I have R and Rstudio installed on an Ubuntu server (14), when I tried to install packages, I get these errors:
>install.packages("nnet")
Installing package into ‘/home/zhge/R/x86_64-pc-linux-gnu-library/3.0’
(as ‘lib’ is unspecified)
--2015-09-08 02:43:31-- https://cran.rstudio.com/src/contrib/nnet_7.3-11.tar.gz Resolving
cran.rstudio.com (cran.rstudio.com)... 54.230.140.42 Connecting to
cran.rstudio.com (cran.rstudio.com)|54.230.140.42|:443... connected.
HTTP request sent, awaiting response... 200 OK Length: 28455 (28K)
[application/x-gzip] Saving to:
‘/tmp/RtmpBT7yHE/downloaded_packages/nnet_7.3-11.tar.gz’
0K .......... .......... ....... 100% 1.20M=0.02s
2015-09-08 02:43:31 (1.20 MB/s) -
‘/tmp/RtmpBT7yHE/downloaded_packages/nnet_7.3-11.tar.gz’ saved
[28455/28455]
/usr/lib/R/bin/R: line 140: /usr/lib/R/etc/ldpaths: Permission denied
/usr/lib/R/bin/R: line 236: /usr/lib/R/etc/ldpaths: Permission denied
Error in file(con, "r") : cannot open the connection Calls:
<Anonymous> -> sub -> grep -> readLines -> file In addition: Warning
message: In file(con, "r") : cannot open file
'/usr/lib/R/etc/Makeconf': Permission denied Warning in
install.packages : installation of package ‘nnet’ had non-zero exit
status
The downloaded source packages are in
‘/tmp/RtmpBT7yHE/downloaded_packages’
UPDATE:
It was just permission issue, all i needed is just:
$ sudo chmod -R 0777 /usr/lib/R/etc/ldpaths
and for the other directories: /usr/lib/R/etc/Makeconf and /usr/lib/R/bin/. I never had this issue before, so it didn't come to me as the problem immediately.
Related
My work laptop has no internet access and I am trying to download the package rgdal.
I have downloaded rgdal_1.4-8.tar.gz, gdal-3.0.4.tar.gz and proj-6.3.2.tar.gz. I tried intalling them via source separately using:
install.packages('.../...tar.gz', type='source', repos=NULL)
but it did not work. Here are the error messages
ERROR: cannot extract package from 'D:/Users/sn/Documents/R source packages/gdal-3.0.4.tar.gz'
Warning in install.packages :
installation of package ‘D:/Users/sn/Documents/R source packages/gdal-3.0.4.tar.gz’ had non-zero exit status
ERROR: cannot extract package from 'D:/Users/sn/Documents/R source packages/proj-6.3.2.tar.gz'
Warning in install.packages :
installation of package ‘D:/Users/sn/Documents/R source packages/proj-6.3.2.tar.gz’ had non-zero exit status
Error in download.file(sprintf("https://github.com/rwinlib/gdal2/archive/v%s.zip", :
cannot open URL 'https://github.com/rwinlib/gdal2/archive/v2.2.3.zip'
In addition: Warning message:
In download.file(sprintf("https://github.com/rwinlib/gdal2/archive/v%s.zip", :
InternetOpenUrl failed: 'A connection with the server could not be established'
Execution halted
make: *** [Makevars.win:27: winlibs] Error 1
ERROR: compilation failed for package 'rgdal'
* removing 'D:/Users/sn/Documents/R/win-library/3.6/rgdal'
Warning in install.packages :
installation of package ‘D:/Users/sn/Documents/R source packages/rgdal_1.4-8.tar.gz’ had non-zero exit status
I was wanting to install XLConnect package so that i could save my databses created from RSQLite in different formats. But when i do
install.packages("XLConnect")
it seems to give error
checking whether Java run-time works... ./configure: line 3747: /usr/lib/jvm/default-java/bin/java: No such file or directory
no
configure: error: Java interpreter '/usr/lib/jvm/default-java/bin/java' does not work
ERROR: configuration failed for package ‘rJava’
* removing ‘/home/mrshekar/R/x86_64-pc-linux-gnu-library/3.4/rJava’
Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status
ERROR: dependency ‘rJava’ is not available for package ‘XLConnectJars’
* removing ‘/home/mrshekar/R/x86_64-pc-linux-gnu-library/3.4/XLConnectJars’
Warning in install.packages :
installation of package ‘XLConnectJars’ had non-zero exit status
ERROR: dependencies ‘XLConnectJars’, ‘rJava’ are not available for package ‘XLConnect’
* removing ‘/home/mrshekar/R/x86_64-pc-linux-gnu-library/3.4/XLConnect’
Warning in install.packages :
installation of package ‘XLConnect’ had non-zero exit status
Now i read on R: rJava package install failing about the
export JAVA_HOME=/usr/lib/jvm/java-6-sun/jre
export PATH=$PATH:$JAVA_HOME/bin
but still the problem seeems to persist. Also if you look at the solution on Error of java path on loading rJava package
sudo R CMD javareconf
It gives the error
*** JAVA_HOME is not a valid path, ignoring
*** Cannot find any Java interpreter
*** Please make sure 'java' is on your PATH or set JAVA_HOME correspondingly
Also for the install JDK answer
apt-get install r-cran-rjava
I get the permission denied error even if i do it on vm-virtual box it gives me permission denied for the ubuntu 18.04 version i have installed and made myself the admin.
