I want to install the Rsymphony package in R 3.1. While installing the following error is thrown:
* package ‘Rsymphony’ successfully unpacked and MD5 sums checked
Cannot find SYMPHONY libraries and headers.
See <https://projects.coin-or.org/SYMPHONY>.
ERROR: configuration failed for package ‘Rsymphony’
So that decided to install the lib's for debian:
apt-get install coinor-libsymphony-dev coinor-libsymphony-doc
However, I still get the same error. Either I missed a certain lib or installed the wrong thing. How can I install the Rsymphony package correctly?
Spec: I'm using R 3.1 and debian 7.8
You may need more libraries -- the r-cran-rsymphony package which I maintain has
Build-Depends: debhelper (>= 7.0.0), r-base-dev (>= 3.1.2), \
cdbs, coinor-libsymphony-dev, coinor-libcgl-dev, autotools-dev
You can ignore cdbs etc if you are not building a package, but you probably want the two coinor-*-dev packages.
I'm using Ubuntu 14.04 and R 3.1. I wanted to update package Rsymphony to version 0.1-19 and got a similar error message as above.
Following Dirk's advise I did apt-get install coinor-libcgl-dev which also installed coinor-libclp-dev, coinor-libcoinutils-dev and coinor-libosi-dev. After that I could install Rsymphony using R's installation mechanism.
apt-get install r-cran-rsymphony worked but installed version 0.1-17-1.
Please install the packages for the library first:
apt-get install coinor-libsymphony-dev coinor-libsymphony-doc
Then install the package from CRAN:
apt-get install r-cran-rsymphony
That did the trick for me:
[Sun|11:39:13][tir on atlas2:~]-> sudo apt-get install r-cran-rsymphony
Reading package lists... Done
Building dependency tree
Reading state information... Done
Suggested packages:
r-cran-runit
The following NEW packages will be installed:
r-cran-rsymphony
0 upgraded, 1 newly installed, 0 to remove and 17 not upgraded.
Need to get 1,748 kB of archives.
After this operation, 3,919 kB of additional disk space will be used.
Get:1 http://in.archive.ubuntu.com/ubuntu/ trusty/universe r-cran-rsymphony amd64 0.1-17-1 [1,748 kB]
Fetched 1,748 kB in 54s (32.1 kB/s)
Selecting previously unselected package r-cran-rsymphony.
(Reading database ... 348392 files and directories currently installed.)
Preparing to unpack .../r-cran-rsymphony_0.1-17-1_amd64.deb ...
Unpacking r-cran-rsymphony (0.1-17-1) ...
Setting up r-cran-rsymphony (0.1-17-1) ...
[Sun|11:40:26][tir on atlas2:~]->
Related
I can not install mariadb-server. I run the following command:
sudo apt install mariadb-server mariadb-client -y
The following message appears:
Building dependency tree... Done
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.
mariadb-client-core-10.5 : Depends: libreadline5 (>= 5.2) but it is not installable
E: Unable to correct problems, you have held broken packages.
How can I fix these dependecies?
Thanks in advance!!!
=========================================
sudo apt install mariadb-client-core-10.5 -y
Reading package lists... Done
Building dependency tree... Done
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.
mariadb-client-core-10.5 : Depends: libreadline5 (>= 5.2) but it is not installable
E: Unable to correct problems, you have held broken packages.
I have tried with aptitude:
** sudo aptitude install mariadb-server **
The following NEW packages will be installed:
gawk{a} libsigsegv2{a} mariadb-server{b}
0 packages upgraded, 3 newly installed, 0 to remove and 19 not upgraded.
Need to get 434 kB of archives. After unpacking 1.772 kB will be used.
The following packages have unmet dependencies:
mariadb-server : Depends: mariadb-server-10.5 (>= 1:10.5.15+maria~focal) but it is not installable
The following actions will resolve these dependencies:
Keep the following packages at their current version:
1) mariadb-server [Not Installed]
Accept this solution? [Y/n/q/?] Y
The following NEW packages will be installed:
gawk{a} libsigsegv2{a}
0 packages upgraded, 2 newly installed, 0 to remove and 19 not upgraded.
Need to get 430 kB of archives. After unpacking 1.761 kB will be used.
