I cannot install qpcR package, using this command in R:
install.packages("qpcR")
Apparently, everything looks fine initially:
Installing package into ‘/home/emanuel/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/qpcR_1.4-1.tar.gz'
Content type 'application/x-gzip' length 4303726 bytes (4.1 MB)
==================================================
downloaded 4.1 MB
* installing *source* package ‘qpcR’ ...
** package ‘qpcR’ 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 registerDynamicSymbol.c -o registerDynamicSymbol.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 smth.c -o smth.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o qpcR.so registerDynamicSymbol.o smth.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
And then things starts to going wrong:
usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
collect2: error: ld returned 1 exit status
/usr/share/R/share/make/shlib.mk:6: recipe for target 'qpcR.so' failed
make: *** [qpcR.so] Error 1
ERROR: compilation failed for package ‘qpcR’
* removing ‘/home/emanuel/R/x86_64-pc-linux-gnu-library/3.4/qpcR’
Warning in install.packages :
installation of package ‘qpcR’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpOPiQkB/downloaded_packages’
Additional (maybe) relevant info:
Before the lines presented above, I was having trouble with another qpcR dependence, the rgl package, and I solved trying all the suggestions from another question: "Error in installing rgl package".
I made a brief search about: "-llpack", "-lblas", "qpcR.so" .Unfortunately nothing seems (to me at least) to be related to my specific problem.
I using Mint with these specifications: Linux version 4.8.0-53-generic (buildd#lgw01-56) (gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.4) ) #56~16.04.1-Ubuntu
R version 3.4.4
R studio Version 1.1.453
Thanks in advance for any help!
satisfy the dependencies using this command in terminal.
sudo apt-get install libblas-dev liblapack-dev
hope this helps (Y)
Related
I've downloaded an old repo on a new laptop (running on MacOS Catalina) and attempted to run a R script.
The repo has a renv lock file - meaning, I should be able to restore all dependencies as they were.
But as I run the renv::restore() command, this error message appears:
Installing pbapply [1.4-3] ...
OK [linked cache]
Installing mvtnorm [1.1-2] ...
FAILED
Error installing package 'mvtnorm':
===================================
* installing to library ‘~/renv/staging/2’
* installing *source* package ‘mvtnorm’ ...
** package ‘mvtnorm’ successfully unpacked and MD5 sums checked
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c C_FORTRAN_interface.c -o C_FORTRAN_interface.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c miwa.c -o miwa.o
gfortran -fPIC -g -O2 -c mvt.f -o mvt.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c mvtnorm-init.c -o mvtnorm-init.o
gfortran -fPIC -g -O2 -c tvpack.f -o tvpack.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o mvtnorm.so C_FORTRAN_interface.o miwa.o mvt.o mvtnorm-init.o tvpack.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [mvtnorm.so] Error 1
ERROR: compilation failed for package ‘mvtnorm’
* removing ‘~/renv/staging/2/mvtnorm’
------------------------------------------------------------------------------
R was unable to find one or more FORTRAN libraries during compilation.
This often implies that the FORTRAN compiler has not been properly configured.
Please see https://stackoverflow.com/q/35999874 for more information.
Reason(s):
- 'ld: library not found for -lgfortran'
Error: install of package 'mvtnorm' failed [error code 1]
Traceback (most recent calls last):
13: renv::restore()
12: renv_restore_run_actions(project, diff, current, lockfile, rebuild)
11: renv_install(records)
10: renv_install_staged(records)
9: renv_install_default(records)
8: handler(package, renv_install_impl(record))
7: renv_install_impl(record)
6: withCallingHandlers(renv_install_package_local(record), error = function(e) {
vwritef("\tFAILED")
writef(e$output)
})
5: renv_install_package_local(record)
4: renv_install_package_local_impl(package, path)
3: r_cmd_install(package, path)
2: r_exec_error(package, output, "install", status)
1: stop(error)
I can't make sense of the link in the error message (copied here: Mac OS X R error "ld: warning: directory not found for option").
From my problem search, I've come across some possible solutions that are above my R knowledge level, e.g.:
"[...] creating the file ~/.R/Makevars within my home directory." (Unable to install fortran based packages in R - "gfortran -m32:not found")
"[...] installed gcc & gcc-fortran and that solved it" (Unable to install a package on R)
Similar ideas here: OS X package installation depends on gfortran-4.8
Some guidance here would be deeply appreciated. Please let me know if there's any other info you need (first time posting here).
Thanks in advance!
