I am trying to install R on CentOS 8 and it requires openblas-0.3.3-5.el8, but using dnf the AppStream repo only gives me openblas-0.3.3-2.el8. Is there any way to force it to install the newer version? Thanks in advance, I am really stuck here.
[bosr#rth.ad.rothschild.com#usd1sapp101 ~]$ sudo dnf install openblas
Last metadata expiration check: 0:39:47 ago on Tue 25 May 2021 06:50:01 PM CEST.
Dependencies resolved.
=================================================================================================
Package Architecture Version Repository Size
=================================================================================================
Installing:
openblas x86_64 0.3.3-2.el8 InstallMedia-AppStream 4.3 M
Transaction Summary
=================================================================================================
Install 1 Package
Total size: 4.3 M
Installed size: 31 M
Is this ok [y/N]: N
If I try to install R, here is the error message I get:
> [bosr#rth.ad.rothschild.com#usd1sapp101 ~]$ sudo dnf update
> CentOS-8 - AppStream 271 MB/s | 5.4 MB 00:00
> CentOS-8 - Base 248 MB/s | 2.2 MB 00:00
> CentOS-8 - PowerTools 5.1 MB/s | 2.0 MB 00:00
> Extra Packages for Enterprise Linux Modular 8 - x86_64 594 kB/s | 610 kB 00:01
> Extra Packages for Enterprise Linux 8 - x86_64 6.4 MB/s | 9.4 MB 00:01
> Error:
> Problem: package R-devel-4.0.5-1.el8.x86_64 requires R-core-devel = 4.0.5-1.el8, but none of the providers can be installed
> - package R-core-devel-4.0.5-1.el8.x86_64 requires openblas-devel, but none of the providers can be installed
> - cannot install the best update candidate for package R-devel-1-1.x86_64
> - nothing provides openblas(x86-32) = 0.3.3-5.el8 needed by openblas-devel-0.3.3-5.el8.i686
> - nothing provides openblas-threads(x86-32) = 0.3.3-5.el8 needed by openblas-devel-0.3.3-5.el8.i686
> - nothing provides openblas(x86-64) = 0.3.3-5.el8 needed by openblas-devel-0.3.3-5.el8.x86_64
> - nothing provides openblas-threads(x86-64) = 0.3.3-5.el8 needed by openblas-devel-0.3.3-5.el8.x86_64
> (try to add '--skip-broken' to skip uninstallable packages or '--nobest' to use not only best candidate packages)
> [bosr#rth.ad.rothschild.com#usd1sapp101 ~]$
The missing packages are in a repo called powertools that is disabled on Centos8 by default. You need to enable this repo then try again. On my GCP VM I ran:
sudo yum install epel-release
sudo yum config-manager --set-enabled powertools
sudo yum install R
I used wget to download the newer version of openblas and openblas-threads. I was then able to install them and then install R. Not sure why the repo wasn't giving me the latest version, but I am good now.
Related
I noticed that having a minimum Bioconductor version of 3.12 and R 4.0 is mandatory for installing ANCOMBC. However I did install it on R 3.6 by doing the following:
Install all dependencies of ANCOMBC using Bioconductor version 3.10 (compatible with R 3.6)
Download the source tar.gz from https://bioconductor.org/packages/release/bioc/html/ANCOMBC.html
sudo R CMD install ANCOMBC_1.4.0.tar.gz
The above was done in a linux (Ubuntu) machine.
Requesting any other recommendations for installing ANCOMBC on R < 4.0. Is the above recommended to do when package mandates minimum R 0f 4.0 but gets successfully installed on lower version?
I have a 3.4 R version on my machine and i want to install the 4 version , after downlowding the package and making it my R version still at 3.4 . what is the problem ? ( i have a ubuntu 16.04 working on my machine )
According to here, the installation requires to add
deb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran40/
in the /etc/apt/sources.list
It is mentioned that
R 4.0 packages for Ubuntu on i386 and amd64 are available for most stable Desktop releases of Ubuntu until their official end of life date. However, only the latest Long Term Support (LTS) release is fully supported. As of April 27, 2020 the supported releases are Xenial Xerus (16.04; LTS), Bionic Beaver and Focal Fossa (20.04, amd64 only). Note, to install R 4.0 packages, a different sources.list entry is needed. See below for details.
