltools)
* installing *source* package ‘base64enc’ ...
** package ‘base64enc’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c base64.c -o base64.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c uriencode.c -o uriencode.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8.c -o utf8.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o base64enc.so base64.o uriencode.o utf8.o -L/usr/lib/R/lib -lR
installing to /home/akriti/R/x86_64-pc-linux-gnu-library/3.2/base64enc/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (base64enc)
* installing *source* package ‘xml2’ ...
** package ‘xml2’ successfully unpacked and MD5 sums checked
Package libxml-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libxml-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libxml-2.0' found
Package libxml-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libxml-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libxml-2.0' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lxml2
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libxml-2.0 was not found. Try installing:
* deb: libxml2-dev (Debian, Ubuntu, etc)
* rpm: libxml2-devel (Fedora, CentOS, RHEL)
* csw: libxml2_dev (Solaris)
If libxml-2.0 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libxml-2.0.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘xml2’
* removing ‘/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/xml2’
Warning in install.packages :
installation of package ‘xml2’ had non-zero exit status
* installing *source* package ‘caTools’ ...
** package ‘caTools’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Gif2R.cpp -o Gif2R.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c GifTools.cpp -o GifTools.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c runfunc.c -o runfunc.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o caTools.so Gif2R.o GifTools.o runfunc.o -L/usr/lib/R/lib -lR
installing to /home/akriti/R/x86_64-pc-linux-gnu-library/3.2/caTools/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (caTools)
* installing *source* package ‘rprojroot’ ...
** package ‘rprojroot’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rprojroot)
ERROR: dependencies ‘curl’, ‘openssl’ are not available for package ‘httr’
* removing ‘/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/httr’
Warning in install.packages :
installation of package ‘httr’ had non-zero exit status
* installing *source* package ‘knitr’ ...
** package ‘knitr’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (knitr)
ERROR: dependencies ‘xml2’, ‘httr’ are not available for package ‘rvest’
* removing ‘/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/rvest’
Warning in install.packages :
installation of package ‘rvest’ had non-zero exit status
* installing *source* package ‘rmarkdown’ ...
** package ‘rmarkdown’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (rmarkdown)
ERROR: dependencies ‘httr’, ‘rvest’, ‘xml2’ are not available for package ‘tidyverse’
* removing ‘/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/tidyverse’
Warning in install.packages :
*installation of package ‘tidyverse’ had non-zero exit status
You find the answer in your error message:
------------------------ ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
* deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
....
....
Copy and paste the following to your Terminal and than try installing tidyverse again. Should solve the problem.
# Required for many packages
sudo apt-get install -y libxml2-dev libcurl4-openssl-dev libssl-dev
The problem occurred because tidyverse has system dependencies (i.e., libcurl4-openssl-dev, libssl-dev, libxml2-dev). I wrote a blog post that explains the solution in more details.
try this , it helped me out
sudo apt-get install -y libxml2-dev libcurl4-openssl-dev libssl-dev
A strategy I have found successful is to install R and R-Studio through anaconda (https://www.anaconda.com/). Create a separate environment for R and use the anaconda navigator to install R-Studio.
(Two great things about this approach: i) dependencies are automatically taken care of in the background ii) your working environment is sandboxed against accidents ... unless you're looking for trouble :-) )
I had the same issue with RStudio on Ubuntu 20.04 but switched to using R and R - Studio through anaconda.Tidyverse can be loaded without issues.
library(tidyverse)
── Attaching packages ─────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.3.1 ──
✓ ggplot2 3.3.5 ✓ purrr 0.3.4
✓ tibble 3.1.2 ✓ dplyr 1.0.7
✓ tidyr 1.1.3 ✓ stringr 1.4.0
✓ readr 1.4.0 ✓ forcats 0.5.1
── Conflicts ────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
x dplyr::filter() masks stats::filter()
x dplyr::lag() masks stats::lag()
Related
When I try to install the car package using the traditional install.packages('car', dependencies=T), the console gives me back the below errors
Error: package ‘R6’ was installed before R 4.0.0: please re-install it
Execution halted
ERROR: lazy loading failed for package ‘httpuv’
* removing ‘/home/fritz/R/x86_64-pc-linux-gnu-library/4.0/httpuv’
Warning in install.packages :
installation of package ‘httpuv’ had non-zero exit status
* installing source package ‘dplyr’ ...
