url <- "http://cran.us.r-project.org/src/contrib/Archive/cldr/cldr_1.1.0.tar.gz"
pkgFile<-"cldr_1.1.0.tar.gz"
download.file(url = url, destfile = pkgFile)
Console
>trying URL 'http://cran.us.r-project.org/src/contrib/Archive/cldr/cldr_1.1.0.tar.gz'
Content type 'application/x-gzip' length 2296083 bytes (2.2 MB)
==============================
downloaded 2.2 MB
install.packages(pkgs = pkgFile, type = "source", repos = NULL)
> Installing package into ‘C: / Users / v - xuawan / Documents / R / win -
library / 3.2’
(as ‘lib’ is unspecified)
* installing * source * package 'cldr' ...
** package 'cldr' successfully unpacked and MD5 sums checked
** libs
> ** * arch - i386
Warning:running command 'make -f "Makevars" -f "C:/PROGRA~1/R/R-32~1.0/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-32~1.0/share/make/winshlib.mk" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="cldr.dll" ' had status 127
ERROR:compilation failed for package 'cldr'
* removing 'C:/Users/v-xuawan/Documents/R/win-library/3.2/cldr'
Warning in install.packages:running command '"C:/PROGRA~1/R/R-32~1.0/bin/x64/R" CMD INSTALL -l "C:\Users\v-xuawan\Documents\R\win-library\3.2" "cldr_1.1.0.tar.gz"' had status 1
Warning in install.packages:installation of package ‘cldr_1.1.0.tar.gz’ had non -
zero exit status
I tried to install package cldr on windows.
I am wondering if any of you know how to solve above error message
Have you installed RTools?
Choose the right version, which belongs to your R version (it seems you use R 3.2)
From the 127 return code, it looks like you don't have a C++ compiler installed on your path. Have you installed the latest Rtools for Windows? It will give you the C++ toolchain you need.
Try this: install.packages("cldr", type="binary"). I was getting same error message for 'backports' package installation.
The same functions can be found in other packages now available on CRAN. They can be installed with the usual install.packages("cld2") and install.packages("cld3"):
cld2 - https://github.com/ropensci/cld2
cld3 - https://github.com/ropensci/cld3
For a quick comparison based on tweets, see this other answer: https://stackoverflow.com/a/46663823/4124601
I was having the same issue on R Cloud for 'raster' package, it's fixed when I've switched to Desktop R Studio. I've seen Desktop R studio downloads other required packages too before installing the one you wanted. I'm not sure if this's the exact case for you, but worth to try!
Related
I am trying to install ‘rmarkdown’ in my RStudio Version 1.4.904 and R version 4.0.3 but getting the following error. I cannot open a new rmarkdown and knit a rmarkdown file. Every time I try, this message pops up,
R Markdown documents requires an updated version of the rmarkdown package. Do you want to install this package now?
Can anyone help me with that?
install.packages(ç, dependencies=TRUE)
Installing package into ‘/Users/Library/R/4.0/library’
(as ‘lib’ is unspecified)
There is a binary version available but the source version is later:
binary source needs_compilation
rmarkdown 2.3 2.4 FALSE
installing the source package ‘rmarkdown’
trying URL 'http://cran.utstat.utoronto.ca/src/contrib/rmarkdown_2.4.tar.gz'
Content type 'application/x-gzip' length 3202546 bytes (3.1 MB)
==================================================
downloaded 3.1 MB
Warning in file(con, "r") :
cannot open file '/var/db/timezone/zoneinfo/+VERSION': No such file or directory
dyld: lazy symbol binding failed: Symbol not found: _utimensat
Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13)
Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: _utimensat
Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13)
Expected in: /usr/lib/libSystem.B.dylib
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 30112 Done echo 'tools:::.install_packages()'
30113 Abort trap: 6 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}
Warning in install.packages :
installation of package ‘rmarkdown’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/70/lgr12kdn6wn_k36sscnc0_dw0000gn/T/Rtmpmc0jUR/downloaded_packages’```
download the binary tgz (https://cran.r-project.org/web/packages/rmarkdown/index.html) and install directly from it.
It should work. I had pretty much the same issue and I solved it that way. Keep me posted!
F
I also faced a similar problem and I spent a half-day on getting the correct solution.
Step I followed:
Uninstalled the existing version
Installed updated version of R - R version 4.0.4 (2021-02-15).
Clicked on File->New file->R markdown. It asked to install Rmarkdown packages.
Noted the packages I need to install
Typed install.packages("rmarkdown", dependencies = TRUE) on R source(can be done on R console)
Then I tried installing Rmarkdown packages individually and it worked for me. Below are the packages I needed to install.
install.packages('knitr')
install.packages('tinytex')
install.packages('base64enc')
install.packages('digest')
install.packages('jsonlite')
install.packages('htmltools')
install.packages('rmarkdown')
A somewhat more technical workaround but it worked for me.
Go to https://cran.r-project.org/ select "Packages" from the menu on the right and navigate until you find the package you need.
