I ran apt-get install openssl
and verified that the new version .1g is installed
root#nyc2-04-www:~# apt-cache policy openssl
openssl:
Installed: 1.0.1g-1
Candidate: 1.0.1g-2
Version table:
1.0.1g-2 0
500 http://http.debian.net/debian/ sid/main amd64 Packages
*** 1.0.1g-1 0
100 /var/lib/dpkg/status
1.0.1e-2+deb7u6 0
500 http://security.debian.org/ wheezy/updates/main amd64 Packages
1.0.1e-2+deb7u4 0
500 http://ftp.us.debian.org/debian/ wheezy/main amd64 Packages
500 http://http.debian.net/debian/ wheezy/main amd64 Packages
However, I notice that even though the new openssl is installed, my servers are still vulnerable unless I do a full apt-get upgrade
See here: http://filippo.io/Heartbleed/#www.uat.phantomjscloud.com
How can I avoid doing the full apt-get upgrade, but ensure the new openssl is being used?
FYI I did verify that doing apt-get upgrade will fix heartbleed (i did that in my production server) But I'm currious as to why updating openssl isn't good enough.
FYI I am using nginx. I also did apt-get install nginx afterwards but that didn't resolve the issue either
UPDATE: running openssl version -a shows that 1.0.1f is still active, even after reboot.
apt-get install libssl1.0.0 fixes the problem
Related
I just bought a new machine and made a fresh installation of Ubuntu 21.10 since I've read that the newer kernel works better with graphics drivers. I'm planning to update to the 22.04 LTS when it will be available. I didn't realize, however, that I might run into challenges with R.
There are plenty of questions here in SO on installing R on Ubuntu, but none seemed recent enough to address the Ubuntu version 21.10.
Ubuntu Packages For R - Full Instructions state that
As of May 19, 2021 the supported releases are
Hirsute Hippo (21.04, amd64 only)
Groovy Gorilla (20.10, amd64 only),
Focal Fossa (20.04; LTS and amd64 only),
Bionic Beaver (18.04; LTS), and
Xenial Xerus (16.04; LTS).
So, if I understand correctly, I have three options:
Uninstall 21.10 and replace with 21.04
Wait for support for 21.10
Install R from source
Now, the question is, have I understood correctly, or could I use, for example, the 21.04 repository (hirsute-cran40/)?
Apparently, it is ok to use a repository of older releases.
I was encouraged by Andre Wildeberg (thanks!) and added the 21.04 repository (hirsute-cran40/) into my /etc/apt/sources.list:
deb https://cloud.r-project.org/bin/linux/ubuntu hirsute-cran40/
Then, you can follow the rest of the CRAN instructions.
Add the relevant GPG key (under "Secure APT", half way through the document):
$ wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
Finally, install R:
$ sudo apt-get update
$ sudo apt-get install r-base
And everything should be working fine.
You need a newer signing key for that repo:
root:~# apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
Warning: apt-key is deprecated. Manage keyring files in trusted.gpg.d instead (see apt-key(8)).
Executing: /tmp/apt-key-gpghome.MsSJzqgwfx/gpg.1.sh --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
gpg: key 51716619E084DAB9: "Michael Rutter <marutter#gmail.com>" 1 new signature
gpg: failed to start agent '/usr/bin/gpg-agent': No such file or directory
gpg: can't connect to the agent: No such file or directory
gpg: Total number processed: 1
gpg: new signatures: 1
root:~# apt update
Get:1 https://cloud.r-project.org/bin/linux/ubuntu hirsute-cran40/ InRelease [3628 B]
Get:2 http://security.ubuntu.com/ubuntu impish-security InRelease [110 kB]
Hit:3 http://archive.ubuntu.com/ubuntu impish InRelease
Get:4 http://archive.ubuntu.com/ubuntu impish-updates InRelease [110 kB]
Get:5 http://archive.ubuntu.com/ubuntu impish-backports InRelease [101 kB]
Fetched 325 kB in 1s (422 kB/s)
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
1 package can be upgraded. Run 'apt list --upgradable' to see it.
root:#
One you have that, impish works fine. That said, hirsute binaries should work too (or even focal binaries, as one does with the 5000+ r-cran-* binaries the 'cran2deb4ubuntu' repo for the LTS release).