E: Could not open lock file /var/lib/dpkg/lock - open (13: Permission denied)
E: Unable to lock the administration directory (/var/lib/dpkg/), are you root?
What should i do? Please help.
When I want to install the package mclust, I get the following error:
> install.packages("mclust")
Installing package into ‘C:/Users/hp1/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
There is a binary version available but the source version is
later:
binary source needs_compilation
mclust 5.2.3 5.3 TRUE
Do you want to install from sources the package which needs compilation?
y/n: y
installing the source package ‘mclust’
trying URL 'https://cran.rstudio.com/src/contrib/mclust_5.3.tar.gz'
Content type 'application/x-gzip' length 2792962 bytes (2.7 MB)
downloaded 2.7 MB
* installing *source* package 'mclust' ...
** package 'mclust' successfully unpacked and MD5 sums checked
** libs
*** arch - i386
gcc -m32 -I"C:/PROGRA~1/R/R-32~1.3/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c init.c -o init.o
gfortran -m32 -O3 -mtune=core2 -c mclust.f -o mclust.o
make: gfortran: Command not found
C:/PROGRA~1/R/R-32~1.3/etc/i386/Makeconf:206: recipe for target 'mclust.o' failed
make: *** [mclust.o] Error 127
Warning: running command 'make -f "Makevars" -f "C:/PROGRA~1/R/R-32~1.3/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-32~1.3/share/make/winshlib.mk" SHLIB="mclust.dll" SHLIB_LIBADD='$(FLIBS)' OBJECTS="init.o mclust.o mclustaddson.o"' had status 2
ERROR: compilation failed for package 'mclust'
* removing 'C:/Users/hp1/Documents/R/win-library/3.2/mclust'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-32~1.3/bin/x64/R" CMD INSTALL -l "C:\Users\hp1\Documents\R\win-library\3.2" C:\Users\hp1\AppData\Local\Temp\RtmpiAzB7h/downloaded_packages/mclust_5.3.tar.gz' had status 1
Warning in install.packages :
installation of package ‘mclust’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\hp1\AppData\Local\Temp\RtmpiAzB7h\downloaded_packages’
When digging for solutions on how to fix it, I came across this where the OP says in a comment that the issue was arising due to missing llpack and lblas libraries, which they fixed by installing lapackdev and blasdev packages. But when I try to install these packages, I get error. I checked all my 12 repositories and tried again, but same result.