Solution
Download and install "gfortran-6.1.pkg (OS X 10.11+, signed, 64-bit)" from this page: https://cran.r-project.org/bin/macosx/tools/
Upon executing 'Rscript -e "install.packages('mclust')"` with R 4.0.1 on Ubuntu 20.04, the process hangs during package preparation. Any idea how to fix or debug this issue?
ENV: R v4.0.1, GCC v9, Ubuntu v20.04
CMD: Rscript -e "install.packages('mclust')"
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/mclust_5.4.6.tar.gz'
Content type 'application/x-gzip' length 2877519 bytes (2.7 MB)
==================================================
downloaded 2.7 MB
* installing *source* package ‘mclust’ ...
** package ‘mclust’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-dEscXG/r-base-4.0.1=. -fstack-protector-strong -c dmvnorm.f -o dmvnorm.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-dEscXG/r-base-4.0.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-dEscXG/r-base-4.0.1=. -fstack-protector-strong -c mclust.f -o mclust.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-dEscXG/r-base-4.0.1=. -fstack-protector-strong -c mclustaddson.f -o mclustaddson.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o mclust.so dmvnorm.o init.o mclust.o mclustaddson.o -llapack -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/00LOCK-mclust/00new/mclust/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Based on the response on R-sig-debian for a similar issue, I figured this issue is due to a bug in the pthread-based versions of Blas and Lapack libraries.
Until the bug is fixed, the workaround is to use libopenblas-openmp-blas and libopenblas-openmp-lapack libraries.
There are two ways to achieve use these libraries.
Uninstall the pthread-based version of the libraries and install the openmp-based version of the libraries.
Switch to openmp-based version of the libraries via update-alternatives. This can be done via sudo update-alternatives --config <name> command with being liblapack.so.3-x86_64-linux-gnu and libblas.so.3-x86_64-linux-gnu.
I have R (version 3.6.3 (2020-02-29), Holding the Windsock) installed on Ubuntu 18.04.4 LTS. When I try to install ggplot2 from source, the installation of dependency package isoband fails with testthat.h not found. The full output:
> install.packages("ggplot2")
Installing package into ‘/home/oszkar/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
also installing the dependency ‘isoband’
trying URL 'https://cloud.r-project.org/src/contrib/isoband_0.2.1.tar.gz'
Content type 'application/x-gzip' length 2293333 bytes (2.2 MB)
==================================================
downloaded 2.2 MB
trying URL 'https://cloud.r-project.org/src/contrib/ggplot2_3.3.0.tar.gz'
Content type 'application/x-gzip' length 3031461 bytes (2.9 MB)
==================================================
downloaded 2.9 MB
* installing *source* package ‘isoband’ ...
** package ‘isoband’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I"/home/oszkar/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include"
-I"/usr/local/lib/R/site-library/testthat/include" -fpic -g -O2
-fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=.
-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/oszkar/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include"
-I"/usr/local/lib/R/site-library/testthat/include" -fpic -g -O2
-fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c clip-lines.cpp -o clip-lines.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I"/home/oszkar/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include"
-I"/usr/local/lib/R/site-library/testthat/include" -fpic -g -O2
-fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c isoband.cpp -o isoband.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I"/home/oszkar/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include"
-I"/usr/local/lib/R/site-library/testthat/include" -fpic -g -O2
-fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c polygon.cpp -o polygon.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I"/home/oszkar/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include"
-I"/usr/local/lib/R/site-library/testthat/include" -fpic -g -O2
-fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c separate-polygons.cpp -o separate-polygons.o
separate-polygons.cpp:4:10: fatal error: testthat.h: No such file or directory
#include <testthat.h>
^~~~~~~~~~~~
compilation terminated.
/usr/lib/R/etc/Makeconf:177: recipe for target 'separate-polygons.o' failed
make: *** [separate-polygons.o] Error 1
ERROR: compilation failed for package ‘isoband’
* removing ‘/home/oszkar/R/x86_64-pc-linux-gnu-library/3.6/isoband’
Warning in install.packages :
installation of package ‘isoband’ had non-zero exit status
ERROR: dependency ‘isoband’ is not available for package ‘ggplot2’
* removing ‘/home/oszkar/R/x86_64-pc-linux-gnu-library/3.6/ggplot2’
Warning in install.packages :
installation of package ‘ggplot2’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmp5aYRcO/downloaded_packages’
I have already tried to install testthat manually, but it seems not to be available for R 3.6.3:
> install.packages("testthat")
...