I am trying to install R-base 4.0, but it keeps installing v3.6. I've tried:
sudo apt install deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/
sudo apt-get install r-base
and v3.6, not 4.0 was installed. Next I tried:
sudo apt install deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/
sudo apt-get upgrade r-base
and it didn't work.
How do I upgrade to Rv4.0? I am using Pop_Os, no Ubuntu. Could that be the issue?
First off, your initial line is wrong. There is not such apt install deb command. You are supposed to edit the apt sources file by hand (though these days there may be GUI solutions to it as well).
Second, you omitted to actually use the new repo by not running sudo apt update (or equally sudo apt-get update). You must update the local indices.
Third, a preferred way is to just upgrade as you (almost) did in the second paragraph. But upgrade takes no package argument!
Fourth, this has nothing to do with Pop!OS as we are talking only about apt and apt-get here.
For completeness, I did a little blog and video about the R 3.6.* to R 4.0.* upgrade. More info here if you care.
PS Fifth, as r2evans noted in the comment, be sure to pick the right distro. I run straight Ubuntu so "focal" it is more me. You probably want R 4.0.* from the Ubuntu build matching your Pop!OS build.
I tried to upgrade the last version of R in my ubuntu server, following other blogs I uninstall R from my server and I tried to install doing these steps:
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/'
sudo apt update
I followed these steps from here https://www.digitalocean.com/community/tutorials/how-to-install-r-on-ubuntu-18-04
When I tried to run the last command: sudo apt-get install r-base
I got this error:
sudo apt install r-base
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
r-base : Depends: r-base-core (>= 4.0.2-1.1804.0) but it is not going to be installed
Depends: r-recommended (= 4.0.2-1.1804.0) but it is not going to be installed
Recommends: r-base-html but it is not going to be installed
apt-cache policy r-base yield:
-base:
Installed: (none)
Candidate: 4.0.2-1.1804.0
Version table:
4.0.2-1.1804.0 500
500 https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/ Packages
4.0.1-1.1804.0 500
500 https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/ Packages
4.0.0-1.1804.0 500
500 https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/ Packages
3.6.3-2 500
500 http://archive.ubuntu.com/ubuntu focal/universe amd64 Packages
3.4.4-1xenial0 500
500 https://cran.rstudio.com/bin/linux/ubuntu xenial/ Packages
3.4.3-1xenial0 500
500 https://cran.rstudio.com/bin/linux/ubuntu xenial/ Packages
3.4.2-2xenial2 500
500 https://cran.rstudio.com/bin/linux/ubuntu xenial/ Packages
3.4.2-1xenial1 500
500 https://cran.rstudio.com/bin/linux/ubuntu xenial/ Packages
3.4.1-2xenial0 500
500 https://cran.rstudio.com/bin/linux/ubuntu xenial/ Packages
3.4.1-1xenial0 500
500 https://cran.rstudio.com/bin/linux/ubuntu xenial/ Packages
3.4.0-1xenial0 500
500 https://cran.rstudio.com/bin/linux/ubuntu xenial/ Packages
3.3.3-1xenial0 500
500 https://cran.rstudio.com/bin/linux/ubuntu xenial/ Packages
3.3.2-1xenial0 500
500 https://cran.rstudio.com/bin/linux/ubuntu xenial/ Packages
3.3.1-1xenial0 500
500 https://cran.rstudio.com/bin/linux/ubuntu xenial/ Packages
3.3.0-2xenial0 500
500 https://cran.rstudio.com/bin/linux/ubuntu xenial/ Packages
3.3.0-1xenial0 500
500 https://cran.rstudio.com/bin/linux/ubuntu xenial/ Packages
3.2.5-1xenial 500
500 https://cran.rstudio.com/bin/linux/ubuntu xenial/ Packages
Thanks for your help!
Your quoted output is partial and we cannot see what is really behind it.
My suspicion is that some other package the binary depends on is too old. In general the apt install command assumes a current system. So maybe try
sudo apt update
sudo apt upgrade
sudo apt install r-base
and update your question with any "odd" errors you are seeing. I maintain the underlying Debian package r-base, and run these same Ubuntu binaries on several machines too without any issues.
I ran into the same issue...what kind of processor are you on? This happened to me because I was installing on an arm64 machine, and the main cran repo does not have packages for that architecture. I removed the reference to the cran repository in /etc/apt/sources.list (just using a text editor) and installed from http://ports.ubuntu.com/ubuntu-ports. This worked fine, but I have an older version of R than what's available on the cran repo. I'll either have to find a different source for the packages, or compile locally, or live with R 3.4.4.