** package ‘dplyr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-8T8CYO/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c chop.cpp -o chop.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-8T8CYO/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c filter.cpp -o filter.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-8T8CYO/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c funs.cpp -o funs.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-8T8CYO/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c group_by.cpp -o group_by.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-8T8CYO/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c group_data.cpp -o group_data.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-8T8CYO/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c imports.cpp -o imports.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-8T8CYO/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.cpp -o init.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-8T8CYO/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c mask.cpp -o mask.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-8T8CYO/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c mutate.cpp -o mutate.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-8T8CYO/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c slice.cpp -o slice.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-8T8CYO/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c summarise.cpp -o summarise.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o dplyr.so chop.o filter.o funs.o group_by.o group_data.o imports.o init.o mask.o mutate.o slice.o summarise.o
-L/usr/lib/R/lib -lR
installing to /home/fritz/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-dplyr/00new/dplyr/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error: package ‘vctrs’ was installed before R 4.0.0: please re-install it
Execution halted
ERROR: lazy loading failed for package ‘dplyr’
* removing ‘/home/fritz/R/x86_64-pc-linux-gnu-library/4.0/dplyr’
Warning in install.packages :
installation of package ‘dplyr’ had non-zero exit status
* installing source package ‘openxlsx’ ...
** package ‘openxlsx’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/fritz/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-8T8CYO/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/fritz/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-8T8CYO/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c helper_functions.cpp -o helper_functions.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/fritz/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-8T8CYO/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c load_workbook.cpp -o load_workbook.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I'/home/fritz/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-8T8CYO/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c openxlsx_init.c -o openxlsx_init.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/fritz/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-8T8CYO/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c read_workbook.cpp -o read_workbook.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/fritz/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-8T8CYO/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c write_data.cpp -o write_data.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/fritz/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-8T8CYO/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c write_file.cpp -o write_file.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/fritz/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-8T8CYO/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c write_file_2.cpp -o write_file_2.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o openxlsx.so RcppExports.o helper_functions.o load_workbook.o openxlsx_init.o read_workbook.o write_data.o
write_file.o write_file_2.o -L/usr/lib/R/lib -lR
installing to /home/fritz/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-openxlsx/00new/openxlsx/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package ‘stringi’ was installed before R 4.0.0: please re-install it
Execution halted
ERROR: lazy loading failed for package ‘openxlsx’
* removing ‘/home/fritz/R/x86_64-pc-linux-gnu-library/4.0/openxlsx’
Warning in install.packages :
installation of package ‘openxlsx’ had non-zero exit status
* installing source package ‘survey’ ...
** package ‘survey’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (survey)
ERROR: dependency ‘dplyr’ is not available for package ‘tidyr’
* removing ‘/home/fritz/R/x86_64-pc-linux-gnu-library/4.0/tidyr’
Warning in install.packages :
installation of package ‘tidyr’ had non-zero exit status
ERROR: dependency ‘hms’ is not available for package ‘readr’
* removing ‘/home/fritz/R/x86_64-pc-linux-gnu-library/4.0/readr’
Warning in install.packages :
installation of package ‘readr’ had non-zero exit status
ERROR: dependency ‘hms’ is not available for package ‘progress’
* removing ‘/home/fritz/R/x86_64-pc-linux-gnu-library/4.0/progress’
Warning in install.packages :
installation of package ‘progress’ had non-zero exit status
* installing source package ‘effects’ ...
** package ‘effects’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (effects)
ERROR: dependency ‘httpuv’ is not available for package ‘shiny’
