I need to install R-INLA on R 4.1.1 (Windows 10). I cannot update the R version due to compatibility issues of the newer R installations with other tools I that use. I tried the line:
remotes::install_version("INLA", version="22.05.03",repos=c(getOption("repos"),INLA="https://inla.r-inla-download.org/R/testing"), dep=TRUE)
As recommended on the INLA website for R 4.1. I get this message in return:
* installing *binary* package 'INLA' ...
cp: unknown option -- )
Try '/usr/bin/cp --help' for more information.
ERROR: installing binary package failed
* removing 'C:/Program Files/R/R-4.1.1/library/INLA'
I have rtools40 installed and added to my path. I have installed the two suggested packages graph and Rgraphviz as recommended.
I have also tried:
devtools::install_github(repo = "https://github.com/hrue/r-inla", ref = "stable", subdir = "rinla", build = FALSE)
But no luck there either.
If I type where cp in the RStudio terminal, I get:
$ where cp
C:\Program Files\Git\usr\bin\cp.exe
C:\rtools40\usr\bin\cp.exe
But I am not sure if this has anything to do with R not finding cp.
Anyone has any advice?
I was having the same problem, and solved it for my Windows 10 machine:
Download the INLA_22.05.03.zip file at https://inla.r-inla-download.org/R/stable/bin/windows/contrib/4.1/
In RStudio, under the Tools menu, select Install Packages, and Install from: Package Archive File. Tell RStudio where the .zip file is located on your local machine. From there it installed fine for me.
Related
I am using this document as a guide
and i ran through this error
Install the project...
-- Install configuration: "RELEASE"
CMake Error at cmake_install.cmake:36 (file):
file cannot create directory: /installation/OpenCV-/share/licenses/opencv4.
Maybe need administrative privileges.
I just encountered the same problem as you. I found out that it is not a permission problem, but a path problem of OpenCV installation.
I use the following method for successfully installing OpenCV4.2.0 to my computer.
Change the path:
-D CMAKE_INSTALL_PREFIX = $cwd/installation/OpenCV-4.2.0
To
-D CMAKE_INSTALL_PREFIX = /usr/local
I'm trying to install the package "Tax4Fun" but keep failing.
I've tried 2 different ways:
install.packages("devtools")
devtools::install_url("http://tax4fun.gobics.de/Tax4Fun/Tax4Fun_0.3.1.tar.gz")
library(Tax4Fun)
The error that I get is:
ERROR: dependency 'biom' is not available for package 'Tax4Fun'
I've also tried installing biom directly
BiocManager::install("biom")
which does not work either
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05)
Installing package(s) 'biom'
Installation path not writeable, unable to update packages: boot, foreign, KernSmooth,
mgcv, nlme, survival
Warning message:
package ‘biom’ is not available (for R version 3.6.1)
The other way I've tried to install Tax4Fun directly is
BiocManager::install("Tax4Fun")
I get the following error code:
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05)
Installing package(s) 'Tax4Fun'
Installation path not writeable, unable to update packages: boot, foreign, KernSmooth,
mgcv, nlme, survival
Warning message:
package ‘Tax4Fun’ is not available (for R version 3.6.1)
Please help :)
You need to install it by downloading the packages from source (http://tax4fun.gobics.de). Then it depends whether you are running on Linux/Mac or Windows.
From the command line, you navigate to the folder containing the .tar.gz downloaded package. Then you should install it using:
R CMD INSTALL Tax4Fun_0.3.1.tar.gz
But dependancies are not installed by default. So you need to install dependancies manually, Qiimer and Biom, which are both deprecated on Cran. You install them using the same command, after you have downloaded the packages from the Cran archives.
Before that, you need to also install their dependancies in R:
install.packages("pheatmap")
install.packages("RJSONIO")
Then you should be able to proceed as mentioned above: install Qiimer and Biom from the command line first. Then Tax4Fun from the command line too.