I know that this is no new question, rather this issue has been raised several times.
I have just switched from Linux Mint 19.1 to 19.3 (new install, not upgrade) and want to install R from scratch.
However, problems arise when I tried to follow this repair guide and in the end, when attempting to run
sudo apt-get install r-base
The terminal replied this
> 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 (>= 3.6.2-1disco) but it is not going to be installed
> Depends: r-recommended (= 3.6.2-1disco) but it is not going to be installed W: Target Packages (Packages) is configured multiple
> times in /etc/apt/sources.list:1 and
> /etc/apt/sources.list.d/additional-repositories.list:2 E: Unable to
> correct problems, you have held broken packages
Now I know that this is a common problem for numerous Linux and R users, and I have read dozens of StackOverflow post regarding this issue. But the problem persists and it is for me nearly impossible to fix, because I have tried to edit the /etc/apt/sources.list and nothing changed.
Any help greatly appreciated!
I got the same problem :
Use deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/ for linux mint version 19.3
and not disco (it's for the last version of Ubuntu)
Building Qt5 toolchain for Raspberry Pi2 Qt apps using Yocto fido See this tutorial. My build machine is NUC with Debian 7.8.
Succeeded to build my image perfectly, but getting error while building my toolchain.
my local.conf, I removed x11 feature
MACHINE = "raspberrypi2"
LICENSE_FLAGS_WHITELIST="commercial license"
DISTRO = "poky"
DL_DIR = "${TOPDIR}/../dl"
PACKAGE_CLASSES = "package_ipk"
DISTRO_FEATURES_remove = "x11 wayland" <=========
# Set Rpi GPU Memory to 128MB
GPU_MEM = "128"
my bblayers.conf
# LAYER_CONF_VERSION is increased each time build/conf/bblayers.conf
# changes incompatibly
LCONF_VERSION = "6"
BBPATH = "${TOPDIR}"
BBFILES ?= ""
BBLAYERS ?= " \
${TOPDIR}/../poky/meta-embarcados \
${TOPDIR}/../poky/meta-embarcados/meta-rpi \
${TOPDIR}/../poky/meta-qt5 \
${TOPDIR}/../poky/meta-raspberrypi \
${TOPDIR}/../poky/meta-openembedded/meta-oe \
${TOPDIR}/../poky/meta-openembedded/meta-ruby \
${TOPDIR}/../poky/meta \
${TOPDIR}/../poky/meta-yocto \
"
I have tried from scratch by removing my build/tmp folder to no avail, I am still getting the x11 dependency issue although it's a removed feature in my local.conf.
ERROR: Unable to install packages. Command '/home/otto/yocto/build/tmp/sysroots/x86_64-linux/usr/bin/opkg-cl -f /home/otto/yocto/build/tmp/work/cortexa7hf-vfp-vfpv4-neon-poky-linux-gnueabi/meta-toolchain-qt5/1.0-r0/opkg.conf -o /home/otto/yocto/build/tmp/work/cortexa7hf-vfp-vfpv4-neon-poky-linux-gnueabi/meta-toolchain-qt5/1.0-r0/sdk/image/opt/poky/1.8/sysroots/cortexa7hf-vfp-vfpv4-neon-poky-linux-gnueabi --force_postinstall --prefer-arch-to-version install packagegroup-core-standalone-sdk-target-dbg packagegroup-core-standalone-sdk-target packagegroup-qt5-toolchain-target' returned 255:
Installing packagegroup-core-standalone-sdk-target-dbg (1.0-r8) on root.
Downloading file:/home/otto/yocto/build/tmp/deploy/ipk/all/packagegroup-core-standalone-sdk-target-dbg_1.0-r8_all.ipk.
and
Configuring glibc-gconv-cp1252.
Configuring libsegfault.
Configuring libgcov-dev.
Configuring glibc-gconv-iso8859-15.
Configuring glibc-gconv-iso8859-1.
Configuring packagegroup-core-standalone-sdk-target.