Download the binary.zip file for your operating system and extract the files.
Copy the extracted folder into the installation directory for your packages. It should be shown somewhere in the error messages from where you attempted to install the package originally. Replace any existing files. Restart RStudio to recognize the updated versions.
S.O.: Linux Ubuntu 14.04 LTS
R: R version 3.2.1 (2015-06-18) -- "World-Famous Astronaut"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: i686-pc-linux-gnu (32-bit)
When I try to install the package rjags, I get the following fatal error:
install.packages("rjags")
Installing package into ‘/home/marco/.rkward/library’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
trying URL 'http://mirrors.softliste.de/cran/src/contrib/rjags_3-15.tar.gz'
Content type 'application/x-gzip' length 66879 bytes (65 KB)
==================================================
downloaded 65 KB
* installing *source* package ‘rjags’ ...
** package ‘rjags’ successfully unpacked and MD5 sums checked
checking for prefix by checking for jags... no
configure: error: "Location of JAGS headers not defined. Use configure arg '--with-jags-include' or environment variable 'JAGS_INCLUDE'"
ERROR: configuration failed for package ‘rjags’
* removing ‘/home/marco/.rkward/library/rjags’
The downloaded source packages are in
‘/tmp/RtmpditLat/downloaded_packages’
Warning message:
In install.packages("rjags") :
installation of package ‘rjags’ had non-zero exit status
Apparently, the first error message is
configure: error: "Location of JAGS headers not defined. Use configure arg '--with-jags-include' or environment variable 'JAGS_INCLUDE'"
How can I solve this?
As a top comment explained, you need JAGS (Just Another Gibbs Sampler) to be installed in your system. Since you're using Ubuntu 14.04, running
sudo apt-get install jags
should be enough. However, in case you're in another distribution (or, for some reason, the code above doesn't work for you), it's a good idea to know how to get JAGS from the source:
Access http://mcmc-jags.sourceforge.net/
Look for the proper version under "Downloads". For instance, Fedora users should look into the Fedora_20 folder of http://download.opensuse.org/repositories/home:/cornell_vrdc/
Don't forget to download both the base as well as the devel versions.
After the installation is successful, you can go back to R (which can stay open during the whole thing, anyway) and install the package you want.
To me, first, I worked with the installation jags by terminal:
sudo apt-get install jags
and then
install.packages("rjags")
And the error was gone.
1) If necessary Download and install R (https://www.r-project.org/) and potentially a user interface to R like R Studio (see here for tips on getting started with R).
2) Download and install JAGS as per operating system requriements. (http://mcmc-jags.sourceforge.net/)
3) Install additional R packages: e.g., in R install.packages("rjags") . In particular, I use the packages rjags to interface with JAGS and coda to process MCMC output.
I would like to use functions in the mvpart package in R. I know it has been removed from CRAN, but I tried installing archive versions available here: http://cran.r-project.org/web/packages/mvpart/index.html
install.packages("D:/mvpart_1.6-2.tar.gz", repos = NULL, type = "source")
I get this result:
Installing package into ‘C:/Users/jk/Documents/R/win-library/3.1’
(as ‘lib’ is unspecified)
* installing source package 'mvpart' ...
** package 'mvpart' successfully unpacked and MD5 sums checked
** libs
*** arch - i386
Warning: running command 'make -f "C:/PROGRA~1/R/R-31~1.3/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-31~1.3/share/make/winshlib.mk" SHLIB="mvpart.dll" OBJECTS="anova.o branch.o bsplit.o choose_surg.o dist.o fix_cp.o formatg.o free_tree.o gini.o graycode.o insert_split.o make_cp_list.o make_cp_table.o mrt.o mysort.o nodesplit.o partition.o poisson.o pred_rpart.o rpart.o rpart_callback.o rpartexp2.o rpcountup.o rpmatrix.o rundown.o rundown2.o s_to_rp.o s_xpred.o surrogate.o usersplit.o vgdist.o xdiss.o xval.o"' had status 127
ERROR: compilation failed for package 'mvpart'
* removing 'C:/Users/jk/Documents/R/win-library/3.1/mvpart'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-31~1.3/bin/x64/R" CMD INSTALL -l "C:\Users\jk\Documents\R\win-library\3.1" "D:/mvpart_1.6-2.tar.gz"' had status 1
Warning in install.packages :
installation of package ‘D:/mvpart_1.6-2.tar.gz’ had non-zero exit status
My questions are: Did I do something wrong here - is there a way to install 'mvpart'? Or, is there another package that will do multivariate partitioning, similar to 'mvpart'?
Option 1:
An archive install must be compiled, as it's stored as source code. Probably, you have not installed the R Tools compiler for Windows. Follow the install instructions here.
