Currently using Ububtu 14.04 with R 3.0 and RStudio. The installation of devtools failed on the installation of the curl package. I had successfully installed Rcpp by a restart previously - So I tried a clean start of R and Rstudio and tried installing package curl first - with the error messages below:
install.packages("curl")
Installing package into ‘/home/freya/R/i686-pc-linux-gnu-library/3.0’
(as ‘lib’ is unspecified)
trying URL 'http://cran.rstudio.com/src/contrib/curl_0.9.2.tar.gz'
Content type 'application/x-gzip' length 244688 bytes (238 Kb)
opened URL
==================================================
downloaded 238 Kb
* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
File curl.h not found. Make sure the curl development library is installed, e.g. libcurl4-openssl-dev (deb) or libcurl-devel (rpm).
ERROR: configuration failed for package ‘curl’
* removing ‘/home/freya/R/i686-pc-linux-gnu-library/3.0/curl’
Warning in install.packages :
installation of package ‘curl’ had non-zero exit status
Any suggestions appreciated, Thanks
KNB
Related
I Tried to install nodejs using nvm on ubuntu 18.04. But everytime it's throwing following error stack
pasindu#pasindu-HP-EliteBook-850-G7-Notebook-PC:~$ nvm install 0.10.35
Downloading and installing node v0.10.35...
Downloading https://nodejs.org/dist/v0.10.35/node-v0.10.35-linux-x64.tar.gz...
Warning: Failed to create the file
Warning: /home/pasindu/.nvm/.cache/bin/node-v0.10.35-linux-x64/node-v0.10.35-li
Warning: nux-x64.tar.gz: Permission denied
curl: (23) Failure writing output to destination
Binary download from https://nodejs.org/dist/v0.10.35/node-v0.10.35-linux-x64.tar.gz failed, trying source.
grep: /home/pasindu/.nvm/.cache/bin/node-v0.10.35-linux-x64/node-v0.10.35-linux-x64.tar.gz: No such file or directory
Provided file to checksum does not exist.
Binary download failed, trying source.
Detected that you have 12 CPU core(s)
Running with 11 threads to speed up the build
Downloading https://nodejs.org/dist/v0.10.35/node-v0.10.35.tar.gz...
Warning: Failed to create the file
Warning: /home/pasindu/.nvm/.cache/src/node-v0.10.35/node-v0.10.35.tar.gz:
Warning: Permission denied
curl: (23) Failure writing output to destination
Binary download from https://nodejs.org/dist/v0.10.35/node-v0.10.35.tar.gz failed, trying source.
grep: /home/pasindu/.nvm/.cache/src/node-v0.10.35/node-v0.10.35.tar.gz: No such file or directory
Provided file to checksum does not exist.
It may be the problem of snap curl, see here, cos I installed curl with snap at first and always encounter this problem, then I removed curl with sudo snap remove curl and reinstall it with sudo apt install curl, my current curl version is 7.68.0. then solved it.
I had to clear the cache:
nvm cache clear.
I've got the error after I tried to install a version of Node, which I've tried to install already, however the installation processs failed at the first time due disconnecting from the internet.
[Trying to] Installing flatpak on Arch linux fails:
$ sudo pacman -S flatpak
resolving dependencies...
:: There are 3 providers available for xdg-desktop-portal-impl:
:: Repository extra
1) xdg-desktop-portal-gtk 2) xdg-desktop-portal-kde
:: Repository community
3) xdg-desktop-portal-wlr
Enter a number (default=1): 1
looking for conflicting packages...
Packages (11) appstream-glib-0.7.18-1 gcab-1.4-1 geoclue-2.5.7-3 geocode-glib-3.26.2-1
gnome-desktop-1:40.0-1 gnome-keyring-1:40.0-1 libstemmer-0+713-2 ostree-2021.1-1
xdg-desktop-portal-1.8.0-1 xdg-desktop-portal-gtk-1.8.0-1 flatpak-1.10.2-1
Total Download Size: 0.63 MiB
Total Installed Size: 29.29 MiB
:: Proceed with installation? [Y/n] Y
:: Retrieving packages...
error: failed retrieving file 'ostree-2021.1-1-x86_64.pkg.tar.zst' from mirror.rackspace.com : The requested URL returned error: 404
error: failed retrieving file 'ostree-2021.1-1-x86_64.pkg.tar.zst' from mirrors.evowise.com : The requested URL returned error: 404
error: failed retrieving file 'ostree-2021.1-1-x86_64.pkg.tar.zst' from mirror.rackspace.com : The requested URL returned error: 404
error: failed retrieving file 'ostree-2021.1-1-x86_64.pkg.tar.zst' from mirror.rackspace.com : The requested URL returned error: 404
warning: failed to retrieve some files
error: failed to commit transaction (failed to retrieve some files)
Errors occurred, no packages were upgraded.