Collected errors:
* satisfy_dependencies_for: Cannot satisfy the following dependencies for packagegroup-qt5-toolchain-target:
* libx11-6 (>= 1.6.2) * libxcb1 (>= 1.11) * libxau6 (>= 1.0.8) * libxdmcp6 (>= 1.1.1) *
* opkg_install_cmd: Cannot install package packagegroup-qt5-toolchain-target.
ERROR: Function failed: do_populate_sdk
ERROR: Logfile of failure stored in: /home/otto/yocto/build/tmp/work/cortexa7hf-vfp-vfpv4-neon-poky-linux-gnueabi/meta-toolchain-qt5/1.0-r0/temp/log.do_populate_sdk.26687
ERROR: Task 7 (/home/otto/yocto/build/../poky/meta-qt5/recipes-qt/meta/meta-toolchain-qt5.bb, do_populate_sdk) failed with exit code '1'
NOTE: Tasks Summary: Attempted 3419 tasks of which 3418 didn't need to be rerun and 1 failed.
No currently running tasks (3418 of 3420)
Summary: 1 task failed:
/home/otto/yocto/build/../poky/meta-qt5/recipes-qt/meta/meta-toolchain-qt5.bb, do_populate_sdk
Summary: There were 2 ERROR messages shown, returning a non-zero exit code.
Any pointers on how to resolve this? why would it still try to compile x11 feature when removed?
(Votes down are Ok, but a comment explaining why you are voting down is better. It's not like I am not trying hard on my side to resolve this critical issue on a Sunday! There is definitely some trolls in the StackExchange community)
Libraries on build machine
This look to be the problem, the installed version is 1.5.0-1+deb7u2 where it requires >=1.6.2. That doesn't answer my question, but that's a hint.
otto#marvin:~/yocto/build$ apt-cache policy libx11-6
libx11-6:
Installed: 2:1.5.0-1+deb7u2
Candidate: 2:1.5.0-1+deb7u2
Version table:
*** 2:1.5.0-1+deb7u2 0
500 http://security.debian.org/ wheezy/updates/main amd64 Packages
100 /var/lib/dpkg/status
2:1.5.0-1+deb7u1 0
500 http://ftp.us.debian.org/debian/ wheezy/main amd64 Packages
500 http://http.debian.net/debian/ wheezy/main amd64 Packages
otto#marvin:~/yocto/build$ apt-cache policy libxcb1
libxcb1:
Installed: 1.8.1-2+deb7u1
Candidate: 1.8.1-2+deb7u1
Version table:
1.10-3~bpo70+1 0
100 http://http.debian.net/debian/ wheezy-backports/main amd64 Packages
*** 1.8.1-2+deb7u1 0
500 http://ftp.us.debian.org/debian/ wheezy/main amd64 Packages
500 http://security.debian.org/ wheezy/updates/main amd64 Packages
500 http://http.debian.net/debian/ wheezy/main amd64 Packages
100 /var/lib/dpkg/status
otto#marvin:~/yocto/build$ apt-cache policy libxau6
libxau6:
Installed: 1:1.0.7-1
Candidate: 1:1.0.7-1
Version table:
*** 1:1.0.7-1 0
500 http://ftp.us.debian.org/debian/ wheezy/main amd64 Packages
500 http://http.debian.net/debian/ wheezy/main amd64 Packages
100 /var/lib/dpkg/status
otto#marvin:~/yocto/build$ apt-cache policy libxdmcp6
libxdmcp6:
Installed: 1:1.1.1-1
Candidate: 1:1.1.1-1
Version table:
*** 1:1.1.1-1 0
500 http://ftp.us.debian.org/debian/ wheezy/main amd64 Packages
500 http://http.debian.net/debian/ wheezy/main amd64 Packages
100 /var/lib/dpkg/status
Upgraded to Debian 8.1 but problem persists
although libx11-6, libxau6, libxdmcp6 satisfy the version requirements, one library doesn't, and I can't install >=1.11 (I think), this is the latest libxcb1 on Jessie that I can get.
otto#marvin:~/yocto$ sudo apt-cache policy libxcb1
libxcb1:
Installed: 1.10-3+b1
Candidate: 1.10-3+b1
Version table:
*** 1.10-3+b1 0
500 http://ftp.us.debian.org/debian/ jessie/main amd64 Packages
500 http://http.debian.net/debian/ jessie/main amd64 Packages
100 /var/lib/dpkg/status
the message
Configuring packagegroup-core-standalone-sdk-target.