* removing ‘/home/fritz/R/x86_64-pc-linux-gnu-library/4.0/shiny’
Warning in install.packages :
installation of package ‘shiny’ had non-zero exit status
ERROR: dependency ‘shiny’ is not available for package ‘miniUI’
* removing ‘/home/fritz/R/x86_64-pc-linux-gnu-library/4.0/miniUI’
Warning in install.packages :
installation of package ‘miniUI’ had non-zero exit status
ERROR: dependencies ‘dplyr’, ‘tidyr’ are not available for package ‘broom’
* removing ‘/home/fritz/R/x86_64-pc-linux-gnu-library/4.0/broom’
Warning in install.packages :
installation of package ‘broom’ had non-zero exit status
ERROR: dependencies ‘hms’, ‘readr’ are not available for package ‘haven’
* removing ‘/home/fritz/R/x86_64-pc-linux-gnu-library/4.0/haven’
Warning in install.packages :
installation of package ‘haven’ had non-zero exit status
ERROR: dependency ‘progress’ is not available for package ‘readxl’
* removing ‘/home/fritz/R/x86_64-pc-linux-gnu-library/4.0/readxl’
Warning in install.packages :
installation of package ‘readxl’ had non-zero exit status
ERROR: dependencies ‘shiny’, ‘miniUI’ are not available for package ‘manipulateWidget’
* removing ‘/home/fritz/R/x86_64-pc-linux-gnu-library/4.0/manipulateWidget’
Warning in install.packages :
installation of package ‘manipulateWidget’ had non-zero exit status
ERROR: dependencies ‘broom’, ‘dplyr’ are not available for package ‘pbkrtest’
* removing ‘/home/fritz/R/x86_64-pc-linux-gnu-library/4.0/pbkrtest’
Warning in install.packages :
installation of package ‘pbkrtest’ had non-zero exit status
ERROR: dependencies ‘haven’, ‘readxl’, ‘openxlsx’ are not available for package ‘rio’
* removing ‘/home/fritz/R/x86_64-pc-linux-gnu-library/4.0/rio’
Warning in install.packages :
installation of package ‘rio’ had non-zero exit status
ERROR: dependencies ‘shiny’, ‘manipulateWidget’ are not available for package ‘rgl’
* removing ‘/home/fritz/R/x86_64-pc-linux-gnu-library/4.0/rgl’
Warning in install.packages :
installation of package ‘rgl’ had non-zero exit status
ERROR: dependencies ‘pbkrtest’, ‘rio’ are not available for package ‘car’
* removing ‘/home/fritz/R/x86_64-pc-linux-gnu-library/4.0/car’
Warning in install.packages :
installation of package ‘car’ had non-zero exit status
ERROR: dependency ‘car’ is not available for package ‘alr4’
* removing ‘/home/fritz/R/x86_64-pc-linux-gnu-library/4.0/alr4’
Warning in install.packages :
installation of package ‘alr4’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmpuw3pOk/downloaded_packages’
I don't know how to resolve the problem, can someone please help me?
I'm trying to install the pcadapt in RStudio using
> remotes::install_github("bcm-uga/pcadapt")
But it gives me the error installation of package ‘bigutilsr’ had non-zero exit status
Downloading GitHub repo bcm-uga/pcadapt#master
Installing 1 packages: bigutilsr
Installing package into ‘/home/jenifer/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
probando la URL 'https://cloud.r-project.org/src/contrib/bigutilsr_0.3.2.tar.gz'
Content type 'application/x-gzip' length 915116 bytes (893 KB)
==================================================
downloaded 893 KB
* installing *source* package ‘bigutilsr’ ...
** package ‘bigutilsr’ successfully unpacked and MD5 sums checked
** libs
g++ -I"/usr/share/R/include" -DNDEBUG -I"/home/jenifer/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -I"/usr/share/R/include" -DNDEBUG -I"/home/jenifer/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ogk.cpp -o ogk.o
g++ -I"/usr/share/R/include" -DNDEBUG -I"/home/jenifer/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rollmean.cpp -o rollmean.o
g++ -I"/usr/share/R/include" -DNDEBUG -I"/home/jenifer/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rowSumsSq.cpp -o rowSumsSq.o
g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -o bigutilsr.so RcppExports.o ogk.o rollmean.o rowSumsSq.o -L/usr/lib/R/lib -lR
installing to /home/jenifer/R/x86_64-pc-linux-gnu-library/3.5/bigutilsr/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: S3 methods ‘eigs.matrix’, ‘eigs.dgeMatrix’, ‘eigs.dgCMatrix’, ‘eigs.dgRMatrix’, ‘eigs.dsyMatrix’, ‘eigs.dsCMatrix’, ‘eigs.dsRMatrix’, ‘eigs.function’, ‘eigs_sym.matrix’, ‘eigs_sym.dgeMatrix’, ‘eigs_sym.dgCMatrix’, ‘eigs_sym.dgRMatrix’, ‘eigs_sym.function’, ‘svds.matrix’, ‘svds.dgeMatrix’, ‘svds.dgCMatrix’, ‘svds.dgRMatrix’, ‘svds.dsyMatrix’, ‘svds.dsCMatrix’, ‘svds.dsRMatrix’, ‘svds.function’ were declared in NAMESPACE but not found
Error in library.dynam(lib, package, package.lib) :
shared object ‘RSpectra.so’ not found
ERROR: lazy loading failed for package ‘bigutilsr’
* removing ‘/home/jenifer/R/x86_64-pc-linux-gnu-library/3.5/bigutilsr’
Error: Failed to install 'pcadapt' from GitHub:
(convertido del aviso) installation of package ‘bigutilsr’ had non-zero exit status
>
I've been searching on google and it seems that if gcc isn't set up correctly, then R tries to compile the packages and it fails (https://community.rstudio.com/t/cannot-install-any-packages-non-zero-exit-status/53310), but I don't know if this is the case, and if it is, I don't know how to solve it.
gcc --version
gcc (Debian 8.3.0-6) 8.3.0
I'm also having similar issues while trying to install adegenet, hierfstat, pegas, poppr and other packages but I will put a post about this with moor details somewhere else ins stackoverflow just to keep it simple and to not give place to confussion with the code.