I want to update R from 3.4.4 to 3.5 on ubuntu. I follow this How to upgrade R in ubuntu? ,but always meet some troubles
my try:
1、su
2、vi /etc/apt/sources.list and add
deb https://mirrors.ustc.edu.cn/CRAN/bin/linux/ubuntu/ xenial/
3、gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
4、gpg -a --export E084DAB9 | sudo apt-key add -
5、sudo apt-get update && sudo apt-get upgrade # meet some troubles
6、apt-get install r-base-dev # also meet some troubles
Err:27 http://ppa.launchpad.net/nebc/bio-linux/ubuntu xenial/main amd64 Packages 404 Not Found
W: GPG error: http://dl.google.com/linux/chrome/deb stable Release: The followin g signatures couldn't be verified because the public key is not available: NO_PU BKEY 6494C6D6997C215E
W: The repository 'http://dl.google.com/linux/chrome/deb stable Release' is not signed.
N: Data from such a repository can't be authenticated and is therefore potential ly dangerous to use.
N: See apt-secure(8) manpage for repository creation and user configuration deta ils.
N: Skipping acquire of configured file 'main/binary-i386/Packages' as repository 'http://dl.google.com/linux/chrome/deb stable InRelease' doesn't support archit ecture 'i386'
W: The repository 'http://ppa.launchpad.net/nebc/bio-linux/ubuntu xenial Release ' does not have a Release file.
N: Data from such a repository can't be authenticated and is therefore potential ly dangerous to use.
N: See apt-secure(8) manpage for repository creation and user configuration deta ils.
E: Failed to fetch http://ppa.launchpad.net/nebc/bio-linux/ubuntu/dists/xenial/m ain/binary-amd64/Packages 404 Not Found
E: Some index files failed to download. They have been ignored, or old ones used instead.
x/ubuntu/dists/xenial/main/binary-amd64/Packages 404 Not Found^C-linu
root#omnisky:~# sudo apt-get install r-base-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
r-base-dev is already the newest version (3.4.4-1xenial0). # why?
The following package was automatically installed and is no longer required:
snapd-login-service
Use 'sudo apt autoremove' to remove it.
0 upgraded, 0 newly installed, 0 to remove and 29 not upgraded.
I'm a newbie to Linux and try to install the latest R version on my Raspberry.
My Raspberry runs on Wheezy 7.8.
I followed instructions on CRAN, so I
added
deb http://cran.rstudio.com/bin/linux/debian wheezy-cran3/
to /etc/apt/sources.list
ran apt-get update which was successful and gave me only a "signature error" for the public key as pointed out on the CRAN-site
ran apt-get install r-base
But the result of the last command is
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
r-base : Depends: r-base-core (>= 3.1.2-1~wheezycran3.0) but it is not going to be installed
Depends: r-recommended (= 3.1.2-1~wheezycran3.0) but it is not going to be installed
Recommends: r-base-html but it is not going to be installed
Recommends: r-doc-html but it is not going to be installed
E: Unable to correct problems, you have held broken packages.
I tried to install R-2.15 before and then run the above commands. R-2.15 could be installed successfuly, but I'd need R-3* really.
I did browse the web, but couldn't find any useful hints for my specific problem, so I appreciate any support you could give me.
Thanks!
If it is of any use:
apt-cache policy r-base gives
r-base:
Installed: (none)
Candidate: 3.1.2-1~wheezycran3.0
Version table:
3.1.2-1~wheezycran3.0 0
500 http://cran.rstudio.com/bin/linux/debian/ wheezy-cran3/ Packages
3.1.0-1~wheezycran3.0 0
500 http://cran.rstudio.com/bin/linux/debian/ wheezy-cran3/ Packages
2.15.1-4 0
500 http://mirrordirector.raspbian.org/raspbian/ wheezy/main armhf Packages
apt-cache policy r-base-core gives
r-base-core:
Installed: (none)
Candidate: 2.15.1-4
Version table:
2.15.1-4 0
500 http://mirrordirector.raspbian.org/raspbian/ wheezy/main armhf Packages
uname -a gives
Linux raspberrypi 3.18.5+ #744 PREEMPT Fri Jan 30 18:19:07 GMT 2015 armv6l GNU/Linux
I had the same situation and decided to install that from the source code instead of install R from the repository(apt-get command).