Once that was done, for me, mvpart installed flawlessly from the downloaded archive:
install.packages("C:/mydownload/path/mvpart_1.6-2.tar.gz", repos = NULL, type = "source")
Option 2:
If Option 1 doesn't get the job done, get the devtools package:
install.packages("devtools")
Use it to get the github version:
devtools::install_github("cran/mvpart")
I believe you'll still need the R tools compiler though
downloading Xcode from either the Apple AppStore or Apple Developer website solved my issues installing mvpart. The app version required iOS 10.13 as of this post, but it was easy to find a compatible older version on the website to download. After you download it, move it to your Applications folder and then open it. After that then the devtools:::install_github() worked for me.
It took a good amount of time to install RMySQL on my Linux machine but I was able to install it after changing environment variables and copy and paste lib.dll file.
However, I'm now trying to install RMySQL on my 64bit window machine, but so far there's no progress yet for two days. It broke down after "running command sh ./configure.win had status 127 error, and I cannot find what this means.
Can anyone shed some lights on this?
install.packages('RMySQL',type='source')
Installing package into ‘C:/Users/chu/Documents/R/win-library/3.1’
(as ‘lib’ is unspecified)
trying URL 'http://cran.rstudio.com/src/contrib/RMySQL_0.9-3.tar.gz'
Content type 'application/x-gzip' length 165363 bytes (161 Kb)
opened URL
downloaded 161 Kb
* installing *source* package 'RMySQL' ...
** package 'RMySQL' successfully unpacked and MD5 sums checked
Warning: running command 'sh ./configure.win' had status 127
ERROR: configuration failed for package 'RMySQL'
* removing 'C:/Users/chu/Documents/R/win-library/3.1/RMySQL'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-31~1.0/bin/x64/R" CMD INSTALL -l "C:\Users\chu\Documents\R\win-library\3.1" C:\Users\chu\AppData\Local\Temp\RtmpKA9e7I/downloaded_packages/RMySQL_0.9-3.tar.gz' had status 1
Warning in install.packages :
installation of package ‘RMySQL’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\chu\AppData\Local\Temp\RtmpKA9e7I\downloaded_packages’
for linux users..
install- libmysql first
sudo apt-get install libmysql++-dev
then try.
I was facing the same error. Given below is the link to a way around that worked for me.
http://www.ahschulz.de/2013/07/23/installing-rmysql-under-windows/
In short, the location of library libmysqll.dll required for compilation, had to be changed from lib folder to bin folder of the home directory set for MySQL in environment variables.
By default, R uses the /tmp directory to install packages. On security conscious machines, the /tmp directory is often marked as “noexec” in the /etc/fstab file. This means that no file under /tmp can ever be executed. Packages that require compilation or that have self-inflating data will fail with the error mentioned.
The solution is to set the TMPDIR environment variable outside R (in your shell), which R will use as the compilation directory. How to do this depends on the shell. bash:
mkdir ~/tmp
export TMPDIR=~/tmp
Then R can compile and install the package.
I ran into the same problem while updating packages on Windows server for latest version of R. I solved it by installing from a .zip file vs .tar.gz.
I actually had to go through the process of first downloading the package, and then installing from it (not from mirror) for other reasons.
Here is what it looked like:
pk <- 'caTools'
download.packages(pk, "R-3.2-packages/" ,type = "win.binary")
install.packages(
dir("R-3.2-packages/",pattern=pk,full.names = TRUE),
repos = NULL,
type = "source")
Hope this helps.
Solution if anyone faced the same problem on windows:
Make sure your MYSQL_HOME environment variable is set correctly and libmysql.dll is copied to bin folder!!!
Run install.packages('RMySQL') then when the "Do you want to install from sources..." window pops up select No.
Then copy the downloaded binary packages location from console.
Go to Packages -> Install, paste the location into Package archive and click Install.
Trying to use Hadleys devtools package I am getting a certification error:
install_github("devtools")
Installing github repo(s) devtools/master from hadley
Installing devtools.zip from https://github.com/hadley/devtools/archive/master.zip
Error in function (type, msg, asError = TRUE) :
Peer certificate cannot be authenticated with given CA certificates
Google search tells me that this is a curl issue. I am no nearer.
Using "git" from the command line I can pick up anything I want from github, - I don't get this error. It only appears when I try to connect to github from R.
I am using ubuntu 12.10, libcurl 7.22.0 and R 3.0
Does anyone have an idea what to do to fix this?
Sincerely
H.
This issue is resolved. There was some mismatch between the version of RCurl and the curl library. Re-installing RCurl fixed the problem.
Try
$ git clone git://github.com/hadley/devtools.git
$ R CMD build devtools
$ R CMD install devtools_1.2.99.tar.gz
or just
$ git clone git://github.com/hadley/devtools.git
$ R CMD install devtools
both worked for me on Ubuntu 12.04. Someone else can weigh in on whether there's any difference in building first then installing from tarball or not. I would guess no, but I have no idea
edit:
trying this on os X
* installing to library ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library’
* installing *source* package ‘devtools’ ...
** libs
sh: make: command not found
ERROR: compilation failed for package ‘devtools’
* removing ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library/devtools’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library/devtools’