Do you want to continue? [Y/n/?] Y
Get: 1 http://es.archive.ubuntu.com/ubuntu impish/main amd64 libsigsegv2 amd64 2.13-1ubuntu2 [14,6 kB]
Get: 2 http://es.archive.ubuntu.com/ubuntu impish/main amd64 gawk amd64 1:5.1.0-1build1 [416 kB]
Fetched 430 kB in 1s (718 kB/s)
Selecting previously unselected package libsigsegv2:amd64.
(Reading database ... 209196 files and directories currently installed.)
Preparing to unpack .../libsigsegv2_2.13-1ubuntu2_amd64.deb ...
Unpacking libsigsegv2:amd64 (2.13-1ubuntu2) ...
Setting up libsigsegv2:amd64 (2.13-1ubuntu2) ...
Selecting previously unselected package gawk.
(Reading database ... 209203 files and directories currently installed.)
Preparing to unpack .../gawk_1%3a5.1.0-1build1_amd64.deb ...
Unpacking gawk (1:5.1.0-1build1) ...
Setting up gawk (1:5.1.0-1build1) ...
Processing triggers for man-db (2.9.4-2) ...
Processing triggers for libc-bin (2.34-0ubuntu3.2) ...
I have installed the client with aptitude:
** sudo aptitude install mariadb-client **
The following NEW packages will be installed:
mariadb-client{b}
0 packages upgraded, 1 newly installed, 0 to remove and 19 not upgraded.
Need to get 3.096 B of archives. After unpacking 10,2 kB will be used.
The following packages have unmet dependencies:
mariadb-client : Depends: mariadb-client-10.5 (>= 1:10.5.15+maria~focal) but it is not installable
The following actions will resolve these dependencies:
Keep the following packages at their current version:
1) mariadb-client [Not Installed]
Accept this solution? [Y/n/q/?]
No packages will be installed, upgraded, or removed.
0 packages upgraded, 0 newly installed, 0 to remove and 19 not upgraded.
Need to get 0 B of archives. After unpacking 0 B will be used.
The client still does not connect....
Command 'mysql' not found, but can be installed with:
sudo apt install mysql-client-core-8.0 # version 8.0.28-0ubuntu0.21.10.3, or
sudo apt install mariadb-client-core-10.5 # version 1:10.5.15-0ubuntu0.21.10.1
juanma#juanma-HP-Laptop-17-ca1xxx:~$ mariadb
Command 'mariadb' not found, but can be installed with:
sudo apt install mariadb-client-core-10.5
juanma#juanma-HP-Laptop-17-ca1xxx:~$ sudo apt install mariadb-client-core-10.5 -y
Reading package lists... Done
Building dependency tree... Done
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.
mariadb-client-core-10.5 : Depends: libreadline5 (>= 5.2) but it is not installable
E: Unable to correct problems, you have held broken packages.
Thanks
============================================================
In the end I have done it with Docker and with a script and it has worked perfectly. Thank you all:
#!/bin/bash
docker run --name mariadbtest -e MYSQL_ROOT_PASSWORD=mypass -p 3306:3306 -d docker.io/library/mariadb:10.3
sudo apt install mysql-client-core-8.0
mysql -h 172.17.0.2 -u root -p
In the end I have done it with Docker and with a script and it has worked perfectly. Thank you all:
#!/bin/bash
docker run --name mariadbtest -e MYSQL_ROOT_PASSWORD=mypass -p 3306:3306 -d docker.io/library/mariadb:10.3
sudo apt install mysql-client-core-8.0
mysql -h 172.17.0.2 -u root -p
I have Fedora Workstation 34.
I have installed gdal-devel rpm on my system:
sudo dnf install gdal-devel
Now I am trying to install the R rgdal package.
But the installation fails with the following error message:
configure: API to be used as yet undetermined, searching ...
configure: error: API to be used not found
ERROR: configuration failed for package ‘rgdal’
* removing ‘/home/raffaele/R/x86_64-redhat-linux-gnu-library/4.0/rgdal’
The downloaded source packages are in
‘/tmp/RtmpZRbq1a/downloaded_packages’
✔ Package 'rgdal' successfully installed.
Warning message:
In utils::install.packages("rgdal", repos = "https://cran.rstudio.com/") :
installation of package ‘rgdal’ had non-zero exit status
Please note that in the above the
Package 'rgdal' successfully installed.
is wrong.
In particular it looks like it can't find an API.
How can I fix this problem and install the rgdal R package?
