Problem with running install.packages()
peculiar97 opened this issue · comments
Hi,
After installing r2u, according to this, in a clean R session inside Ubuntu terminal, when trying to install any packages e.g. :
install.packages("BiocManager")
I see the following error:
Error: dbus: Call failed: Launch helper exited with unknown return code 1
I checked the /var/log/syslog and I found this error:
Traceback (most recent call last):
org.r_project.linux1[44262]: File "/usr/local/lib/R/site-library/bspm/service/bspm.py", line 150, in <module>
org.r_project.linux1[44262]: read_conf()
org.r_project.linux1[44262]: File "/usr/local/lib/R/site-library/bspm/service/bspm.py", line 16, in read_conf
org.r_project.linux1[44262]: conf = backend.discover()
org.r_project.linux1[44262]: File "/usr/local/lib/R/site-library/bspm/service/backend/apt.py", line 15, in discover
org.r_project.linux1[44262]: cache_update(partial(cache.update, aprogress), force=True)
org.r_project.linux1[44262]: File "/usr/local/lib/R/site-library/bspm/service/backend/_utils.py", line 33, in cache_update
org.r_project.linux1[44262]: method()
org.r_project.linux1[44262]: File "/usr/lib/python3/dist-packages/apt/cache.py", line 573, in update
org.r_project.linux1[44262]: raise FetchFailedException(e)
dbus-daemon[726]: [system] Activated service 'org.r_project.linux1' failed: Launch helper exited with unknown return code 1The R version is
R version 4.3.2 (2023-10-31) -- "Eye Holes"
The operating system:
Distributor ID: Ubuntu Description: Ubuntu 22.04.3 LTS Release: 22.04 Codename: jammy
Any help would be greatly appreciated!
Hi there, and thanks for trying r2u!
I can take a closer look later but this looks very much like a standard issue of not being able to dispatch to bspm ... because bspm was not installed as root. Check a few of our older issue tickets, check the bspm repo and its issues, and just do
sudo Rscript -e `bspm::dispable(); install.packages("bspm")`
after which bspm, as a key part, should be back 'at system level' and be able to talk to dpkg and apt via systemd.
Dear Dirk,
Thanks for your prompt answer.
For Installation of bspm I followed the instructions at bspm reop for ubuntu. and I run all the codes as the root.
Runnnig this code
sudo Rscript -e 'bspm::dispable(); install.packages("bspm")'
gave
Tracing function "install.packages" in package "utils"
Error: 'dispable' is not an exported object from 'namespace:bspm'
Execution halted
I should also add if I install the packages by apt e.g.
sudo apt install r-cran-ggplot2
everything is OK!
But I am not able to use install.packages.
That was my typo which gets the error. My apologies. Please try again with
sudo Rscript -e 'bspm::disable(); install.packages("bspm")'
(bspm has only two user-facing function enable() and disable(), I fat-fingered.)
That you can in fact install via apt proves my point: your setup is correct, you have the correct repo entries -- we just have to ensure the added cherry of bspm is installed just right so that it can elevate the R installation request to a system command. You are close.
I got surprised since there is no dispable() ;)
trying the corrected code
sudo Rscript -e 'bspm::disable(); install.packages("bspm")'
and then running
install.packages("BiocManager")
gave
Hit https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/ InRelease
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Error: Closer!! Any idea why launchpad times out?
(Also: formatting trick here. Use three backticks, followed a languages symbol so eg
```r
res <- lm(y ~ x, data=D)
```
will produce
res <- lm(y ~ x, data=D)But to prove the point over here things are peachy -- using Docker just to simulate an 'empty' system:
edd@rob:~$ docker run --rm -ti rocker/r2u Rscript -e 'install.packages("BiocManager")'
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Install system packages as root...
Reading package lists... Done
Building dependency tree... Don
Reading state information... Done
Reading package lists... Done
Building dependency tree...
Reading state information... Done
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Selecting previously unselected package r-cran-biocmanager.
(Reading database ... 18320 file
Preparing to unpack .../r-cran-biocmanager_1.30.22-1.ca2204.1_all.deb ...
Unpacking r-cran-bio
Setting up r-cran-biocmanager (1.30.22-1.ca2204.1) ...
edd@rob:~$ So far so good!
Runnig
sudo docker run --rm -ti rocker/r2u Rscript -e 'install.packages("BiocManager")'
Unable to find image 'rocker/r2u:latest' locally
latest: Pulling from rocker/r2u
e96e057aae67: Pull complete
a8390eea866c: Pull complete
145fd72d096e: Pull complete
Digest: sha256:ad84e9056a4b097c162124a62f5d3d15c86a8297d1e632810e2d591cd57ce05b
Status: Downloaded newer image for rocker/r2u:latest
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Install system packages as root...