If somebody can help me, I will appreciate it very much
Cheers
I am using this site for reference:
http://r4ds.had.co.nz/introduction.html
but I am unable to install the tidyverse package. Using dependencies = TRUE did not help. What else can I do?
installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lcurl
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
* deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
* rpm: libcurl-devel (Fedora, CentOS, RHEL)
* csw: libcurl_dev (Solaris)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘curl’
* removing ‘/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/curl’
Warning in install.packages :
installation of package ‘curl’ had non-zero exit status
* installing *source* package ‘openssl’ ...
** package ‘openssl’ successfully unpacked and MD5 sums checked
Using PKG_CFLAGS=
Using PKG_LIBS=-lssl -lcrypto
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because openssl was not found. Try installing:
* deb: libssl-dev (Debian, Ubuntu, etc)
* rpm: openssl-devel (Fedora, CentOS, RHEL)
* csw: libssl_dev (Solaris)
* brew: openssl#1.1 (Mac OSX)
If openssl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘openssl’
* removing ‘/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/openssl’
Warning in install.packages :
installation of package ‘openssl’ had non-zero exit status
* installing *source* package ‘evaluate’ ...
** package ‘evaluate’ successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (evaluate)
* installing *source* package ‘highr’ ...
** package ‘highr’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (highr)
* installing *source* package ‘markdown’ ...
** package ‘markdown’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rbase64.c -o Rbase64.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rmarkdown.c -o Rmarkdown.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c autolink.c -o autolink.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c buffer.c -o buffer.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c houdini_href_e.c -o houdini_href_e.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c houdini_html_e.c -o houdini_html_e.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c html.c -o html.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c html_smartypants.c -o html_smartypants.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c markdown.c -o markdown.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stack.c -o stack.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o markdown.so Rbase64.o Rinit.o Rmarkdown.o autolink.o buffer.o houdini_href_e.o houdini_html_e.o html.o html_smartypants.o markdown.o stack.o -L/usr/lib/R/lib -lR
installing to /home/akriti/R/x86_64-pc-linux-gnu-library/3.2/markdown/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (markdown)
* installing *source* package ‘yaml’ ...
** package ‘yaml’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c api.c -o api.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dumper.c -o dumper.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c emitter.c -o emitter.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c implicit.c -o implicit.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c loader.c -o loader.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c parser.c -o parser.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c r-ext.c -o r-ext.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c reader.c -o reader.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c scanner.c -o scanner.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c writer.c -o writer.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o yaml.so api.o dumper.o emitter.o implicit.o loader.o parser.o r-ext.o reader.o scanner.o writer.o -L/usr/lib/R/lib -lR
installing to /home/akriti/R/x86_64-pc-linux-gnu-library/3.2/yaml/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (yaml)
* installing *source* package ‘htmltools’ ...
** package ‘htmltools’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -I"/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -I/usr/share/R/include -DNDEBUG -I"/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c template.cpp -o template.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o htmltools.so RcppExports.o template.o -L/usr/lib/R/lib -lR
installing to /home/akriti/R/x86_64-pc-linux-gnu-library/3.2/htmltools/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (htmltools)
* installing *source* package ‘base64enc’ ...
** package ‘base64enc’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c base64.c -o base64.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c uriencode.c -o uriencode.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utf8.c -o utf8.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o base64enc.so base64.o uriencode.o utf8.o -L/usr/lib/R/lib -lR
installing to /home/akriti/R/x86_64-pc-linux-gnu-library/3.2/base64enc/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (base64enc)
* installing *source* package ‘xml2’ ...
** package ‘xml2’ successfully unpacked and MD5 sums checked
Package libxml-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libxml-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libxml-2.0' found
Package libxml-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libxml-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libxml-2.0' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lxml2
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libxml-2.0 was not found. Try installing:
* deb: libxml2-dev (Debian, Ubuntu, etc)
* rpm: libxml2-devel (Fedora, CentOS, RHEL)
* csw: libxml2_dev (Solaris)
If libxml-2.0 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libxml-2.0.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘xml2’
* removing ‘/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/xml2’
Warning in install.packages :
installation of package ‘xml2’ had non-zero exit status
* installing *source* package ‘caTools’ ...
** package ‘caTools’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Gif2R.cpp -o Gif2R.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c GifTools.cpp -o GifTools.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c runfunc.c -o runfunc.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o caTools.so Gif2R.o GifTools.o runfunc.o -L/usr/lib/R/lib -lR
installing to /home/akriti/R/x86_64-pc-linux-gnu-library/3.2/caTools/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (caTools)
* installing *source* package ‘rprojroot’ ...
