today I upgraded to R 3.3.0... oh boy.. wish I stayed at the previous version.
The last few hours I have been trying to solve some issues to install car and sjPlot, but problems remain.
When installing sjPlot everything goes fine, but when setting the library, I get this error:
error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘quantreg’
Error: package or namespace load failed for ‘sjPlot’
Something similar occurs with car, during installation:
installing the source package ‘quantreg’
trying URL 'https://lib.ugent.be/CRAN/src/contrib/quantreg_5.26.tar.gz'
Content type 'unknown' length 1720216 bytes (1.6 MB)
==================================================
downloaded 1.6 MB
* installing *source* package ‘quantreg’ ...
** package ‘quantreg’ successfully unpacked and MD5 sums checked
** libs
gfortran-4.8 -fPIC -g -O2 -c akj.f -o akj.o
gfortran-4.8 -fPIC -g -O2 -c boot.f -o boot.o
gfortran-4.8 -fPIC -g -O2 -c bound.f -o bound.o
gfortran-4.8 -fPIC -g -O2 -c boundc.f -o boundc.o
gfortran-4.8 -fPIC -g -O2 -c brute.f -o brute.o
/var/folders/lp/ndh7gxxs6vn0ldd3fqblq7k80000gn/T//ccbxq8DR.s:37:expecting string instruction after `rep'
make: *** [brute.o] Error 1
ERROR: compilation failed for package ‘quantreg’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/quantreg’
The downloaded source packages are in
‘/private/var/folders/lp/ndh7gxxs6vn0ldd3fqblq7k80000gn/T/RtmpNPzXls/downloaded_packages’
Warning message:
In install.packages("car") :
installation of package ‘quantreg’ had non-zero exit status
Any thoughts on what I can do to solve this??
Thanks
Related
I'm new in R and I've been having some issues installing Hmisc package in order to elaborate a Spearman's correlation heatmap. The warning and error are as follows:
18 warnings generated.
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c bilinear.f -o bilinear.o
make: gfortran: No such file or directory
make: *** [bilinear.o] Error 1
ERROR: compilation failed for package ‘interp’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/interp’
Warning in install.packages :
installation of package ‘interp’ had non-zero exit status
* installing *source* package ‘polspline’ ...
** package ‘polspline’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c allpack.f -o allpack.o
make: gfortran: No such file or directory
make: *** [allpack.o] Error 1
ERROR: compilation failed for package ‘polspline’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/polspline’
Warning in install.packages :
installation of package ‘polspline’ had non-zero exit status
* installing *source* package ‘VGAM’ ...
** package ‘VGAM’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c VGAM_init.c -o VGAM_init.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c caqo3.c -o caqo3.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c ei.f -o ei.o
make: gfortran: No such file or directory
make: *** [ei.o] Error 1
ERROR: compilation failed for package ‘VGAM’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/VGAM’
Warning in install.packages :
installation of package ‘VGAM’ had non-zero exit status
ERROR: dependency ‘interp’ is not available for package ‘latticeExtra’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/latticeExtra’
Warning in install.packages :
installation of package ‘latticeExtra’ had non-zero exit status
ERROR: dependency ‘latticeExtra’ is not available for package ‘Hmisc’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Hmisc’
Warning in install.packages :
installation of package ‘Hmisc’ had non-zero exit status
ERROR: dependencies ‘Hmisc’, ‘polspline’ are not available for package ‘rms’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rms’
Warning in install.packages :
installation of package ‘rms’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/8b/43x_77fx1p73gb68h2418m5r0000gn/T/RtmpIhACeD/downloaded_packages.
PS. I'm also a Mac user, and I've trying to solve it as some of you guys have suggested in other similar questions,
I've used:
-adding dependencies=true in the script.
-installing tydiverse package
-installing backports
I'm trying to install MVN package:
> install.packages("MVN")
probando la URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.5/MVN_5.5.tgz'
Content type 'application/x-gzip' length 382369 bytes (373 KB)
==================================================
downloaded 373 KB
The downloaded binary packages are in
/var/folders/79/xxghr9tj65789879v41wrp6h0000gn/T//Rtmp4bpod5/downloaded_packages
but when I do library(MVN) it says me that Error: package or namespace load failed for ‘MVN’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘rrcov’
so when I try to install it:
> install.packages("rrcov")
There is a binary version available but the source version is later:
binary source needs_compilation
rrcov 1.4-4 1.4-7 TRUE
Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes
installing the source package ‘rrcov’
probando la URL 'https://cran.rstudio.com/src/contrib/rrcov_1.4-7.tar.gz'
Content type 'application/x-gzip' length 965680 bytes (943 KB)
==================================================
downloaded 943 KB
* installing *source* package ‘rrcov’ ...
** package ‘rrcov’ 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 R-rng4ftn.c -o R-rng4ftn.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c covOPW.c -o covOPW.o
gfortran -fPIC -g -O2 -c ds11.f -o ds11.o
gfortran: warning: couldn’t understand kern.osversion ‘15.6.0
f951: internal compiler error: Illegal instruction: 4
f951: internal compiler error: Abort trap: 6
gfortran: internal compiler error: Abort trap: 6 (program f951)
make: *** [ds11.o] Abort trap: 6
ERROR: compilation failed for package ‘rrcov’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rrcov’
Warning in install.packages :
installation of package ‘rrcov’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/79/xxghr9tj65789879v41wrp6h0000gn/T/Rtmp4bpod5/downloaded_packages’
I've searched how to fix that, installing XCode, reinstalling r, and nothing. I need this package to perfom some multivariate analysis for my thesis but I do not know how to fix it.