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Get:1 https://r2u.stat.illinois.edu/ubuntu jammy/main all r-cran-biocmanager all 1.30.22-1.ca2204.1 [479 kB]
Fetched 479 kB in 0s (0 B/s)
Selecting previously unselected package r-cran-biocmanager.
(Reading database ... 18320 files and directories currently installed.)
Preparing to unpack .../r-cran-biocmanager_1.30.22-1.ca2204.1_all.deb ...
Unpacking r-cran-biocmanager (1.30.22-1.ca2204.1) ...
Setting up r-cran-biocmanager (1.30.22-1.ca2204.1) ...If on your 'real' system some apt repos give you errors you can always temporarily comment them out. These issues are really orthogonal to your use of bspm and we should get that issu squashed. The other one may be a tempoary glitch.
Inside the rstudio, still I get dbus error!
> install.packages("BiocManager")
Error in install.packages : dbus: Call failed: Launch helper exited with unknown return code 1
> install.packages("rmarkdown")
Error in install.packages : dbus: Call failed: Launch helper exited with unknown return code 1This is my R session info
> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices datasets utils methods base
loaded via a namespace (and not attached):
[1] compiler_4.3.2 tools_4.3.2 bspm_0.5.5 Maybe search the old issues, and/or search at the bspm repo. There was a reason for something, and as I recall also a workaround -- maybe again the 'did you install bspm as root' ?
At one point I thought it would not work at all but that is not true. All I can tell you is 'it works here'.
Quick 'proof' from my laptop after first uninstalling a package to be able to show an actual installation:
> install.packages("RcppExamples")
Install system packages...
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
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> Bspm is installed as root.
Interestingly, when I disable bspm
bspm::disable()
install.packages("BiocManager")it works as a charm and starts installing the desired package.
That could have been it. Maybe I have ~/.Rprofile set up in such a way that I do not enable bspm.
But then .... if it doesn't use bspm, it doesn't use r2u?
But it seems bspm is still running in background
bspm::disable()
install.packages("BiocManager")
Installing package into ‘/home/mah/R/x86_64-pc-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/BiocManager_1.30.22.tar.gz'
Content type 'application/x-gzip' length 582690 bytes (569 KB)
==================================================
downloaded 569 KB
Tracing function "install.packages" in package "utils"
Tracing function "install.packages" in package "utils"
* installing *source* package ‘BiocManager’ ...
** package ‘BiocManager’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Tracing function "install.packages" in package "utils"
Tracing function "install.packages" in package "utils"
** help
*** installing help indices
** building package indices
Tracing function "install.packages" in package "utils"
Tracing function "install.packages" in package "utils"
** installing vignettes
** testing if installed package can be loaded from temporary location
Tracing function "install.packages" in package "utils"
Tracing function "install.packages" in package "utils"
** testing if installed package can be loaded from final location
Tracing function "install.packages" in package "utils"
Tracing function "install.packages" in package "utils"
** testing if installed package keeps a record of temporary installation path
* DONE (BiocManager)
The downloaded source packages are in
‘/tmp/RtmpKqm1Tx/downloaded_packagesOk, only you are on your machine. Maybe you followed my advice and added bspm::enable() to /etc/R/Profile ? Then fresh R session will be using it, and you see the Tracing ... messages you quote.
bspm is good. You need if you want install.packages() to call apt.
As also stated, bspm must also be installed correctly (as root user) to be able to do that. That is about all I can repeat to you. Some of the rest you may have to debug locally.
Ok, only you are on your machine. Maybe you followed my advice and added bspm::enable() to /etc/R/Profile ? Then fresh R session will be using it, and you see the Tracing ... messages you quote.
bspm is good. You need if you want install.packages() to call apt.
As also stated, bspm must also be installed correctly (as root user) to be able to do that. That is about all I can repeat to you. Some of the rest you may have to debug locally.
But something seems wrong at your end. You have both install.packages() traced and local installation from source. But I am out of ideas about what may be different.
One idea: try running Rscript -e 'bspm::shadowed_packages()'. It may reveal multiple bspm installations. Or maybe the one you made as root went into root's own local installation path.
Tried running shawdow_packages, but nothing came out
sudo Rscript -e 'bspm::shadowed_packages()'
[1] Package LibPath Version Shadow.LibPath Shadow.Version
[6] Shadow.Newer
<0 rows> (or 0-length row.names)Evenmore, I tried to remove all the possible installation of "bspm" using
library(utils)
# Remove the package
remove.packages("bspm")
# If the package is installed in multiple libraries, specify the library path
# Get the library path
path.lib <- .libPaths()
# Remove the package from a specific library
remove.packages("bspm", lib = path.lib[1]) # change the index based on your library pathand reinstalled using the source version
sudo R CMD INSTALL bspm_0.5.5.tar.gz
* installing to library ‘/usr/local/lib/R/site-library’
* installing *source* package ‘bspm’ ...