What's the correct way to download and install flatpack on Linux?
Update the system with
pacman -Syu and try again
buy I highly recommend going with AUR packages
Note that it is not advisable to install an individual package after -Sy or -Syy. If you need to update your mirrors with -y to install a package, you should combine it with a full system upgrade -u:
sudo pacman -Syu flatpak
You might not see immediate breakage with -Sy <package>, but eventually something will break with continued use. If <package> happens to pull in new lib versions, then any program that depends on those libs will break since they will still be built against the old libs.
Solved it with running sudo pacman -Syy first
This is sometimes happen. you can solve it using pacman -Syu flatpak.
If it didn't solve then you have to change your repository server either from /etc/pacman or /etc/pacman.d/mirrorlist.
Passing on knowledge I just learned in the hopes of reducing the
headache others may experience with native gem extensions like I've
had.
TL;DR - Had an issue with bundle install. Read mkmf.log as mentioned in the error. The log had another error that I googled. Installed
necessary library. Afterwards, bundle install was successful.
Trying to install gems using bundler and getting errors about building gem native extensions:
$ bundle install
Fetching gem metadata from https://rubygems.org/...........
Fetching version metadata from https://rubygems.org/..
Resolving dependencies...
Installing daemons 1.2.3
Installing eventmachine 1.0.8 with native extensions
Gem::Ext::BuildError: ERROR: Failed to build gem native extension.
current directory: /usr/local/rvm/gems/ruby-2.3.0/gems/eventmachine-1.0.8/ext
/usr/local/rvm/rubies/ruby-2.3.0/bin/ruby -r ./siteconf20160309-8483-1so3k75.rb extconf.rb
*** extconf.rb failed ***
Could not create Makefile due to some reason, probably lack of necessary
libraries and/or headers. Check the mkmf.log file for more details. You may
need configuration options.
<...>
To see why this extension failed to compile, please check the mkmf.log which can be found here:
/usr/local/rvm/gems/ruby-2.3.0/extensions/x86_64-linux/2.3.0/eventmachine-1.0.8/mkmf.log
extconf failed, exit code 1
<...>
Installing mysql2 0.4.3 with native extensions
Gem::Ext::BuildError: ERROR: Failed to build gem native extension.
current directory: /usr/local/rvm/gems/ruby-2.3.0/gems/mysql2-0.4.3/ext/mysql2
/usr/local/rvm/rubies/ruby-2.3.0/bin/ruby -r ./siteconf20160309-8483-1oxfnj5.rb extconf.rb
checking for ruby/thread.h... *** extconf.rb failed ***
Could not create Makefile due to some reason, probably lack of necessary
libraries and/or headers. Check the mkmf.log file for more details. You may
need configuration options.
<...>
To see why this extension failed to compile, please check the mkmf.log which can be found here:
/usr/local/rvm/gems/ruby-2.3.0/extensions/x86_64-linux/2.3.0/mysql2-0.4.3/mkmf.log
extconf failed, exit code 1
<...>
Installing rack 1.6.4
Installing tilt 2.0.1
Using bundler 1.11.2
An error occurred while installing eventmachine (1.0.8), and Bundler cannot continue.
Make sure that `gem install eventmachine -v '1.0.8'` succeeds before bundling.
Passing on knowledge I just learned in the hopes of reducing the
headache others may experience with native gem extensions like I've
had.
TL;DR - Had an issue with bundle install. Read mkmf.log as mentioned in the error. The log had another error that I googled. Installed
necessary library. Afterwards, bundle install was successful.
I see that the errors point me to mkmf.log and where it's located. I open it up and check the error. Among other things it mentions the following on lines 2 and 3.