The above instructions are for Debian/Ubuntu or similar. Dependencies in Linux need to be installed separately as indicated in the CRAN for rgdal. On Fedora use
sudo dnf install gdal-devel proj-devel
Not that proj-devel is necessary to prevent the error "configure: error: API to be used not found". After which in R you can use install.packages("rgdal"). Using the package manager is also a good solution.
Based on the instructions by dncgst, I would suggest first installing the packages libgdal-dev and libproj-dev:
sudo apt-get install gdal-bin proj-bin libgdal-dev libproj-dev
I discovered you can install the binaries directly from the package manager
sudo dnf install R-rgdal
Recently I had to update R from 3.4.4 to 3.5 for installing bioconductor packages. For doing that I followed the steps on this link.
But now I have the problem that r studio do not work for the problem:
R shared library (/usr/local/lib/R/lib/libR.so) not found. If this is
a custom build of R, was it built with the --enable-R-shlib option?
For that reason I tried to reinstall R 3.4.4 with the command:
sudo apt-get install r-base
But it returns me this error:
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-recommended (= 3.5.1-2xenial) but it is not
going to be installed
E: Unable to correct problems, you have held broken packages.
Does anyone know how to remove completely R (3.5) and installing again the 3.4 version?
Thank you all.
Edit: R works on command line with the 3.5 version and I cannot install other packages like:
$ sudo apt-get install libgdal-dev
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:
libgdal-dev : Depends: libarmadillo-dev but it is not going to be installed
Depends: libdap-dev but it is not going to be installed
Depends: libgeotiff-dev but it is not going to be installed
Depends: libgif-dev but it is not going to be installed
Depends: libhdf4-alt-dev but it is not going to be installed
Depends: libhdf5-dev but it is not going to be installed
Depends: libjpeg-dev
Depends: libmysqlclient-dev but it is not going to be installed
Depends: libnetcdf-dev but it is not going to be installed
Depends: libpoppler-private-dev but it is not going to be installed
Depends: libpq-dev but it is not going to be installed
Depends: libtiff-dev
Depends: libxml2-dev but it is not going to be installed
E: Unable to correct problems, you have held broken packages.
When I install a fcitx related package an error show that qtbase-abi-5-5-1 is needed but not installed.
wsx#wsx:~/Downloads$ sudo apt install ./fcitx-frontend-qt5-rstudio_1.0.5-1ubuntu1~qt542_amd64.deb ./libfcitx-qt5-1-rstudio_1.0.5-1ubuntu1~qt542_amd64.deb
Reading package lists... Done
Building dependency tree
Reading state information... Done
Note, selecting 'fcitx-frontend-qt5-rstudio' instead of './fcitx-frontend-qt5-rstudio_1.0.5-1ubuntu1~qt542_amd64.deb'
Note, selecting 'libfcitx-qt5-1-rstudio' instead of './libfcitx-qt5-1-rstudio_1.0.5-1ubuntu1~qt542_amd64.deb'
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:
fcitx-frontend-qt5-rstudio : Depends: qtbase-abi-5-5-1 but it is not installable
E: Unable to correct problems, you have held broken packages.
I tried using command sodu apt install qtbase-abi-5 to find the package but failed. I then download the .deb package from https://ubuntu.pkgs.org/16.04/ubuntu-updates-main-amd64/libqt5core5a_5.5.1+dfsg-16ubuntu7.5_amd64.deb.html but it was not work, the page show that this .deb package provide the qtbase-abi-5 package. Interestingly, I can find few information about this error by google. Some info from Ask ubuntu forum say that it seems the qtbase-abi-5 is not included in libqt5core5a.
I don't know how to fix it. Can you give me some suggestion or some link which do can download qtbase-abi-5 ?
Thanks #GAD3R for your answer, I am sorry that it fails.
wsx#wsx:~$ sudo apt-cache search qtbase-abi
libqt5core5a - Qt 5 core module
wsx#wsx:~$ sudo apt install libqt5core5a
Reading package lists... Done
Building dependency tree
Reading state information... Done
libqt5core5a is already the newest version (5.9.1+dfsg-10ubuntu1).