Collected errors:
* satisfy_dependencies_for: Cannot satisfy the following dependencies for packagegroup-qt5-toolchain-target:
* libx11-6 (>= 1.6.2) * libxcb1 (>= 1.11) * libxau6 (>= 1.0.8) * libxdmcp6 (>= 1.1.1) *
* opkg_install_cmd: Cannot install package packagegroup-qt5-toolchain-target.
ERROR: Function failed: do_populate_sdk
ERROR: Logfile of failure stored in: /home/otto/yocto/build/tmp/work/cortexa7hf-vfp-vfpv4-neon-poky-linux-gnueabi/meta-toolchain-qt5/1.0-r0/temp/log.do_populate_sdk.12273
ERROR: Task 7 (/home/otto/yocto/build/../poky/meta-qt5/recipes-qt/meta/meta-toolchain-qt5.bb, do_populate_sdk) failed with exit code '1'
NOTE: Tasks Summary: Attempted 3419 tasks of which 3418 didn't need to be rerun and 1 failed.
No currently running tasks (3418 of 3420)
Summary: 1 task failed:
/home/otto/yocto/build/../poky/meta-qt5/recipes-qt/meta/meta-toolchain-qt5.bb, do_populate_sdk
Summary: There were 2 ERROR messages shown, returning a non-zero exit code.
Identified failing command
/home/otto/yocto/build/tmp/sysroots/x86_64-linux/usr/bin/opkg-cl -f /home/otto/yocto/build/tmp/work/cortexa7hf-vfp-vfpv4-neon-poky-linux-gnueabi/meta-toolchain-qt5/1.0-r0/opkg.conf -o /home/otto/yocto/build/tmp/work/cortexa7hf-vfp-vfpv4-neon-poky-linux-gnueabi/meta-toolchain-qt5/1.0-r0/sdk/image/opt/poky/1.8/sysroots/cortexa7hf-vfp-vfpv4-neon-poky-linux-gnueabi --force_postinstall --prefer-arch-to-version install packagegroup-qt5-toolchain-target
definitely something in the packagegroup-qt5-toolchain-target
This sounds similar to the experience I had where I built for X11 then subsequently turned it off with DISTRO_FEATURES_remove = "x11".
As far as I could see there was still a dependency on X11 somewhere in the license manifest, from what I recall there was a header file used Xauth in pango/cairo that's stubbed out without X11.
The problem went away when I built for a different MACHINE, so I would suggest launching a completely fresh build without X11 after clearing your SSTATE_CACHE.
I've downloaded cloudera-manager-installer.bin from CDH's official site. But when I trying to install it, the program hangs at 40% progress.
The installation log looks like this:
Loading mirror speeds from cached hostfile
* epel: mirrors.neusoft.edu.cn
* rpmforge: ftp.riken.jp
Setting up Install Process
Resolving Dependencies
--> Running transaction check
---> Package cloudera-manager-server.x86_64 0:4.8.2-1.cm482.p0.101.el6 will be installed
--> Processing Dependency: cloudera-manager-daemons = 4.8.2 for package: cloudera-manager-server-4.8.2-1.cm482.p0.101.el6.x86_64
--> Running transaction check
---> Package cloudera-manager-daemons.x86_64 0:4.8.2-1.cm482.p0.101.el6 will be installed
--> Finished Dependency Resolution
Dependencies Resolved
================================================================================
Package Arch Version Repository Size
================================================================================
Installing:
cloudera-manager-server x86_64 4.8.2-1.cm482.p0.101.el6 cloudera-manager 7.7 k
Installing for dependencies:
cloudera-manager-daemons
x86_64 4.8.2-1.cm482.p0.101.el6 cloudera-manager 148 M
Transaction Summary
================================================================================
Install 2 Package(s)
Total download size: 148 M
Installed size: 203 M
Downloading Packages:
I can access archive.cloudera.com from my server.
How can I deal with this problem ?
Try the following
sudo unmount cm_processes
sudo rm -Rf /var/run/cloudera*
Doing it solved this for me.