I am trying to install the xps package from http://www.bioconductor.org/packages/release/bioc/html/xps.html
for R 3.0.3 on Windows 8.1 x64.
When I try:
source("http://bioconductor.org/biocLite.R")
biocLite("xps")
I get the following messages:
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.3.
Installing package(s) 'xps'
package ‘xps’ is available as a source package but not as a binary
Warning message:
package ‘xps’ is not available (for R version 3.0.3)
So I try installing by downloading the package source for xps
When I try to install it I get the following message:
* installing *source* package 'xps' ...
testing for presence of ROOT...
perl: not found
found of ROOT in directory C:\root\/bin...OK
** libs
running 'src/Makefile.win' ...
Syntax error: Unterminated quoted string
Syntax error: Unterminated quoted string
g++ -pipe -mwindows -I/include -include w32pragma.h -O2 -DWIN32 -c TMLMath.cxx
cc1plus.exe: fatal error: w32pragma.h: No such file or directory
compilation terminated.
make: *** [TMLMath.o] Error 1
Warning: running command 'make --no-print-directory -f "Makefile.win"' had status 2
ERROR: compilation failed for package 'xps'
* removing 'D:/Program Files/R/R-3.0.3/library/xps'
The xps landing page says that xps is not available for 64-bit windows. If you run 32-bit R you'll be able to install the binary with biocLite.
Related
I am trying to install GDINA on MRAN 4.0.2 on Ubuntu 18.04 server and I am getting below error. Please advise how may I do the installation. GDINA is installing on previous version of MRAN and R 4.0.3 on this same machine but failing on MRAN 4.0.2.
Microsoft R Open 4.0.2
The enhanced R distribution from Microsoft
Microsoft packages Copyright (C) 2020 Microsoft Corporation
Using the Intel MKL for parallel mathematical computing (using 1 cores).
Default CRAN mirror snapshot taken on 2020-07-16.
See: https://mran.microsoft.com/.
* installing *source* package ‘GDINA’ ...
** package ‘GDINA’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
...
. _<removing some g++ compilation outputs>_
g++ -shared -L/opt/microsoft/ropen/4.0.2/lib64/R/lib -o GDINA.so Lik.o Lik2.o LouisC.o Mord.o Mstep.o NgRg.o RcppExports.o SE.o aggregateCol.o fitstats.o scorep.o sequP.o util.o varsigma.o Microsoft R Open 4.0.2 The enhanced R distribution from Microsoft Microsoft packages Copyright (C) 2020 Microsoft Corporation Using the Intel MKL for parallel mathematical computing (using 1 cores). Default CRAN mirror snapshot taken on 2020-07-16. See: https://mran.microsoft.com/. -L/opt/microsoft/ropen/4.0.2/lib64/R/lib -lRlapack -L/opt/microsoft/ropen/4.0.2/lib64/R/lib -lRblas -lgfortran -lm -L/opt/microsoft/ropen/4.0.2/lib64/R/lib -lR
g++: error: Microsoft: No such file or directory
g++: error: R: No such file or directory
g++: error: Open: No such file or directory
g++: error: 4.0.2: No such file or directory
...
g++: error: 2020-07-16.: No such file or directory
g++: error: See:: No such file or directory
g++: error: https://mran.microsoft.com/.: No such file or directory
/opt/microsoft/ropen/4.0.2/lib64/R/share/make/shlib.mk:6: recipe for target 'GDINA.so' failed
make: *** [GDINA.so] Error 1
ERROR: compilation failed for package ‘GDINA’
* removing ‘/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/GDINA’
Warning in install.packages :
installation of package ‘GDINA’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpTrbkOd/downloaded_packages’
I am trying to install rJava but it is not working. No matter which version of Java I install, I always get the same error. I already tried to install previous Java versions but that is not working. I also tried to set JAVA_HOME to the JDK folder but nothing seems to work. I am using Windows10.
Code and error:
> install.packages("rJava")
Installing package into ‘C:/Users/x/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
There is a binary version available but the source version is later:
binary source needs_compilation
rJava 0.9-12 0.9-13 TRUE
installing the source package ‘rJava’
trying URL 'https://cran.rstudio.com/src/contrib/rJava_0.9-13.tar.gz'
Content type 'application/x-gzip' length 664898 bytes (649 KB)
downloaded 649 KB
* installing *source* package 'rJava' ...