/usr/bin/ld: cannot find -lgmp
collect2: error: ld returned 1 exit status
I know from the error while during bundle install that it could be missing a library. So I search for a package called gmp. I find 2 libraries, one called libgmp10 and the other libgmp10-dev.
$ apt-cache search -n gmp
libgmp-dev - Multiprecision arithmetic library developers tools
libgmp10 - Multiprecision arithmetic library
<...>
I search my installed packages to see if I need to get one.
$ dpkg --get-selections | grep gmp
libgmp10:amd64 install
Since libgmp10 is already there, I try installing libgmp-dev. Then I run retry installing my gems, and it works!
$ sudo apt-get install libgmp-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following extra packages will be installed:
libgmpxx4ldbl
Suggested packages:
libgmp10-doc libmpfr-dev
The following NEW packages will be installed:
libgmp-dev libgmpxx4ldbl
0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
Need to get 300 kB of archives.
After this operation, 1,675 kB of additional disk space will be used.
Do you want to continue? [Y/n]
Get:1 http://us.archive.ubuntu.com/ubuntu/ trusty/main libgmpxx4ldbl amd64 2:5.1.3+dfsg-1ubuntu1 [8,736 B]
Get:2 http://us.archive.ubuntu.com/ubuntu/ trusty/main libgmp-dev amd64 2:5.1.3+dfsg-1ubuntu1 [292 kB]
Fetched 300 kB in 0s (411 kB/s)
Selecting previously unselected package libgmpxx4ldbl:amd64.
(Reading database ... 218685 files and directories currently installed.)
Preparing to unpack .../libgmpxx4ldbl_2%3a5.1.3+dfsg-1ubuntu1_amd64.deb ...
Unpacking libgmpxx4ldbl:amd64 (2:5.1.3+dfsg-1ubuntu1) ...
Selecting previously unselected package libgmp-dev:amd64.
Preparing to unpack .../libgmp-dev_2%3a5.1.3+dfsg-1ubuntu1_amd64.deb ...
Unpacking libgmp-dev:amd64 (2:5.1.3+dfsg-1ubuntu1) ...
Setting up libgmpxx4ldbl:amd64 (2:5.1.3+dfsg-1ubuntu1) ...
Setting up libgmp-dev:amd64 (2:5.1.3+dfsg-1ubuntu1) ...
Processing triggers for libc-bin (2.19-0ubuntu6.7) ...
$ bundle install
Fetching gem metadata from https://rubygems.org/...........
Fetching version metadata from https://rubygems.org/..
Resolving dependencies...
Using daemons 1.2.3
Installing eventmachine 1.0.8 with native extensions
Installing mysql2 0.4.3 with native extensions
Using rack 1.6.4
Using tilt 2.0.1
Using bundler 1.11.2
Installing rack-protection 1.5.3
Installing thin 1.6.4 with native extensions
Installing sinatra 1.4.6
Bundle complete! 3 Gemfile dependencies, 9 gems now installed.
Use `bundle show [gemname]` to see where a bundled gem is installed.
I am trying to install the R 3.0.2 devtools package on Ubuntu 14.04 as follows:
install.packages("devtools")
I get the following results:
Installing package into ‘/home/jim/R/x86_64-pc-linux-gnu-library/3.0’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Warning: dependency ‘xml2’ is not available
also installing the dependency ‘rversions’
trying URL 'http://cran.rstudio.com/src/contrib/rversions_1.0.1.tar.gz'
Content type 'application/x-gzip' length 4624 bytes
opened URL
==================================================
downloaded 4624 bytes
trying URL 'http://cran.rstudio.com/src/contrib/devtools_1.8.0.tar.gz'
Content type 'application/x-gzip' length 141487 bytes (138 Kb)
opened URL
==================================================
downloaded 138 Kb
ERROR: dependency ‘xml2’ is not available for package ‘rversions’
* removing ‘/home/jim/R/x86_64-pc-linux-gnu-library/3.0/rversions’
ERROR: dependency ‘rversions’ is not available for package ‘devtools’
* removing ‘/home/jim/R/x86_64-pc-linux-gnu-library/3.0/devtools’
The downloaded source packages are in
‘/tmp/RtmpmDzsRJ/downloaded_packages’
Warning messages:
1: In install.packages("devtools") :
installation of package ‘rversions’ had non-zero exit status
2: In install.packages("devtools") :
installation of package ‘devtools’ had non-zero exit status
It appears there is a dependency on a package named xml2. Does anyone know where I can find this package and how I can install it.