> install.packages("lapackdev")
Installing package into ‘C:/Users/hp1/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘lapackdev’ is not available (for R version 3.2.3)
> setRepositories(graphics = getOption("menu.graphics"),
+ ind = NULL, addURLs = character())
--- Please select repositories for use in this session ---
1: + CRAN 2: BioC software
3: BioC annotation 4: BioC experiment
5: BioC extra 6: + CRAN (extras)
7: Omegahat 8: R-Forge
9: rforge.net 10: CRAN (extras, https)
11: R-Forge [https] 12: rforge.net [https]
Enter one or more numbers separated by spaces, or an empty line to cancel
1: 1 2 3 4 5 6 7 8 9 10 11 12
> install.packages("lapackdev")
Warning in install.packages :
cannot open URL 'http://www.omegahat.org/R/src/contrib/PACKAGES.gz': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'http://www.omegahat.org/R/src/contrib/PACKAGES': HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository http://www.omegahat.org/R/src/contrib:
cannot open URL 'http://www.omegahat.org/R/src/contrib/PACKAGES'
Warning in install.packages :
cannot open URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES.gz': HTTP status was '400 Bad Request'
Warning in install.packages :
cannot open URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES': HTTP status was '400 Bad Request'
Warning in install.packages :
unable to access index for repository https://R-Forge.R-project.org/src/contrib:
cannot open URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES'
Installing package into ‘C:/Users/hp1/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
Warning in install.packages :
cannot open URL 'http://www.omegahat.org/R/src/contrib/PACKAGES.gz': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'http://www.omegahat.org/R/src/contrib/PACKAGES': HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository http://www.omegahat.org/R/src/contrib:
cannot open URL 'http://www.omegahat.org/R/src/contrib/PACKAGES'
Warning in install.packages :
cannot open URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES.gz': HTTP status was '400 Bad Request'
Warning in install.packages :
cannot open URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES': HTTP status was '400 Bad Request'
Warning in install.packages :
unable to access index for repository https://R-Forge.R-project.org/src/contrib:
cannot open URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES'
Warning in install.packages :
package ‘lapackdev’ is not available (for R version 3.2.3)
Warning in install.packages :
cannot open URL 'http://www.omegahat.org/R/bin/windows/contrib/3.2/PACKAGES.gz': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'http://www.omegahat.org/R/bin/windows/contrib/3.2/PACKAGES': HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository http://www.omegahat.org/R/bin/windows/contrib/3.2:
cannot open URL 'http://www.omegahat.org/R/bin/windows/contrib/3.2/PACKAGES'
Warning in install.packages :
cannot open URL 'http://www.rforge.net/bin/windows/contrib/3.2/PACKAGES.gz': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'http://www.rforge.net/bin/windows/contrib/3.2/PACKAGES': HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository http://www.rforge.net/bin/windows/contrib/3.2:
cannot open URL 'http://www.rforge.net/bin/windows/contrib/3.2/PACKAGES'
Warning in install.packages :
cannot open URL 'https://R-Forge.R-project.org/bin/windows/contrib/3.2/PACKAGES.gz': HTTP status was '400 Bad Request'
Warning in install.packages :
cannot open URL 'https://R-Forge.R-project.org/bin/windows/contrib/3.2/PACKAGES': HTTP status was '400 Bad Request'
Warning in install.packages :
unable to access index for repository https://R-Forge.R-project.org/bin/windows/contrib/3.2:
cannot open URL 'https://R-Forge.R-project.org/bin/windows/contrib/3.2/PACKAGES'
Warning in install.packages :
cannot open URL 'https://www.rforge.net/bin/windows/contrib/3.2/PACKAGES.gz': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'https://www.rforge.net/bin/windows/contrib/3.2/PACKAGES': HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository https://www.rforge.net/bin/windows/contrib/3.2:
cannot open URL 'https://www.rforge.net/bin/windows/contrib/3.2/PACKAGES'
Same with blasdev:
> install.packages("blasdev")
Warning in install.packages :
cannot open URL 'http://www.omegahat.org/R/src/contrib/PACKAGES.gz': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'http://www.omegahat.org/R/src/contrib/PACKAGES': HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository http://www.omegahat.org/R/src/contrib:
cannot open URL 'http://www.omegahat.org/R/src/contrib/PACKAGES'
Warning in install.packages :
cannot open URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES.gz': HTTP status was '400 Bad Request'
Warning in install.packages :
cannot open URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES': HTTP status was '400 Bad Request'
Warning in install.packages :
unable to access index for repository https://R-Forge.R-project.org/src/contrib:
cannot open URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES'
Installing package into ‘C:/Users/hp1/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
Warning in install.packages :
cannot open URL 'http://www.omegahat.org/R/src/contrib/PACKAGES.gz': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'http://www.omegahat.org/R/src/contrib/PACKAGES': HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository http://www.omegahat.org/R/src/contrib:
cannot open URL 'http://www.omegahat.org/R/src/contrib/PACKAGES'
Warning in install.packages :
cannot open URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES.gz': HTTP status was '400 Bad Request'
Warning in install.packages :
cannot open URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES': HTTP status was '400 Bad Request'
Warning in install.packages :
unable to access index for repository https://R-Forge.R-project.org/src/contrib:
cannot open URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES'
Warning in install.packages :
package ‘blasdev’ is not available (for R version 3.2.3)
Warning in install.packages :
cannot open URL 'http://www.omegahat.org/R/bin/windows/contrib/3.2/PACKAGES.gz': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'http://www.omegahat.org/R/bin/windows/contrib/3.2/PACKAGES': HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository http://www.omegahat.org/R/bin/windows/contrib/3.2:
cannot open URL 'http://www.omegahat.org/R/bin/windows/contrib/3.2/PACKAGES'
Warning in install.packages :
cannot open URL 'http://www.rforge.net/bin/windows/contrib/3.2/PACKAGES.gz': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'http://www.rforge.net/bin/windows/contrib/3.2/PACKAGES': HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository http://www.rforge.net/bin/windows/contrib/3.2:
cannot open URL 'http://www.rforge.net/bin/windows/contrib/3.2/PACKAGES'
Warning in install.packages :
cannot open URL 'https://R-Forge.R-project.org/bin/windows/contrib/3.2/PACKAGES.gz': HTTP status was '400 Bad Request'
Warning in install.packages :
cannot open URL 'https://R-Forge.R-project.org/bin/windows/contrib/3.2/PACKAGES': HTTP status was '400 Bad Request'
Warning in install.packages :
unable to access index for repository https://R-Forge.R-project.org/bin/windows/contrib/3.2:
cannot open URL 'https://R-Forge.R-project.org/bin/windows/contrib/3.2/PACKAGES'
Warning in install.packages :
cannot open URL 'https://www.rforge.net/bin/windows/contrib/3.2/PACKAGES.gz': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'https://www.rforge.net/bin/windows/contrib/3.2/PACKAGES': HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository https://www.rforge.net/bin/windows/contrib/3.2:
cannot open URL 'https://www.rforge.net/bin/windows/contrib/3.2/PACKAGES'
What is going on and how do I get mclust to install?
I am answering my own question as the following solved the issue (i.e., mclust was installed successfully) without needing to install the 2 packages I mention in the question. So, this might help someone facing difficulty install mclust.
I updated R version from 3.25 to 3.4, and R studio version from 0.9 to the latest (1.0.143 at the time of writing this answer), and this seems to have solved the issue.
Im trying to update the codetools package and get the same error is I use update.package() or install.package(), as shown below. Any insight is appreciated:
R> install.packages("codetools", lib = "/usr/lib/R/library")
trying URL 'https://cran.rstudio.com/src/contrib/codetools_0.2-14.tar.gz'
Content type 'application/x-gzip' length 12938 bytes (12 KB)
==================================================
downloaded 12 KB
* installing *source* package ‘codetools’ ...
** package ‘codetools’ successfully unpacked and MD5 sums checked
mv: cannot move ‘/usr/lib/R/library/codetools’ to ‘/usr/lib/R/library/00LOCK-codetools/codetools’: Permission denied
Warning in file.copy(f, instdir, TRUE) : problem copying ./NAMESPACE to /usr/lib/R/library/codetools/NAMESPACE: Permission denied
Warning in file(file, ifelse(append, "a", "w")) : cannot open file '/usr/lib/R/library/codetools/DESCRIPTION': Permission denied
Error in file(file, ifelse(append, "a", "w")) : cannot open the connection
ERROR: installing package DESCRIPTION failed for package ‘codetools’
* removing ‘/usr/lib/R/library/codetools’
Warning in install.packages : installation of package ‘codetools’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpiJWb8L/downloaded_packages’
Updating HTML index of packages in '.Library'
Warning in install.packages : cannot create file '/usr/share/R/doc/html/packages.html', reason 'Permission denied'
Warning in install.packages : cannot update HTML package index
Permission denied sounds like you don't have administrator permission on that system. Try running R as root (or with sudo) and see if it works then.
In an R package, I have a figure (jpeg) located under man/figures, which is added to a Rd file with,
\if{html}{\figure{supplydemand.jpg}{Supply-demand}}
\if{latex}{\figure{supplydemand}{Supply-demand}}
After updating to roxygen2 4.0.1, I get the error:
==> roxygen2::roxygenize('.', roclets=c('rd', 'collate', 'namespace'))
Error in file(con, "r") : cannot open the connection
Calls: suppressPackageStartupMessages ... <Anonymous> -> first_time -> vapply -> FUN -> readLines -> file
In addition: Warning message:
In file(con, "r") : cannot open file './man/figures': Permission denied
Execution halted
Exited with status 1.
If I remove the code to insert the figure, I still get this error. Only when I remove the subdir man/figures does roxygen2 work OK.
I assume this is a bug in roxygen2 or is there a workaround?