If you are running on Windows you should have quite the same issues, but the installation of the different packages and dependancies is different. You can have a look at the readme at http://tax4fun.gobics.de
C:\Work\R contains the R-3.1.1.tar.gz file
I have build R source(R-3.1.1) in windows 8 from the following commands
cd C:\Work\R
tar --no-same-owner -xf R-3.1.1.tar.gz
cd C:\Work\R\R-3.1.1\src\gnuwin32\
make all recommended
Add the following path to the Environment variables
C:\Work\R\R-3.1.1\bin\i386
Enter the R.exe in command promt
I got the following Error
Fatal error unable to open the base package
System information
Windows 8, 64 bit operating System, x64 –based processor
How to resolve this error?
If you are using R, you can download the newest version from here and then simply install it.
If you have an older version and want only to download the new one, use those commands inside R:
# installing/loading the package:
if(!require(installr)) {
install.packages("installr"); require(installr)} #load / install+load installr
# using the package:
updateR() # this will start the updating process of your R installation. It will check for newer versions, and if one is available, will guide you through the decisions you'd need to make.
We can resolve this issue by using the following command before build the R source code
Set TMPDIR=c:\cygwin64\bin
Here c:\cygwin64\bin is the cygwin installed location in Windows 8 machine.
Here I have mentioned the R source code build steps:
Install cygwin setup
Install RTools
Create the R_HOME file in the directory like C:\R_HOME
Place the R source code tar file in the R_HOME
Add the following path in environment variable in first
c:\Rtools\bin\;c:\Rtools\gcc-4.6.3\bin;C:\cygwin64\bin\;C:\Program Files (x86)\HTML Help Workshop\;C:\R_HOME\R-3.1.1\bin\;
Enter the following command in the command prompt
Set TMPDIR=C:\cygwin64\bin
Set working directory as C:\R_HOME
Enter the following command
tar --no-same-owner -xf R-3.1.1.tar.gz
Copy the Tcl source from c:\R (it will be created while installing RTools)
Set the working directory as follow in command prompt
C:\R_HOME\R-3.1.1\src\gnuwin32
Enter the following command
Make all recommended
Enter the R.exe command in command prompt. We can enter the R terminal
I am trying to build an R package using RStudio on Windows 8 Pro. When I attempt to build the package by running build() I get the error:
"C:/Program Files/R/R-30~1.2/bin/x64/R" --vanilla CMD build "H:\File Assembly\FileAssembler" \
--no-manual --no-resave-data
'C:\Program' is not recognized as an internal or external command, operable program or batch file.
Error: Command failed (1)
I already have MiKTEX installed and I have checked this by:
Sys.which("pdflatex")
pdflatex
"C:\\Program Files (x86)\\MIKTEX~1.9\\miktex\\bin\\pdflatex.exe"
The R version I am using is: R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
Loading library(devtools) and running find_rtools(T) gives:
find_rtools(T)
Scanning path...
ls : c:\Rtools\bin\ls.exe
gcc: c:\Rtools\GCC-46~1.3\bin\gcc.exe
VERSION.txt
Rtools version 3.1.0.1942
Version: 3.1
[1] TRUE
In addition, the path for rtools exes are:
Sys.which("ls.exe")
ls.exe
"c:\\Rtools\\bin\\ls.exe"
Sys.which("gcc.exe")
gcc.exe
"c:\\Rtools\\GCC-46~1.3\\bin\\gcc.exe"
And checking the path in R:
Sys.getenv('PATH')
[1] "C:\\Program Files\\R\\R-3.0.2\\bin\\x64;c:\\Rtools\\bin;c:\\Rtools\\gcc-4.6.3\\bin;……other paths…………;C:\\Program Files (x86)\\MiKTeX 2.9\\miktex\\bin\\"
I would really appreciate help with identifying what I have missed out.
This is a common error caused by a space in the install location path (C:\Program Files). The solution, and the official R recommendation is that you never install R in a location with spaces in it on Windows if you want to be able to install packages from source.
from http://cran.r-project.org/bin/windows/rw-FAQ.html#How-do-I-install-R-for-Windows_003f:
If you want to be able to build packages from sources, we recommend
that you choose an installation path not containing spaces.