** package ‘rprojroot’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rprojroot)
ERROR: dependencies ‘curl’, ‘openssl’ are not available for package ‘httr’
* removing ‘/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/httr’
Warning in install.packages :
installation of package ‘httr’ had non-zero exit status
* installing *source* package ‘knitr’ ...
** package ‘knitr’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (knitr)
ERROR: dependencies ‘xml2’, ‘httr’ are not available for package ‘rvest’
* removing ‘/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/rvest’
Warning in install.packages :
installation of package ‘rvest’ had non-zero exit status
* installing *source* package ‘rmarkdown’ ...
** package ‘rmarkdown’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (rmarkdown)
ERROR: dependencies ‘httr’, ‘rvest’, ‘xml2’ are not available for package ‘tidyverse’
* removing ‘/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/tidyverse’
Warning in install.packages :
*installation of package ‘tidyverse’ had non-zero exit status
You find the answer in your error message:
------------------------ ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
* deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
....
....
Copy and paste the following to your Terminal and than try installing tidyverse again. Should solve the problem.
# Required for many packages
sudo apt-get install -y libxml2-dev libcurl4-openssl-dev libssl-dev
The problem occurred because tidyverse has system dependencies (i.e., libcurl4-openssl-dev, libssl-dev, libxml2-dev). I wrote a blog post that explains the solution in more details.
try this , it helped me out
sudo apt-get install -y libxml2-dev libcurl4-openssl-dev libssl-dev
A strategy I have found successful is to install R and R-Studio through anaconda (https://www.anaconda.com/). Create a separate environment for R and use the anaconda navigator to install R-Studio.
(Two great things about this approach: i) dependencies are automatically taken care of in the background ii) your working environment is sandboxed against accidents ... unless you're looking for trouble :-) )
I had the same issue with RStudio on Ubuntu 20.04 but switched to using R and R - Studio through anaconda.Tidyverse can be loaded without issues.
library(tidyverse)
── Attaching packages ─────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.3.1 ──
✓ ggplot2 3.3.5 ✓ purrr 0.3.4
✓ tibble 3.1.2 ✓ dplyr 1.0.7
✓ tidyr 1.1.3 ✓ stringr 1.4.0
✓ readr 1.4.0 ✓ forcats 0.5.1
── Conflicts ────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
x dplyr::filter() masks stats::filter()
x dplyr::lag() masks stats::lag()
While installing the package RcppArmadillo, I am getting below error.
installing to /usr/lib64/R/library/RcppArmadillo/libs
** R
** inst
** preparing package for lazy loading
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object 'SHLIB.maker' not found
Error : unable to load R code in package ‘RcppArmadillo’
ERROR: lazy loading failed for package ‘RcppArmadillo’
* removing ‘/usr/lib64/R/library/RcppArmadillo’
Warning message:
In install.packages("RcppArmadillo_0.3.920.1.tar.gz", repos = NULL, :
installation of package ‘RcppArmadillo_0.3.920.1.tar.gz’ had non-zero exit status
You need to add R's repository to your system:
Use your favorite text editor (I'm using gedit as an example) to open /etc/apt/sources.list:
sudo gedit /etc/apt/sources.list
Add this line to the file (if this is slow, use another mirror. You may also want to change precise into the codename for your Ubuntu version --- e.g., trusty for 12.04):
deb http://cran.rstudio.com/bin/linux/ubuntu precise/
This works for me install.packages('RcppArmadillo')
> install.packages('RcppArmadillo')
Installing package into ‘/home/priyankara/R/i686-pc-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
trying URL 'http://mirror.bjtu.edu.cn/cran/src/contrib/RcppArmadillo_0.5.300.4.tar.gz'
Content type 'application/octet-stream' length 967193 bytes (944 KB)
==================================================
downloaded 944 KB
* installing *source* package ‘RcppArmadillo’ ...
** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
* checking LAPACK_LIBS: divide-and-conquer complex SVD available via system LAPACK
** libs
g++ -I/usr/share/R/include -DNDEBUG -I"/home/priyankara/R/i686-pc-linux-gnu-library/3.2/Rcpp/include" -I../inst/include -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppArmadillo.cpp -o RcppArmadillo.o
g++ -I/usr/share/R/include -DNDEBUG -I"/home/priyankara/R/i686-pc-linux-gnu-library/3.2/Rcpp/include" -I../inst/include -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -I/usr/share/R/include -DNDEBUG -I"/home/priyankara/R/i686-pc-linux-gnu-library/3.2/Rcpp/include" -I../inst/include -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c fastLm.cpp -o fastLm.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /home/priyankara/R/i686-pc-linux-gnu-library/3.2/RcppArmadillo/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RcppArmadillo)
I am running ubuntu 14.10, late beta, up-to-date.