Error: package or namespace load failed for ‘pkgload’:
.onLoad failed in loadNamespace() for 'pkgload', details:
call: NULL
error: package ‘testthat’ was installed by an R version with different internals;
it needs to be reinstalled for use with this R version
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/oszkar/R/x86_64-pc-linux-gnu-library/3.6/pkgload’
Warning in install.packages :
installation of package ‘pkgload’ had non-zero exit status
ERROR: dependency ‘pkgload’ is not available for package ‘testthat’
* removing ‘/home/oszkar/R/x86_64-pc-linux-gnu-library/3.6/testthat’
Warning in install.packages :
installation of package ‘testthat’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmp5aYRcO/downloaded_packages’
Any idea would be appreciated.
Solved. The cause of the problem was that after a series of Ubuntu and R upgrades there were some outdated packages installed from source remained on my system.
First I opened up an R console and looking for the paths for R packages built with pre 3.6 version:
> unique(subset(as.data.frame(installed.packages()),
grepl("^3\\.[^6]", Built))[, "LibPath"])
[1] /usr/local/lib/R/site-library /usr/lib/R/library
As it is not possible to apply remove.packages() on these outdated packages, I switched to bash, and listed all the package paths:
>grep 'Built: R 3.[0-5]' /usr/local/lib/R/site-library/*/DESCRIPTION /usr/lib/R/library/*/
DESCRIPTION
I have removed (simply deleted from /usr/local/lib/R/site-library/ and /usr/lib/R/library/) the packages on the previous commands output, and now everything works.
I need to access an Azure SQL Database from an R notebook in Databricks. To do this I aimed to use the odbc package, which installed fine on my local instance of R.
I have tried to install the package to the cluster using Databricks' interface, which always fails. I have also tried the following code within a notebook:
install.packages("odbc")
which results in:
Installing package into ‘/databricks/spark/R/lib’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/odbc_1.1.6.tar.gz'
Content type 'application/x-gzip' length 288033 bytes (281 KB)
==================================================
downloaded 281 KB
* installing *source* package ‘odbc’ ...
** package ‘odbc’ successfully unpacked and MD5 sums checked
PKG_CFLAGS=
PKG_LIBS=-lodbc
<stdin>:1:17: fatal error: sql.h: No such file or directory
compilation terminated.
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because odbc was not found. Try installing:
* deb: unixodbc-dev (Debian, Ubuntu, etc)
* rpm: unixODBC-devel (Fedora, CentOS, RHEL)
* csw: unixodbc_dev (Solaris)
* brew: unixodbc (Mac OSX)
To use a custom odbc set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘odbc’
* removing ‘/databricks/spark/R/lib/odbc’
The downloaded source packages are in
‘/tmp/RtmpqHp2QM/downloaded_packages’
I have also tried installing from github:
library(devtools)
devtools::install_github("r-dbi/odbc")
Which gives a different error:
Downloading GitHub repo r-dbi/odbc#master
Installing 3 packages: assertthat, BH, Rcpp
Installing packages into ‘/databricks/spark/R/lib’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/assertthat_0.2.1.tar.gz'
Content type 'application/x-gzip' length 12742 bytes (12 KB)
==================================================
downloaded 12 KB
trying URL 'https://cloud.r-project.org/src/contrib/BH_1.69.0-1.tar.gz'
Content type 'application/x-gzip' length 12378154 bytes (11.8 MB)
==================================================
downloaded 11.8 MB
trying URL 'https://cloud.r-project.org/src/contrib/Rcpp_1.0.1.tar.gz'
Content type 'application/x-gzip' length 3661123 bytes (3.5 MB)
==================================================
downloaded 3.5 MB
* installing *source* package ‘assertthat’ ...
** package ‘assertthat’ 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 (assertthat)
* installing *source* package ‘BH’ ...
** package ‘BH’ successfully unpacked and MD5 sums checked
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (BH)
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Date.cpp -o Date.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Module.cpp -o Module.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rcpp_init.cpp -o Rcpp_init.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c api.cpp -o api.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c attributes.cpp -o attributes.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c barrier.cpp -o barrier.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o -L/usr/lib/R/lib -lR
installing to /databricks/spark/R/lib/Rcpp/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 (Rcpp)
The downloaded source packages are in
‘/tmp/RtmpqHp2QM/downloaded_packages’
Error in processx::run(bin, args = real_cmdargs, stdout_line_callback = real_callback(stdout), :
System command error
In addition: Warning messages:
1: In install.packages("odbc") :
installation of package ‘odbc’ had non-zero exit status
2: In install.packages("odbc") :
installation of package ‘odbc’ had non-zero exit status
Any idea why this package will not install on Databricks when it works fine locally and when all other packages I have tried install on Databricks work fine using the same syntax?