** package 'rJava' successfully unpacked and MD5 sums checked
** using staged installation
Generate Windows-specific files (src/jvm-w32) ...
make: Entering directory '/cygdrive/c/Users/x/AppData/Local/Temp/RtmpQffZ3r/R.INSTALL35acefc1be9/rJava/src/jvm-w32'
C:/RBuildTools/3.5/mingw_64/bin/dlltool --as C:/RBuildTools/3.5/mingw_64/bin/as --input-def jvm64.def --kill-at --dllname jvm.dll --output-lib libjvm.dll.a
C:/RBuildTools/3.5/mingw_64/bin/gcc -O2 -c -o findjava.o findjava.c
C:/RBuildTools/3.5/mingw_64/bin/gcc -s -o findjava.exe findjava.o
make: Leaving directory '/cygdrive/c/Users/x/AppData/Local/Temp/RtmpQffZ3r/R.INSTALL35acefc1be9/rJava/src/jvm-w32'
Find Java...
JAVA_HOME=C:/PROGRA~1/Java/JDK18~1.0_2/jre
=== Building JRI ===
JAVA_HOME=C:/PROGRA~1/Java/JDK18~1.0_2/jre
R_HOME=C:/PROGRA~1/R/R-36~1.3
JDK has no javah.exe - using javac -h . instead
Creating Makefiles ...
Configuration done.
make -C src JRI.jar
make[1]: Entering directory '/cygdrive/c/Users/x/AppData/Local/Temp/RtmpQffZ3r/R.INSTALL35acefc1be9/rJava/jri/src'
C:/PROGRA~1/Java/JDK18~1.0_2/jre/bin/javac -h . -d . ../RList.java ../RBool.java ../RVector.java ../RMainLoopCallbacks.java ../RConsoleOutputStream.java ../Mutex.java ../Rengine.java ../REXP.java ../RFactor.java ../package-info.java
sh: C:/PROGRA~1/Java/JDK18~1.0_2/jre/bin/javac: No such file or directory
make[1]: *** [Makefile.all:41: org/rosuda/JRI/Rengine.class] Error 127
make[1]: Leaving directory '/cygdrive/c/Users/x/AppData/Local/Temp/RtmpQffZ3r/R.INSTALL35acefc1be9/rJava/jri/src'
make: *** [Makefile.all:19: src/JRI.jar] Error 2
**** WARNING: JRI could NOT be built
Set IGNORE=1 if you want to build rJava anyway.
ERROR: configuration failed for package 'rJava'
* removing 'C:/Users/x/Documents/R/win-library/3.6/rJava'
Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status
Thank you for your help!
I would not recommend installing rJava from sources, because it is entirely unnecessary and compiling packages on Windows requires much better knowledge of tools, Java and your system. Since you are using Windows, please install rJava from CRAN using
install.packages("rJava", type="win.binary")
OS: Ubuntu 18.04
R version: 3.4.3 and 3.4.4
I tried to install tuneR with install.packages("tuneR") in R 3.4.3 and R 3.4.4 but I get this error:
* installing *source* package ‘signal’ ...
package ‘signal’ successfully unpacked and MD5 sums checked
libs
gfortran -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -c dpchim.f -o dpchim.o
/bin/bash: gfortran: command not found
/usr/lib/R/etc/Makeconf:182: recipe for target 'dpchim.o' failed
make: *** [dpchim.o] Error 127
ERROR: compilation failed for package ‘signal’
* removing ‘/home/helias/R/x86_64-pc-linux-gnu-library/3.4/signal’
ERROR: dependency ‘signal’ is not available for package ‘tuneR’
* removing ‘/home/helias/R/x86_64-pc-linux-gnu-library/3.4/tuneR’
The downloaded source packages are in
‘/tmp/RtmpL1f4HR/downloaded_packages’
Warning messages:
1: In install.packages("tuneR") :
installation of package ‘signal’ had non-zero exit status
2: In install.packages("tuneR") :
installation of package ‘tuneR’ had non-zero exit status
(I also used RStudio)
I solved installing gfortran and after re-run install.packages("tuneR")
sudo apt install gfortran
You can try downloading the source and install from RStudio. tuneR is available at:
https://CRAN.R-project.org/package=tuneR
Download the .tar.gz file and install locally. You can install using through RStudio (Packages tab -> change install from: Package), or you can install through the terminal using
R CMD INSTALL -l /path tuneR.tar.gz
Another option is
> library(devtools)
> install_github("cran/tuneR")
I am on mavericks 10.9.2 and running R 3.0.2:
20:35:19/Spectral $R
R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin10.8.0 (64-bit)
Let us try to install the kernlab package from source (not doing from source had worse errors)
install.packages("kernlab", type="source")
We get pretty far in compiling but at the end the linker fails:
-Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64'
ld: warning: directory not found for option '-L/usr/local/lib/x86_64'
ld: warning: directory not found for option '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [kernlab.so] Error 1
ERROR: compilation failed for package ‘kernlab’
* removing ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library/kernlab’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library/kernlab’
The downloaded source packages are in
‘/private/var/folders/k4/l5ww32y14svd5wmkgzzftl9m0000gn/T/RtmpyBfij3/downloaded_packages’
Warning message:
In install.packages("kernlab", type = "source") :
installation of package ‘kernlab’ had non-zero exit status
UPDATE
Per Comments I updated to latest (3.12) R. I also did a
brew install gfortran
which was successful
But compiling R from source still has issues with -lgfortran:
install.packages("kernlab", type="source")
..
ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [kernlab.so] Error 1
ERROR: compilation failed for package ‘kernlab’
* removing ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/kernlab’
The downloaded source packages are in
‘/private/var/folders/k4/l5ww32y14svd5wmkgzzftl9m0000gn/T/RtmpugQtXD/downloaded_packages’
The XCode is 5.1.1 (updated just now - that is newest available for 10.9.2)
Here is info on command line tools:
pkgutil --pkg-info=com.apple.pkg.CLTools_Executables
package-id: com.apple.pkg.CLTools_Executables
version: 6.1.0.0.1.1413057044
volume: /
location: /
install-time: 1415295324
groups: com.apple.FindSystemFiles.pkg-group com.apple.DevToolsBoth.pkg-group com.apple.DevToolsNonRelocatableShared.pkg-group
Here is gfortran info:
09:54:46/spectral $gfortran -v
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/local/Cellar/gfortran/4.8.2/gfortran/libexec/gcc/x86_64-apple-darwin13.0.0/4.8.2/lto-wrapper
Target: x86_64-apple-darwin13.0.0
Configured with: ../configure --prefix=/usr/local/Cellar/gfortran/4.8.2/gfortran --datarootdir=/usr/local/Cellar/gfortran/4.8.2/share --bindir=/usr/local/Cellar/gfortran/4.8.2/bin --enable-languages=fortran --with-system-zlib --with-gmp=/usr/local/opt/gmp --with-mpfr=/usr/local/opt/mpfr --with-mpc=/usr/local/opt/libmpc --with-cloog=/usr/local/opt/cloog --with-isl=/usr/local/opt/isl --disable-cloog-version-check --disable-isl-version-check --enable-checking=release --disable-stage1-checking --disable-libstdcxx --enable-lto --disable-nls --disable-multilib
Thread model: posix
gcc version 4.8.2 (GCC)
The installation worked when performed directly through RStudio. It is not clear why that would make the difference, but the problem is resolved.
When I run the code to install BigVis package from GitHub as follows,
devtools::install_github("bigvis")
I get the following output:
Installing github repo bigvis/master from hadley
Downloading master.zip from https://github.com/hadley/bigvis/archive/master.zip
Installing package from /var/folders/dl/hhhtf5f52hz7qrw93wfyk_6h0000gn/T//RtmpgkDD2j/master.zip
arguments 'minimized' and 'invisible' are for Windows only
Installing bigvis
'/Library/Frameworks/R.framework/Resources/bin/R' \
--vanilla CMD INSTALL \
'/private/var/folders/dl/hhhtf5f52hz7qrw93wfyk_6h0000gn/T/RtmpgkDD2j/devtools259f1fe8bc61/bigvis-master' \
--library='/Library/Frameworks/R.framework/Versions/3.0/Resources/library' \
--install-tests
* installing *source* package 'bigvis' ...
** libs
sh: make: command not found
ERROR: compilation failed for package 'bigvis'
* removing '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/bigvis'
Error: Command failed (1)
DO YOU HAVE ANY IDEA HOW I MAY FIX IT? THANKS
The error message sh: make: command not found tells you that the program sh could not find the program make. So my crystal ball tells me you might need to install GNU make. But I know nothing about RStudio nor BigVis.