I have already installed the following:
sudo apt-get install libxml2-dev
sudo apt-get install libcurl4-openssl-dev
sudo apt-get install libcurl4-gnutls-dev
sudo apt-get install curl
If R is installed in Ubuntu using the software center, the stable version at the time of the Ubuntu build is built is included. Hence R 3.0.2 is installed.
Adding the following to /etc/apt/sources.list:
deb http://cran.rstudio.com/bin/linux/ubuntu trusty/
resulted in the current version (R 3.2.0) being loaded.
I had to install the following OpenSSL library
sudo apt-get install libssl-dev
and then I was able to start R and successfully install 'devtools'
Many thanks to Dirk and Pascal for their advice.
Another solution (on version R 3.2.2) is to installing lxml:
$ apt-get install libxml2-dev libxslt-dev
which successfully removed the R error:
Error: configuration failed for package ‘xml2’
appearing in R when running
install.packages("devtools")
I get the this error when i try yo install phpmyadmin on CentOS 6.5 VPS using this.
COMMAND :
sudo yum install phpmyadmin
ERROR :
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
* base: mirror.solarvps.com
* epel: epel.mirror.constant.com
* extras: mirror.wiredtree.com
* rpmforge: repoforge.mirror.constant.com
* updates: mirrors.lga7.us.voxel.net
Setting up Install Process
Resolving Dependencies
--> Running transaction check
---> Package phpmyadmin.noarch 0:2.11.11.3-2.el6.rf will be installed
--> Processing Dependency: php-mbstring >= 4.1.0 for package: phpmyadmin-2.11.11.3-2.el6.rf.noarch
--> Running transaction check
---> Package php-mbstring.x86_64 0:5.3.3-27.el6_5 will be installed
--> Processing Dependency: php-common(x86-64) = 5.3.3-27.el6_5 for package: php-mbstring-5.3.3-27.el6_5.x86_64
--> Finished Dependency Resolution
Error: Package: php-mbstring-5.3.3-27.el6_5.x86_64 (updates)
Requires: php-common(x86-64) = 5.3.3-27.el6_5
Installed: php-common-5.4.30-1.el6.remi.x86_64 (#remi)
php-common(x86-64) = 5.4.30-1.el6.remi
Available: php-common-5.3.3-26.el6.x86_64 (base)
php-common(x86-64) = 5.3.3-26.el6
Available: php-common-5.3.3-27.el6_5.x86_64 (updates)
php-common(x86-64) = 5.3.3-27.el6_5
You could try using --skip-broken to work around the problem
You could try running: rpm -Va --nofiles --nodigest
Somebody please Help. Thanx in advance
You've installed a more recent PHP version (5.4.30-1) from another source (#remi) than the officials (base) repository provides. Now you're trying to install the phpMyAdmin package, which depends on php-mbstring. php-mbstring is the actual problem here -- it's being automatically installed because phpmyadmin depends on it, but the version you're attempting to install isn't compatible with the rest of your PHP installation.
The solution is easy, though, since remi also provides phpmyadmin (quite a bit more recent version than you're attempting to install, too!). Just install phpmyadmin and php-common from the remi repository like you installed PHP. There are some instructions at http://blog.famillecollet.com/pages/Config-en if you forgot, but you managed to install the upgraded PHP already so you should be able to get the remi phpmyadmin installed pretty easily.
OR....
Download phpMyAdmin from http://www.phpmyadmin.net and uncompress it to your web root and forget about the package. php-mbstring isn't strictly required to run the application anyway, so you don't even need to worry about that part as long as you meet the other requirements.
You installed php5.4 from remi repository.
phpmyadmin needs php to work; but you are installing phpmyadmin from the official repository and that phpmyadmin version needs php5.3.
I guess you don't want to go back to php5.3, so just run this command:
yum --enablerepo=remi install phpmyadmin
If you didn't add remi repositories to you CentOS, you will have to previously run:
sudo rpm -Uvh http://download.fedoraproject.org/pub/epel/6/i386/epel-release-6-8.noarch.rpm
sudo rpm -Uvh http://rpms.famillecollet.com/enterprise/remi-release-6.rpm