Best option to access a SQL Database is using the preinstalled JDBC connectivity (see the Documentation).
If you want to use ODBC this requires (as mentioned in one of the comments) unix odbc. Good practice to install multiple packages is using init-scripts. Following python code is for creating an init-script for pyodbc installation.
script = """
sudo apt-get -q -y install unixodbc unixodbc-dev
sudo apt-get -q -y install python3-dev
sudo pip install pyodbc
curl https://packages.microsoft.com/keys/microsoft.asc | apt-key add -
sudo curl https://packages.microsoft.com/config/ubuntu/16.04/prod.list > /etc/apt/sources.list.d/mssql-release.list
sudo apt-get update
sudo ACCEPT_EULA=Y apt-get -q -y install msodbcsql
"""
dbutils.fs.put("/databricks/init/pyodbc/pyodbc.sh", script, True)
Hope this helps.
When I go to my app address for a simple histogram app I get the following error:
An error has occurred
The application failed to start.
The application exited during initialization.
Error in eval(expr, envir, enclos) : The Shiny package was not found
in the library. Ensure that Shiny is installed and is available in the
Library of the user you're running this application as. Calls: local
-> eval.parent -> eval -> eval -> eval -> eval Execution halted
So I try to reinstall the shiny package and I get this message which I am having trouble interpreting into the next course of action. Maybe I need to be explicit about install dependencies?
xxxxxxxxxxxx:~$ sudo su - \
> -c "R -e \"install.packages('shiny', repos='http://cran.rstudio.com/')\""
R version 3.1.0 RC (2014-04-05 r65382) -- "Spring Dance"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> install.packages('shiny', repos='http://cran.rstudio.com/')
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
also installing the dependencies ‘Rcpp’, ‘httpuv’
trying URL 'http://cran.rstudio.com/src/contrib/Rcpp_0.11.1.tar.gz'
Content type 'application/x-gzip' length 2003515 bytes (1.9 Mb)
opened URL
==================================================
downloaded 1.9 Mb
trying URL 'http://cran.rstudio.com/src/contrib/httpuv_1.3.0.tar.gz'
Content type 'application/x-gzip' length 423739 bytes (413 Kb)
opened URL
==================================================
downloaded 413 Kb
trying URL 'http://cran.rstudio.com/src/contrib/shiny_0.9.1.tar.gz'
Content type 'application/x-gzip' length 958658 bytes (936 Kb)
opened URL
==================================================
downloaded 936 Kb
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -g -c Date.cpp -o Date.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -g -c Module.cpp -o Module.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -g -c Rcpp_init.cpp -o Rcpp_init.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -g -c api.cpp -o api.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -g -c attributes.cpp -o attributes.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -g -c barrier.cpp -o barrier.o
g++ -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/Rcpp/libs
** R
** inst
** preparing package for lazy loading
Error : package ‘codetools’ was built before R 3.0.0: please re-install it
Error : unable to load R code in package ‘Rcpp’
ERROR: lazy loading failed for package ‘Rcpp’
* removing ‘/usr/local/lib/R/site-library/Rcpp’
ERROR: dependency ‘Rcpp’ is not available for package ‘httpuv’
* removing ‘/usr/local/lib/R/site-library/httpuv’
ERROR: dependency ‘httpuv’ is not available for package ‘shiny’
* removing ‘/usr/local/lib/R/site-library/shiny’
The downloaded source packages are in
‘/tmp/RtmpRLRUsk/downloaded_packages’
Warning messages:
1: In install.packages("shiny", repos = "http://cran.rstudio.com/") :
installation of package ‘Rcpp’ had non-zero exit status
2: In install.packages("shiny", repos = "http://cran.rstudio.com/") :
installation of package ‘httpuv’ had non-zero exit status
3: In install.packages("shiny", repos = "http://cran.rstudio.com/") :
installation of package ‘shiny’ had non-zero exit status
After installing the codetools package according to jdharrison's advice, I retried installing shiny and then stated that I needed to reinstall RJSONIO. I then installed RJSONIO and tried installing shiny again. Now it is asking me for package caTools. When I install caTools it asks for bittops. I then try installing caTools again and it needs package digest. I install that, try shiny again and it asks for xtable. I install xtable and now shiny installs! now shiny server is working.