Any help will be appreciated.
Thanks!
I am using an iOS 10.11.6
I am having an issue when installing the "mclust" package on rstudio.
Here is the warning message:
>install.packages("mclust")
trying URL 'https://cran.rstudio.com/src/contrib/mclust_5.4.tar.gz'
Content type 'application/x-gzip' length 2535477 bytes (2.4 MB)
==================================================
downloaded 2.4 MB
* installing *source* package ‘mclust’ ...
** package ‘mclust’ successfully unpacked and MD5 sums checked
** libs
/home/usr/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -
I/home/usr/anaconda3/lib/R/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2
-I/home/usr/anaconda3/include -fpic -march=nocona -mtune=haswell -
ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -
I/home/usr/anaconda3/include -c init.c -o init.o
make: /home/usr/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc: Command
not found
/home/usr/anaconda3/lib/R/etc/Makeconf:160: recipe for target 'init.o'
failed
make: *** [init.o] Error 127
ERROR: compilation failed for package ‘mclust’
* removing ‘/home/usr/anaconda3/lib/R/library/mclust’
Warning in install.packages :
installation of package ‘mclust’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpGCCIZS/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
In addition, I also tried to access the directory /home.usr/anaconda3/x86_64-conda_cos6-linux-gnu-cc ,which apparently doesn't exist.
I have a 5 node BigInsights hadoop cluster in Bluemix. I am getting error, when I am trying to install H2O ai R in BigInsights cluster.
install.packages("h2o", type="source", repos=(c("http://h2o-release.s3.amazonaws.com/h2o/rel-turing/3/R")))
ERROR: dependencies ‘statmod’, ‘RCurl’, ‘jsonlite’ are not available for package ‘h2o’
* removing ‘/home/opus/R/x86_64-redhat-linux-gnu-library/3.3/h2o’
The downloaded source packages are in
‘/tmp/RtmpJmcuyB/downloaded_packages’
Warning message:
In install.packages("h2o", type = "source", repos = (c("http://h2o-release.s3.amazonaws.com/h2o/rel-turing/3/R"))) :
installation of package ‘h2o’ had non-zero exit status
When I try to install 'RCurl' package of R in BigInsights cluster, getting the error message as:
trying URL 'https://cran.fhcrc.org/src/contrib/RCurl_1.95-4.8.tar.gz'
Content type 'application/x-gzip' length 916934 bytes (895 KB)
==================================================
downloaded 895 KB
* installing *source* package ‘bitops’ ...
** package ‘bitops’ successfully unpacked and MD5 sums checked
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c bit-ops.c -o bit-ops.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c cksum.c -o cksum.o
gcc -m64 -std=gnu99 -shared -L/usr/lib64/R/lib -o bitops.so bit-ops.o cksum.o -L/usr/lib64/R/lib -lR
installing to /home/opus/R/x86_64-redhat-linux-gnu-library/3.3/bitops/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
converting help for package ‘bitops’
finding HTML links ... done
bitAnd html
bitFlip html
bitShiftL html
cksum html
** building package indices
** testing if installed package can be loaded
* DONE (bitops)
* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/home/opus/R/x86_64-redhat-linux-gnu-library/3.3/RCurl’
The downloaded source packages are in
‘/tmp/RtmpJmcuyB/downloaded_packages’
Warning message:
In install.packages("RCurl") :
installation of package ‘RCurl’ had non-zero exit status
Please help me to resolve the issue and help would be much appreciated.
It looks like you are trying to install on Linux.
You need to install the development files for libcurl first.
eg
apt-get install libcurl4-openssl-dev
or
yum install libcurl-devel
install.packages('forecast')
Installing package into ‘/usr/lib64/R/library’
(as ‘lib’ is unspecified)
trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/forecast_5.4.tar.gz'
Content type 'application/x-gzip' length 150965 bytes (147 Kb)
opened URL
downloaded 147 Kb
installing source package ‘forecast’ ...
package ‘forecast’ successfully unpacked and MD5 sums checked
libs
g++ -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RcppArmadillo/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c calcBATS.cpp -o calcBATS.o
In file included from calcBATS.cpp:1:0:
calcBATS.h:36:27: fatal error: RcppArmadillo.h: No such file or directory
#include
^
compilation terminated.
make: * [calcBATS.o] Error 1
ERROR: compilation failed for package ‘forecast’
* removing ‘/usr/lib64/R/library/forecast’
The downloaded source packages are in
‘/tmp/RtmpJRX18M/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("forecast") :
installation of package ‘forecast’ had non-zero exit status
Looks like there is a missing package dependence, RcppArmadillo.
install.packages("RcppArmadillo")
Then:
install.packages('forecast')
add within your lifecycle configuration
conda install -y -c r r-forecast