** package ‘bspm’ successfully unpacked and MD5 sums checked
** using staged installation
* installing /usr/share/dbus-1/system-services/org.r_project.linux1.service
* installing /etc/dbus-1/system.d/org.r_project.linux1.conf
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (bspm)Still I see the dbus error after enabling the bspm.
Anyway, Dirk thank you very much for the brainstorming and your feedback!
Can we recap completely what works and does not work on your machine?
- You can install via
apti.e.sudo apt install r-cran-ggplot2works (and preferably the logs show it being installed from r2u not plain ubuntu (per the download path) and the version number is 3.4.4-1.ca2204.1 - You can or cannot install via
bspmand thenaptoutside of RStudio? DoesRscript -e 'install.packages("ggplot2")'fetch that same binary? (You may have to uninstall, which may be tricky because of depends so maybe play with a 'leaf' package with no dependencies likefortunes). - You cannot install from RStudio
One issue could be that you lack the Python packages bspm needs: python3-apt, python3-dbus, python3-gi -- Do you have those?
For your record, I prepared real-time answers for the questions
- You can install via
apti.e.sudo apt install r-cran-ggplot2works (and preferably the logs show it being installed from r2u not plain ubuntu (per the download path) and the version number is 3.4.4-1.ca2204.1
sudo apt install r-cran-ggplot2
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
r-cran-ggplot2 is already the newest version (3.4.4-1.ca2204.1).
0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
- You can or cannot install via bspm and then apt outside of RStudio? Does Rscript -e 'install.packages("ggplot2")' fetch that same binary? (You may have to uninstall, which may be tricky because of depends so maybe play with a 'leaf' package with no dependencies like fortunes).
sudo Rscript -e 'install.packages("ggplot2")'
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Error:
Execution halted3.You cannot install from RStudio
install.packages("ggplot2")
Error in install.packages : dbus: Call failed: Launch helper exited with unknown return code 1One issue could be that you lack the Python packages bspm needs: python3-apt, python3-dbus, python3-gi -- Do you have those?
dpkg -s python3-apt python3-dbus python3-gi
Package: python3-apt
Status: install ok installed
Priority: important
Section: python
Installed-Size: 705
Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Architecture: amd64
Multi-Arch: allowed
Source: python-apt
Version: 2.4.0ubuntu2
Replaces: python-apt (<< 0.7.98+nmu1)
Provides: python3.10-apt
Depends: python3 (<< 3.11), python3 (>= 3.10~), python3:any, libapt-pkg6.0 (>= 1.9.11~), libc6 (>= 2.33), libgcc-s1 (>= 3.3.1), libstdc++6 (>= 11), python-apt-common, distro-info-data
Recommends: lsb-release, iso-codes
Suggests: python3-apt-dbg, python-apt-doc, apt
Breaks: apt-xapian-index (<< 0.51~), kthresher (<= 1.4.0-1), python-apt (<< 0.7.98+nmu1)
Description: Python 3 interface to libapt-pkg
The apt_pkg Python 3 interface will provide full access to the internal
libapt-pkg structures allowing Python 3 programs to easily perform a
variety of functions, such as:
.
- Access to the APT configuration system
- Access to the APT package information database
- Parsing of Debian package control files, and other files with a
similar structure
.
The included 'aptsources' Python interface provides an abstraction of
the sources.list configuration on the repository and the distro level.
Original-Maintainer: APT Development Team <deity@lists.debian.org>
Package: python3-dbus
Status: install ok installed
Priority: important
Section: python
Installed-Size: 417
Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Architecture: amd64
Source: dbus-python
Version: 1.2.18-3build1
Provides: python3.10-dbus
Depends: python3 (<< 3.11), python3 (>= 3.10~), python3:any, libc6 (>= 2.4), libdbus-1-3 (>= 1.9.14), libglib2.0-0 (>= 2.40)
Recommends: python3-gi
Suggests: python-dbus-doc
Description: simple interprocess messaging system (Python 3 interface)
D-Bus is a message bus, used for sending messages between applications.
Conceptually, it fits somewhere in between raw sockets and CORBA in
terms of complexity.
.
This package provides a Python 3 interface to D-Bus.
.
See the dbus description for more information about D-Bus in general.