I had the same problem.
Took some time to find that Rcmd.exe was removed by the Kaspersky antivirus.
once I detected that it was easy to fix.
good luck
Offer
I just did a clean install of Windows 7. I've installed Apache, Mysql
and PHP 5.3.5 all separated (not using XAMPP/others).
I'm getting the following error in the install: ERROR: unable to unpack phar://C:/Web/php-5.3.5/PEAR/go-pear.phar/PEAR/go-pear-tarballs/Structures_Graph-1.0.2.tar
The full stack trace is:
C:\Web\php-5.3.5>go-pear.bat
Are you installing a system-wide PEAR or a local copy?
(system|local) [system] : system
Below is a suggested file layout for your new PEAR installation. To change individual locations, type the number in front of the directory. Type 'all' to change all of them or simply press Enter to accept these locations.
1. Installation base ($prefix) : C:\Web\php-5.3.5
2. Temporary directory for processing : C:\Web\php-5.3.5\tmp
3. Temporary directory for downloads : C:\Web\php-5.3.5\tmp
4. Binaries directory : C:\Web\php-5.3.5
5. PHP code directory ($php_dir) : C:\Web\php-5.3.5\pear
6. Documentation directory : C:\Web\php-5.3.5\docs
7. Data directory : C:\Web\php-5.3.5\data
8. User-modifiable configuration files directory : C:\Web\php-5.3.5\cfg
9. Public Web Files directory : C:\Web\php-5.3.5\www
10. Tests directory : C:\Web\php-5.3.5\tests
11. Name of configuration file : C:\Web\php-5.3.5\pear.ini
12. Path to CLI php.exe : C:\Web\php-5.3.5
1-12, 'all' or Enter to continue:
Beginning install...
Configuration written to C:\Web\php-5.3.5\pear.ini...
Initialized registry...
Preparing to install...
installing phar://C:/Web/php-5.3.5/PEAR/go-pear.phar/PEAR/go-pear-tarballs/Archive_Tar-1.3.3.tar...
installing phar://C:/Web/php-5.3.5/PEAR/go-pear.phar/PEAR/go-pear-tarballs/Console_Getopt-1.2.3.tar...
installing phar://C:/Web/php-5.3.5/PEAR/go-pear.phar/PEAR/go-pear-tarballs/PEAR-1.8.0.tar...
installing phar://C:/Web/php-5.3.5/PEAR/go-pear.phar/PEAR/go-pear-tarballs/Structures_Graph-1.0.2.tar...
installing phar://C:/Web/php-5.3.5/PEAR/go-pear.phar/PEAR/go-pear-tarballs/XML_Util-1.2.1.tar...
install ok: channel://pear.php.net/Archive_Tar-1.3.3
install ok: channel://pear.php.net/Console_Getopt-1.2.3
ERROR: unable to unpack phar://C:/Web/php-5.3.5/PEAR/go-pear.phar/PEAR/go-pear-tarballs/Structures_Graph-1.0.2.tar
install ok: channel://pear.php.net/XML_Util-1.2.1
install ok: channel://pear.php.net/PEAR-1.8.0
PEAR: Optional feature webinstaller available (PEAR's web-based installer)
PEAR: Optional feature gtkinstaller available (PEAR's PHP-GTK-based installer)
PEAR: Optional feature gtk2installer available (PEAR's' PHP-GTK2-based installer)
PEAR: To install optional features use "pear install pear/PEAR#featurename"
** WARNING! Old version found at C:\Web\php-5.3.5, please remove it or be sure t
o use the new c:\web\php-5.3.5\pear.bat command
The 'pear' command is now at your service at c:\web\php-5.3.5\pear.bat
* WINDOWS ENVIRONMENT VARIABLES *
For convenience, a REG file is available under C:\Web\php-5.3.5\PEAR_ENV.reg .
This file creates ENV variables for the current user.
Double-click this file to add it to the current user registry.