I would like to try a garch model in R 3.1.1. specifically, an MA(1) or ARMA(1,1) with a volatility component.
first, I need to install a garch package. (arima seems part of default R, but not garima.) a well-recommended package among others for garch is guarch.
> install.packages("ruguarch")
...
ERROR: dependency 'ks' is not available for package 'rugarch'
* removing '/usr/local/lib/R/site-library/rugarch'
The downloaded source packages are in
'/tmp/RtmpUBvb9C/downloaded_packages'
Warning messages:
1: In install.packages("rugarch") :
installation of package 'rgl' had non-zero exit status
2: In install.packages("rugarch") :
installation of package 'ks' had non-zero exit status
3: In install.packages("rugarch") :
installation of package 'rugarch' had non-zero exit status
on the solo ks install,
> install.packages("ks")
...
checking for X... no
configure: error: X11 not found but required, configure aborted.
of course, even if I get this to work, it will only be step 1. then I need to find a package that can give me a half-life. (I am not a TS expert or an R expert, and perhaps not really an expert on anything. I hope these questions are not obscure.) I must admit that I only know the half-life of an AR1, not the half-life of an MA1, much less that of a GARIMA(?,1,0,1).
A few quick points:
You have typos in your question. It is rugarch, not guarch
rugarch by Alexios is a very powerful, and very demanding package. It relies on a (large) number of other packages. Your installation failed, among other things, because you did not have as many preconditions met as you could have.
With that, for starters do a sudo apt-get install r-cran-rcpparmadillo r-cran-rgl. Particularly rgl is tricky as you need to realize that you need OpenGL headers, so why not take the binary package. Ditto for RcppArmadillo which will also get you Rcpp.
Once you do that, chances are that the installation succeeds. I just tested in a virtual machine with Ubuntu 14.04, and it was no problem. If things fail, examine build failures closely.
For reference, below is the installation on a system which already had a number of other packages installed, including Rcpp and rgl, but which still needed a large number for rugarch. This is eunning inside a Docker container, henec the root user and funky hostname. install.r is a helper script from the littler package.
root#96097d7112b1:/# install.r rugarch
install.r rugarch
also installing the dependencies 'truncnorm', 'misc3d', 'multicool', 'DistributionUtils', 'GeneralizedHyperbolic', 'RUnit', 'Rsolnp', 'nloptr', 'ks', 'numDeriv', 'spd', 'xts', 'chron', 'SkewHyperbolic', 'expm', 'RcppArmadillo'
trying URL [.... downloads omitted to keep this within 30kb limit for SO... ]
* installing *source* package 'truncnorm' ...
** package 'truncnorm' successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rtruncnorm.c -o rtruncnorm.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c truncnorm.c -o truncnorm.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c zeroin.c -o zeroin.o
gcc -std=gnu99 -shared -Wl,-z,relro -o truncnorm.so rtruncnorm.o truncnorm.o zeroin.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/truncnorm/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (truncnorm)
* installing *source* package 'misc3d' ...
** package 'misc3d' successfully unpacked and MD5 sums checked
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (misc3d)
* installing *source* package 'multicool' ...
** package 'multicool' successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c multicool.cpp -o multicool.o
g++ -shared -Wl,-z,relro -o multicool.so multicool.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/multicool/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (multicool)
* installing *source* package 'RUnit' ...
** package 'RUnit' successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RUnit)
* installing *source* package 'nloptr' ...
** package 'nloptr' successfully unpacked and MD5 sums checked
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking for pkg-config... no
configure: Now testing for NLopt header file.
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking nlopt.h usability... no
checking nlopt.h presence... no
checking for nlopt.h... no
configure: Need to download and build NLopt
trying URL 'http://ab-initio.mit.edu/nlopt/nlopt-2.4.2.tar.gz'
Content type 'application/x-gzip' length 2361992 bytes (2.3 Mb)
opened URL
==================================================
downloaded 2.3 Mb
configure: Starting to install library to /tmp/RtmphBrgVr/R.INSTALL2431668f0e2/nloptr/nlopt-2.4.2
configure: Done installing library to /tmp/RtmphBrgVr/R.INSTALL2431668f0e2/nloptr/nlopt-2.4.2
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c dummy.cpp -o dummy.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/tmp/RtmphBrgVr/R.INSTALL2431668f0e2/nloptr/nlopt-2.4.2/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c nloptr.c -o nloptr.o
g++ -shared -Wl,-z,relro -o nloptr.so dummy.o nloptr.o -lm /tmp/RtmphBrgVr/R.INSTALL2431668f0e2/nloptr/nlopt-2.4.2/lib/libnlopt_cxx.a -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/nloptr/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (nloptr)
* installing *source* package 'numDeriv' ...