0 upgraded, 0 newly installed, 0 to remove and 19 not upgraded.
wsx#wsx:~$ sudo apt install ./Downloads/fcitx-frontend-qt5-rstudio_1.0.5-1ubuntu1~qt542_amd64.deb ./Downloads/libfcitx-qt5-1-rstudio_1.0.5-1ubuntu1~qt542_amd64.deb
Reading package lists... Done
Building dependency tree
Reading state information... Done
Note, selecting 'fcitx-frontend-qt5-rstudio' instead of './Downloads/fcitx-frontend-qt5-rstudio_1.0.5-1ubuntu1~qt542_amd64.deb'
Note, selecting 'libfcitx-qt5-1-rstudio' instead of './Downloads/libfcitx-qt5-1-rstudio_1.0.5-1ubuntu1~qt542_amd64.deb'
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:
fcitx-frontend-qt5-rstudio : Depends: qtbase-abi-5-5-1 but it is not installable
E: Unable to correct problems, you have held broken packages.
Can anyone run following commands successfully?
$ wget http://ikuya.info/tmp/fcitx-qt5-rstudio-qt542.tar.gz
$ tar xf fcitx-qt5-rstudio-qt542.tar.gz
$ sudo apt install ./fcitx-frontend-qt5-rstudio_1.0.5-1ubuntu1~qt542_amd64.deb ./libfcitx-qt5-1-rstudio_1.0.5-1ubuntu1~qt542_amd64.deb
The package libqt5core5a provide qtbase-abi-5-5-1.
apt-cache search qtbase-abi
libqt5core5a - Qt 5 core module
To install the qtbase-abi-5-5-1 , run the following command :
sudo apt update
sudo apt upgrade
sudo apt dist-upgrade
sudo apt install libqt5core5a
I need to install rvest package for R version 3.1.2 (2014-10-31)
I get these errors:
checking whether the C++ compiler supports the long long type... no
*** stringi cannot be built. Upgrade your C++ compiler's settings
ERROR: configuration failed for package ‘stringi’
* removing ‘/usr/local/lib64/R/library/stringi’
ERROR: dependency ‘stringi’ is not available for package ‘stringr’
* removing ‘/usr/local/lib64/R/library/stringr’
ERROR: dependency ‘stringr’ is not available for package ‘httr’
* removing ‘/usr/local/lib64/R/library/httr’
ERROR: dependency ‘stringr’ is not available for package ‘selectr’
* removing ‘/usr/local/lib64/R/library/selectr’
ERROR: dependencies ‘httr’, ‘selectr’ are not available for package ‘rvest’
* removing ‘/usr/local/lib64/R/library/rvest’
Any ideas on how I could install R package rvest?
My system is Ubuntu 14.04 with R:3.2.3, and I had the same problem.
Then I checked err meg and tried to install library of libcurl4-openssl-dev and libxml2-dev:
sudo apt-get install libcurl4-openssl-dev
sudo apt-get install libxml2-dev
After installed, install.packages("rvest") was successful.
I needed dependencies such as Rcurl, XML, rvest, xml2, when I was trying to install tidyverse, DESeq2, RUVSeq in Rstudio Version 1.1.456 on a fresh installed Ubuntu 18.04. Anyway, there were a bunch of missing dependencies. This answer might fit better as a comment for Ubuntu 18.04, but I don't have that many reputation. So just trying to make a summary of solutions works for Ubuntu 18.04 here.
In the terminal, run:
sudo apt-get install libcurl4-openssl-dev libssl-dev
sudo apt-get install libxml2-dev
Then within Rstudio,
install.packages("xml2")
install.packages("rvest")
install.packages("tidyverse") # might need other dependencies installed in Rstudio
Got tidyverse!
In the terminal:
sudo apt-get install libmysqlclient-dev ## for RMySQL
Then within the Rstudio
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
biocLite('RUVSeq') ## might have messages as following
installation path not writeable, unable to update packages: cluster, foreign, MASS, Matrix, mgcv, nlme, survival
In the terminal:
sudo R ## give R the root permission
## in the R session within the terminal
pks <- c('cluster', 'foreign', 'MASS', 'Matrix', 'mgcv', 'nlme', 'survival')
install.packages(pks)
q()
That's my own experience. Hope this one has a good Generalizability.
I was able to build the stringi package as this:
install.packages('stringi', configure.args='--disable-cxx11')
My answer is definitely late to this question. Nevertheless, somebody may find it useful.
I run into the same problem so I run this command on the shell:
sudo apt-get upgrade pkg-config
It worked for me.