C:\Web\php-5.3.5>
After days of googling I've found an answer. Here is it. How to solve:
With admin permission (start cmd with admin privileges):
Run the go-pear.bat that comes with the default PHP installation. It'll installs PEAR, but it's going to generate an error when installing Structures_Graph. IMO Pear needs this package to generate the package dependency (graph), since it's missing it not allow us to install or upgrade any other package.
Download and uncompress Structures_Graph from the pear.php.net website (direct link). Then copy the Structure folder into the PEAR folder. The archive has three folders: docs, Structures, tests. We only need the Structures one. Copy the Structures folder to your PHP_ROOT_DIRECTORY\PEAR directory. So if you installed PHP on C:\Web\php-5.3.5 copy the Structures folder to C:\Web\php-5.3.5\PEAR\, the result should be: C:\Web\php-5.3.5\PEAR\Structures
Do pear install Structures_Graph. Even though the files are present, Structures_Graph is not really installed (we had a problem during installation). So we need to run the command above.
Do pear upgrade PEAR. This upgrades PEAR itself to the current version.
Do pear upgrade Console_Getopt. This upgrades Console_Getopt to the current version and now we can manage and install any pear package.
Marcos Roriz solution does indeed work, but to clarify point 2:
The uncompressed "Structures" folder (inside the tgz) needs to be placed inside the folder: "PEAR\pear" -> e.g. C:\wamp\bin\php\php5.3.5\PEAR\pear
This is a combination of the things you need to do and a couple of new tweaks. Worked on WinXP Pro with WAMP (Wampserver 2.2.1)
Change your go-pear.bat file:
#ECHO OFF
set PHP_BIN=php.exe
%PHP_BIN% -d output_buffering=0 -d phar.require_hash=0 PEAR\go-pear.phar
pause
Run it - go-pear.bat
Now you've go a Pear install with a missing graph.php
Download and uncompress Structures_Graph from the pear.php.net website. Copy the Structure folder into the PEAR folder so that the key files are located as such:
PEAR\Structures\Graph.php
PEAR\Structures\Graph\Node.php
Change this line in Node.php:
require_once '/Structures/Graph.php';
Execute in the PEAR directory:
pear upgrade=all
That did it for me.
First of all, run as administrator.
Then - try to write something in target directory in the console to isolate any remaining permissions problems.
I've been having many issues after upgrading my wampserver which now comes with php 5.3.5.
I have solved the problem by installing php 5.3.0 alongside and using it to run the installer found at http://pear.php.net/go-pear. I set the php cli setting to the php5.3.5 folder without any issues.
This might be wampserver specific. To gauge if you are experiencing a similar problem here are some of the issues I encountered:
Using the go-pear.bat packaged with php5.3.5 i had the same unable to unpack error as the original poster.
Using the go-pear.bat packaged with php5.3.0 i was able to complete the installation but the pear installer was v1.8.0
Using the installer on the pear site mentioned previously with php5.3.5 i had an error "Warning: rmdir(D:\temp): Directory not empty in D:\go-pear.php on line 1237". Looking at the stack trace the Archive_Tar class was throwing an error and the installer was failing to clean up after itself.
the web frontend not write correct paths to pear.ini
ig phph setting is magic_quotes_gpc = On
its doubles all slashes "\" in paths to "\" is it a bug ?
Than the packages for example can be unpacked (wrong paths ?)
"unable to unpack" Message when installing packages
http://pear.php.net/bugs/bug.php?id=18212
I tried all of the above with no luck. After downloading and extracting the "Structures" folder I had to edit all paths and add "PEAR/". Then I was able to do "pear install Structures_Graph" and then "pear upgrade-all"
Graph.php
require_once 'PEAR/Structures/Graph/Node.php';
Node.php
require_once 'PEAR/Structures/Graph.php';
AcyclicTest.php
require_once 'PEAR/Structures/Graph.php';
require_once 'PEAR/Structures/Graph/Node.php';
TopologicalSorter.php
require_once 'PEAR/Structures/Graph.php';
require_once 'PEAR/Structures/Graph/Node.php';
require_once 'PEAR/Structures/Graph/Manipulator/AcyclicTest.php';