** package 'numDeriv' successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'Guide.Stex'
** testing if installed package can be loaded
* DONE (numDeriv)
* installing *source* package 'spd' ...
** package 'spd' successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
Creating a generic function from function 'gpdfit' in package 'spd'
Creating a generic function from function 'spdfit' in package 'spd'
Creating a generic function from function 'pspd' in package 'spd'
Creating a generic function from function 'dspd' in package 'spd'
Creating a generic function from function 'qspd' in package 'spd'
Creating a generic function from function 'rspd' in package 'spd'
Creating a generic function for 'plot' from package 'graphics' in package 'spd'
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (spd)
* installing *source* package 'xts' ...
** package 'xts' successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c add_class.c -o add_class.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c any.c -o any.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c attr.c -o attr.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c binsearch.c -o binsearch.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c coredata.c -o coredata.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c diff.c -o diff.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c dimnames.c -o dimnames.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c endpoints.c -o endpoints.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c extract_col.c -o extract_col.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c isOrdered.c -o isOrdered.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c isXts.c -o isXts.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c leadingNA.c -o leadingNA.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c merge.c -o merge.o
gfortran -fpic -g -O2 -fstack-protector-strong -c period.max.f -o period.max.o
gfortran -fpic -g -O2 -fstack-protector-strong -c period.min.f -o period.min.o
gfortran -fpic -g -O2 -fstack-protector-strong -c period.prod.f -o period.prod.o
gfortran -fpic -g -O2 -fstack-protector-strong -c period.sum.f -o period.sum.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rbind.c -o rbind.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rollfun.c -o rollfun.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c runSum.c -o runSum.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c startofyear.c -o startofyear.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c subset.c -o subset.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c subset.old.c -o subset.old.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c toperiod.c -o toperiod.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c totalcols.c -o totalcols.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c tryXts.c -o tryXts.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c unique.time.c -o unique.time.o
gcc -std=gnu99 -shared -Wl,-z,relro -o xts.so add_class.o any.o attr.o binsearch.o coredata.o diff.o dimnames.o endpoints.o extract_col.o init.o isOrdered.o isXts.o leadingNA.o merge.o period.max.o period.min.o period.prod.o period.sum.o rbind.o rollfun.o runSum.o startofyear.o subset.o subset.old.o toperiod.o totalcols.o tryXts.o unique.time.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/xts/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (xts)
* installing *source* package 'chron' ...
** package 'chron' successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c chron_strs.c -o chron_strs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c unpaste.c -o unpaste.o
gcc -std=gnu99 -shared -Wl,-z,relro -o chron.so chron_strs.o init.o unpaste.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/chron/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (chron)
* installing *source* package 'expm' ...
** package 'expm' successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c R_dgebal.c -o R_dgebal.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c expm-eigen.c -o expm-eigen.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c expm.c -o expm.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c logm-eigen.c -o logm-eigen.o
gfortran -fpic -g -O2 -fstack-protector-strong -c matexp.f -o matexp.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c matpow.c -o matpow.o
gfortran -fpic -g -O2 -fstack-protector-strong -c matrexp.f -o matrexp.o
gfortran -fpic -g -O2 -fstack-protector-strong -c matrexpO.f -o matrexpO.o
gfortran -fpic -g -O2 -fstack-protector-strong -c mexp-common.f -o mexp-common.o
gcc -std=gnu99 -shared -Wl,-z,relro -o expm.so R_dgebal.o expm-eigen.o expm.o init.o logm-eigen.o matexp.o matpow.o matrexp.o matrexpO.o mexp-common.o -llapack -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/expm/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (expm)
* installing *source* package 'RcppArmadillo' ...
** package 'RcppArmadillo' successfully unpacked and MD5 sums checked
* checking LAPACK_LIBS: divide-and-conquer complex SVD available via system LAPACK
** libs
g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I../inst/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppArmadillo.cpp -o RcppArmadillo.o
g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I../inst/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I../inst/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c fastLm.cpp -o fastLm.o
g++ -shared -Wl,-z,relro -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/RcppArmadillo/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RcppArmadillo)
* installing *source* package 'DistributionUtils' ...
** package 'DistributionUtils' successfully unpacked and MD5 sums checked
** libs
gfortran -fpic -g -O2 -fstack-protector-strong -c IncompleteBessel.f -o IncompleteBessel.o
gcc -std=gnu99 -shared -Wl,-z,relro -o DistributionUtils.so IncompleteBessel.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/DistributionUtils/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (DistributionUtils)
* installing *source* package 'Rsolnp' ...
** package 'Rsolnp' successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (Rsolnp)
* installing *source* package 'ks' ...
