$ sudo R CMD INSTALL bspm_[version].tar.gz
+$ sudo R CMD INSTALL bspm_[version].tar.gz
Further configuration options:
- If you plan to run it only as root (e.g., in a docker container), then you don’t need the D-Bus service, so you can disable its installation by adding
--configure-args="--without-dbus-service".
@@ -142,55 +142,55 @@
To enable it by default, put the following into the Rprofile.site:
-> bspm::enable() # wrap it in suppressMessages() to avoid the initial message
> bspm::enable() # wrap it in suppressMessages() to avoid the initial message
Then, run install.packages as usual, and available system packages will be automatically installed.
Fedora
There are thousands of binary packages available via the iucar/cran Copr repo. The bspm package is available as R-CoprManager, and enabled by default:
-
$ sudo dnf install 'dnf-command(copr)'
-$ sudo dnf copr enable iucar/cran
-$ sudo dnf install R-CoprManager
+
$ sudo dnf install 'dnf-command(copr)'
+$ sudo dnf copr enable iucar/cran
+$ sudo dnf install R-CoprManager
Ubuntu
There are thousands of binary packages available via the c2d4u.team/c2d4u4.0+ PPA repo:
-
$ sudo add-apt-repository ppa:marutter/rrutter4.0 # R v4.0 and higher
-$ sudo add-apt-repository ppa:c2d4u.team/c2d4u4.0+ # R packages
-$ sudo apt-get update && sudo apt-get install python3-{dbus,gi,apt}
+
$ sudo add-apt-repository ppa:marutter/rrutter4.0 # R v4.0 and higher
+$ sudo add-apt-repository ppa:c2d4u.team/c2d4u4.0+ # R packages
+$ sudo apt-get update && sudo apt-get install python3-{dbus,gi,apt}
Then, install bspm as a system package from CRAN:
-
$ sudo Rscript -e 'install.packages("bspm", repos="https://cran.r-project.org")'
+
$ sudo Rscript -e 'install.packages("bspm", repos="https://cran.r-project.org")'
Then, to enable it system-wide (alternatively, use your .Rprofile):
-
$ echo "bspm::enable()" | sudo tee -a /etc/R/Rprofile.site
+
$ echo "bspm::enable()" | sudo tee -a /etc/R/Rprofile.site
openSUSE
There are thousands of binary packages available via the autoCRAN OBS repo:
-
$ sudo zypper ar -r https://download.opensuse.org/repositories/devel:/languages:/R:/patched/openSUSE_Tumbleweed/devel:languages:R:patched.repo
-$ sudo zypper ar -r https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
-$ sudo zypper install R-patched python3-dnf python38-dbus-python python3-gobject
-$ sudo ln -s /etc/zypp/repos.d /etc/yum.repos.d
+
$ sudo zypper ar -r https://download.opensuse.org/repositories/devel:/languages:/R:/patched/openSUSE_Tumbleweed/devel:languages:R:patched.repo
+$ sudo zypper ar -r https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
+$ sudo zypper install R-patched python3-dnf python38-dbus-python python3-gobject
+$ sudo ln -s /etc/zypp/repos.d /etc/yum.repos.d
Then, install bspm as a system package from CRAN:
-
$ sudo Rscript -e 'install.packages("bspm", repos="https://cran.r-project.org")'
+
$ sudo Rscript -e 'install.packages("bspm", repos="https://cran.r-project.org")'
Then, to enable it system-wide (alternatively, use your .Rprofile):
-
$ echo "bspm::enable()" | sudo tee -a /usr/lib64/R/etc/Rprofile.site
+
$ echo "bspm::enable()" | sudo tee -a /usr/lib64/R/etc/Rprofile.site
Sometimes, a restart is required so that the new systemd service is recognized.
Arch
There are a number of binary CRAN packages available via the ArchRPkgs repo as well as Bioconductor packages via the BioArchLinux repo:
-
$ echo -e "\n[desolve]\nServer = https://desolve.ru/archrepo/\$arch" \
- "\n[bioarchlinux]\nServer = https://repo.bioarchlinux.org/\$arch" \
- | sudo tee -a /etc/pacman.conf
-$ sudo pacman -Sy && sudo pacman -S r pyalpm python-{dbus,gobject}
+
$ echo -e "\n[desolve]\nServer = https://desolve.ru/archrepo/\$arch" \
+ "\n[bioarchlinux]\nServer = https://repo.bioarchlinux.org/\$arch" \
+ | sudo tee -a /etc/pacman.conf
+$ sudo pacman -Sy && sudo pacman -S r pyalpm python-{dbus,gobject}
Then, install bspm as a system package from CRAN:
-
$ sudo Rscript -e 'install.packages("bspm", repos="https://cran.r-project.org")'
+
$ sudo Rscript -e 'install.packages("bspm", repos="https://cran.r-project.org")'
Then, to enable it system-wide (alternatively, use your .Rprofile):
-
$ echo "bspm::enable()" | sudo tee -a /usr/lib64/R/etc/Rprofile.site
+
$ echo "bspm::enable()" | sudo tee -a /usr/lib64/R/etc/Rprofile.site
Symptom: you tried to install a package and you got this message.
-
> install.packages(<some_package>)
-Error in install.packages : cannot connect to the system package manager
+
> install.packages(<some_package>)
+Error in install.packages : cannot connect to the system package manager
This usually happens when bspm was installed in the user library or, as a system package, it is not properly configured for some reason. The solution is:
- First and foremost, uninstall any copy of
bspm in your user library.
- Reinstall with admin privileges, e.g.:
-
$ sudo Rscript --vanilla -e 'install.packages("bspm", repos="https://cran.r-project.org")'
+
$ sudo Rscript --vanilla -e 'install.packages("bspm", repos="https://cran.r-project.org")'
diff --git a/docs/news/index.html b/docs/news/index.html
index e4caf7f..f2135c5 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -1,5 +1,5 @@
-Changelog • bspmChangelog • bspm
@@ -10,7 +10,7 @@