Original-Maintainer: Utopia Maintenance Team <pkg-utopia-maintainers@lists.alioth.debian.org>
Homepage: https://www.freedesktop.org/wiki/Software/DBusBindings#Python
Package: python3-gi
Status: install ok installed
Priority: important
Section: python
Installed-Size: 747
Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Architecture: amd64
Multi-Arch: allowed
Source: pygobject
Version: 3.42.1-0ubuntu1
Depends: gir1.2-glib-2.0 (>= 1.48.0), python3 (<< 3.11), python3 (>= 3.10~), python3:any, libc6 (>= 2.14), libffi8 (>= 3.4), libgirepository-1.0-1 (>= 1.62.0-4~), libgirepository-1.0-1-with-libffi8 (>= 1.62.0-4~), libglib2.0-0 (>= 2.56.0)
Description: Python 3 bindings for gobject-introspection libraries
GObject is an abstraction layer that allows programming with an object
paradigm that is compatible with many languages. It is a part of Glib,
the core library used to build GTK+ and GNOME.
.
This package contains the Python 3 binding generator for libraries that
support gobject-introspection, i. e. which ship a gir1.2-<name>-<version>
package. With these packages, the libraries can be used from Python 3.
Homepage: https://wiki.gnome.org/Projects/PyGObject
Original-Maintainer: Debian GNOME Maintainers <pkg-gnome-maintainers@lists.alioth.debian.org>-
is good
-
fails for the reason I told you about yesterday and which you can fix but haven't, you seem to have apt entries pointing to repositories which no longer supply a PACKAGES file. That is not a bspm issue.
-
also good.
I am out of ideas now, sorry. Paging @Enchufa2 who may have clearer eyes and may spot something I missed.
2. fails for the reason I told you about yesterday and which you can fix but haven't, you seem to have apt entries pointing to repositories which no longer supply a PACKAGES file. That is not a bspm issue.
Sorry, I did not get that. Do you suggest this workaround?
sudo Rscript -e 'bspm::disable(); install.packages("ggplot2")'Quoting from your second post that showed that:
sudo Rscript -e 'install.packages("ggplot2")'
Hit http://pl.archive.ubuntu.com/ubuntu jammy InRelease
Hit http://security.ubuntu.com/ubuntu jammy-security InRelease
Hit http://pl.archive.ubuntu.com/ubuntu jammy-updates InRelease
Hit http://pl.archive.ubuntu.com/ubuntu jammy-backports InRelease
Hit https://download.docker.com/linux/ubuntu jammy InRelease
Hit https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/ InRelease
Hit https://dl.google.com/linux/chrome/deb stable InRelease
Hit https://ppa.launchpadcontent.net/c2d4u.team/c2d4u4.0+/ubuntu jammy InRelease
Hit https://ppa.launchpadcontent.net/eugenesan/ppa/ubuntu jammy InRelease
Hit https://download.sublimetext.com apt/stable/ InRelease
Ign https://r2u.stat.illinois.edu/ubuntu jammy InRelease
Hit https://ppa.launchpadcontent.net/marutter/rrutter4.0/ubuntu jammy InRelease
Ign https://ppa.launchpadcontent.net/nomacs/stable/ubuntu jammy InRelease
Hit https://r2u.stat.illinois.edu/ubuntu jammy Release
Ign https://ppa.launchpadcontent.net/oguzhaninan/stacer/ubuntu jammy InRelease
Hit https://packages.microsoft.com/repos/edge stable InRelease
Hit https://ppa.launchpadcontent.net/slgobinath/safeeyes/ubuntu jammy InRelease
Hit https://ppa.launchpadcontent.net/ubuntuhandbook1/audacity/ubuntu jammy InRelease
Err https://ppa.launchpadcontent.net/nomacs/stable/ubuntu jammy Release
404 Not Found [IP: 185.125.190.80 443]
Err https://ppa.launchpadcontent.net/oguzhaninan/stacer/ubuntu jammy Release
404 Not Found [IP: 185.125.190.80 443]
Fetched 0 B in 0s (0 B/s)
Error:
Execution halted
IP address 185.125.190.80 is launchpadcontent.net. I recommend you comment out the entries one by one to identify the ones leading to the 404 which in turn leads to 'Error: Execution halted'. We want to avoid such errors so that we can refresh apt indices and use it. It looks like you have one or two bad ones among multiple candidate repos.
I'm out of ideas too. Could you @peculiar97 please share the output of
Rscript -e '.libPaths()'and
sudo Rscript -e '.libPaths()'?
@eddelbuettel is right! the culprits were these troublesome repos that led to "404 Not Found" error. Commenting out these repos solved the problem!
Thanks @eddelbuettel & @Enchufa2 for making such a responsive community around r2u & bspm.
Yay! Annoying that such a little hickup can block things, isn't it? The error message is not the greatest but it does say 'error' so we are being warned ...
Glad you are up and running with r2u. I am continuing to get a lot of use out of it, and having bspm makes it so much nicer too.