Here is the command I run on my Raspberry Pi 2.
I could install and run R(3.1.2) sucessfully.
It might not be complete answer for you because I might already installed the library like gcc you did not have before. If you encounter the other issue, please let me know. I would like to solve it.
Just as a side note on this topic, because sudo make install process took a long time(maybe over a hour. I'm not sure because I feel asleep before I knew it...), I recommend you to do this when you have enough or before going to sleep like me.
wget http://cran.rstudio.com/src/base/R-3/R-3.1.2.tar.gz
mkdir R_HOME
mv R-3.1.2.tar.gz R_HOME/
cd R_HOME/
tar zxvf R-3.1.2.tar.gz
cd R-3.1.2/
sudo apt-get install gfortran libreadline6-dev libx11-dev libxt-dev
./configure
make
sudo make install
R
The cause of your problem is likely that the cran repository provides armel versions of the packages, and not armhf (which is the expected architecture for your RPI). If this is right, then you have two solutions:
The first work-around could be to download the armel version of the packages and then force their installation despite the architecture mismatch. It is supposed to work according to the Debian wiki, although you may experience performance issues:
The CPU in the Raspberry Pi implements the ARMv6 ISA (with VFP2) and
is thus incompatible with the Debian armhf port baseline of ARMv7+VFP3
and ARM hardware-floating-point ports for other distributions, which
all have the same baseline. It is compatible with Debian armel
(armv4t, soft(emulated) FP), but floating-point tasks will be slow
when running the Debian armel port.
To do that, you can try to reinstall the packages by specifying the armel architecture, for example:
apt-get install r-base:armel
If it doesn't work this way, you can otherwise download the packages from http://cran.r-project.org/bin/linux/debian/wheezy-cran3/ and install them manually using a commandline like:
dpkg --install --force-architecture xxxx_armel.deb yyyy_armel.deb zzzz_armel.deb
The other solution would be to compile R from its source.
I solved my initial question by upgrading Wheezy to Jessie. I am not an expert, but Jessie seems to be the current testing version of Debian, while Wheezy is the stable release - see here.
For upgrading, I followed the instructions here, or here, or here. Note: Upgrading takes quite a while and during the process you're required to answer some questions.
A word of caution though: Jessie is still testing and some people recommend not to use it yet, for a discussion see e.g. here.
I did set it up completely from a new completely new image, and it works well.
After having upgraded to Jessie I installed R-3.1.1. using
sudo apt-get install r-base
And I'd like to thank all those who have answered my question and given alternative ways of solving the problem above.
I'm able to install R-3.1.2 into raspbian using answer from teramonagi. I confirm it can install successfully on Raspberry Pi model B/B+.
However, before you can actually use R (install packages and run some R scripts), you have to increase the swap file size for Raspberry Pi due to lack of RAM (This service works very similar to page file in window, it kicks in when RAM usage is high). You can configure it by edit one of the config file by enter command below in LX terminal.
sudo nano /etc/dphys-swapfile
CONF_SWAPSIZE=100 #(change 100 to 512 or 1024, up to you, save the file)
sudo /etc/init.d/dphys-swapfile stop
sudo /etc/init.d/dphys-swapfile start #(restart swap file service with new swap file size)
Take note though, some users argued that increase swap file size can actually ruin your SD card. So apply this change at your own risk. I've been running my Pi with this configuration for my R automation for 1 month now. No issue so far.
Hope this helps.
Edit: If you are using model B/B+, i recommend to configure swap file size first then compile R.
That's what I've done to update my r-base on wheezy:
HOW TO UPDATE r-base 2.15 to 3.x ON DEBIAN WHEEZY
add these lines at the end of "/etc/apt/sources.list"
deb http://cran.revolutionanalytics.com/bin/linux/debian wheezy-cran3/
deb-src http://cran.revolutionanalytics.com/bin/linux/debian wheezy-cran3/
add the missing publich key of cran
gpg --keyserver pgpkeys.mit.edu --recv-key 06F90DE5381BA480
gpg -a --export 06F90DE5381BA480 | sudo apt-key add -
update and upgrade
apt-get update
aptitude -t wheezy-cran3 install r-base r-base-dev