** package 'ks' successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ks.c -o ks.o
gcc -std=gnu99 -shared -Wl,-z,relro -o ks.so ks.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/ks/libs
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
RGL: unable to open X11 display
Warning in fun(libname, pkgname) : error in rgl_init
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
RGL: unable to open X11 display
Warning in fun(libname, pkgname) : error in rgl_init
* DONE (ks)
* installing *source* package 'GeneralizedHyperbolic' ...
** package 'GeneralizedHyperbolic' successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (GeneralizedHyperbolic)
* installing *source* package 'SkewHyperbolic' ...
** package 'SkewHyperbolic' successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (SkewHyperbolic)
* installing *source* package 'rugarch' ...
** package 'rugarch' successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c distributions.c -o distributions.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c filters.c -o filters.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c fracdiff.c -o fracdiff.o
gfortran -fpic -g -O2 -fstack-protector-strong -c fracimport.f -o fracimport.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c garchmodels.c -o garchmodels.o
g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c garchsim.cpp -o garchsim.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c gig.c -o gig.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c nig.c -o nig.o
g++ -shared -Wl,-z,relro -o rugarch.so distributions.o filters.o fracdiff.o fracimport.o garchmodels.o garchsim.o gig.o nig.o -llapack -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/rugarch/libs
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
RGL: unable to open X11 display
Warning in fun(libname, pkgname) : error in rgl_init
Creating a generic function from function 'ugarchspec' in package 'rugarch'
Creating a generic function from function 'getspec' in package 'rugarch'
Creating a generic function from function 'ugarchfilter' in package 'rugarch'
Creating a generic function from function 'ugarchfit' in package 'rugarch'
Creating a generic function from function 'ugarchforecast' in package 'rugarch'
Creating a generic function from function 'ugarchsim' in package 'rugarch'
Creating a generic function from function 'ugarchpath' in package 'rugarch'
Creating a generic function from function 'resume' in package 'rugarch'
Creating a generic function from function 'ugarchroll' in package 'rugarch'
Creating a generic function from function 'ugarchdistribution' in package 'rugarch'
Creating a generic function from function 'ugarchboot' in package 'rugarch'
Creating a generic function for 'plot' from package 'graphics' in package 'rugarch'
Creating a generic function from function 'report' in package 'rugarch'
Creating a generic function for 'coef' from package 'stats' in package 'rugarch'
Creating a generic function for 'as.data.frame' from package 'base' in package 'rugarch'
Creating a generic function for 'residuals' from package 'stats' in package 'rugarch'
Creating a generic function from function 'sigma' in package 'rugarch'
Creating a generic function from function 'nyblom' in package 'rugarch'
Creating a generic function from function 'signbias' in package 'rugarch'
Creating a generic function from function 'gof' in package 'rugarch'
Creating a generic function from function 'infocriteria' in package 'rugarch'
Creating a generic function from function 'likelihood' in package 'rugarch'
Creating a generic function for 'fitted' from package 'stats' in package 'rugarch'
Creating a generic function from function 'reduce' in package 'rugarch'
Creating a generic function for 'quantile' from package 'stats' in package 'rugarch'
Creating a generic function from function 'pit' in package 'rugarch'
Creating a generic function from function 'newsimpact' in package 'rugarch'
Creating a generic function from function 'halflife' in package 'rugarch'
Creating a generic function from function 'persistence' in package 'rugarch'
Creating a generic function from function 'uncvariance' in package 'rugarch'
Creating a generic function from function 'uncmean' in package 'rugarch'
Creating a generic function from function 'multispec' in package 'rugarch'
Creating a generic function from function 'multifit' in package 'rugarch'
Creating a generic function from function 'multifilter' in package 'rugarch'
Creating a generic function from function 'multiforecast' in package 'rugarch'
Creating a generic function from function 'fpm' in package 'rugarch'
Creating a generic function from function 'convergence' in package 'rugarch'
Creating a generic function for 'vcov' from package 'stats' in package 'rugarch'
Creating a generic function from function 'arfimaspec' in package 'rugarch'
Creating a generic function from function 'arfimafit' in package 'rugarch'
Creating a generic function from function 'arfimafilter' in package 'rugarch'
Creating a generic function from function 'arfimaforecast' in package 'rugarch'
Creating a generic function from function 'arfimasim' in package 'rugarch'
Creating a generic function from function 'arfimapath' in package 'rugarch'
Creating a generic function from function 'arfimaroll' in package 'rugarch'
Creating a generic function from function 'arfimadistribution' in package 'rugarch'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
RGL: unable to open X11 display
Warning in fun(libname, pkgname) : error in rgl_init
* DONE (rugarch)
The downloaded source packages are in
'/tmp/downloaded_packages'
root#96097d7112b1:/#