I am experiencing similar problems to user Aurele in this forum: https://community.rstudio.com/t/cannot-install-rstudio-desktop-on-my-linux-machine-permission-problem/7264. My error message:
~/Downloads$ sudo dpkg -i rstudio-xenial-1.1.463-amd64.deb
(Reading database ... 239410 files and directories currently installed.)
Preparing to unpack rstudio-xenial-1.1.463-amd64.deb ...
Unpacking rstudio (1.1.463) ...
dpkg: error processing archive rstudio-xenial-1.1.463-amd64.deb (--install):
unable to open '/usr/lib/rstudio/www/rstudio/0E471A7ED100AFCB82EF81C71F4D11F4.cache.js.dpkg-new': Operation not permitted
Processing triggers for shared-mime-info (1.9-2) ...
Processing triggers for hicolor-icon-theme (0.17-2) ...
Processing triggers for gnome-menus (3.13.3-11ubuntu1.1) ...
Processing triggers for desktop-file-utils (0.23-1ubuntu3.18.04.1) ...
Processing triggers for mime-support (3.60ubuntu1) ...
Errors were encountered while processing:
rstudio-xenial-1.1.463-amd64.deb
I tried installing other older versions of rstudio (rstudio-1.0.153-amd64.deb, rstudio-0.99.903-i386.deb)
~/Downloads$ sudo gdebi rstudio-1.0.153-amd64.deb
Reading package lists... Done
Building dependency tree
Reading state information... Done
Reading state information... Done
RStudio
RStudio is a set of integrated tools designed to help you be more productive with R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, and workspace management.
Do you want to install the software package? [y/N]:y
(Reading database ... 239410 files and directories currently installed.)
Preparing to unpack rstudio-1.0.153-amd64.deb ...
Unpacking rstudio (1.0.153) ...
dpkg: error processing archive rstudio-1.0.153-amd64.deb (--install):
unable to open '/usr/lib/rstudio/bin/r-ldpath.dpkg-new': Operation not permitted
Processing triggers for shared-mime-info (1.9-2) ...
Processing triggers for hicolor-icon-theme (0.17-2) ...
Processing triggers for gnome-menus (3.13.3-11ubuntu1.1) ...
Processing triggers for desktop-file-utils (0.23-1ubuntu3.18.04.1) ...
Processing triggers for mime-support (3.60ubuntu1) ...
Errors were encountered while processing:
rstudio-1.0.153-amd64.deb
~/Downloads$ sudo dpkg -i rstudio-0.99.903-i386.deb
Selecting previously unselected package rstudio:i386.
(Reading database ... 239410 files and directories currently installed.)
Preparing to unpack rstudio-0.99.903-i386.deb ...
Unpacking rstudio:i386 (0.99.903) ...
dpkg: error processing archive rstudio-0.99.903-i386.deb (--install):
unable to create new file '/var/lib/dpkg/info/rstudio.list-new': Operation not permitted
Processing triggers for shared-mime-info (1.9-2) ...
Processing triggers for gnome-menus (3.13.3-11ubuntu1.1) ...
Processing triggers for desktop-file-utils (0.23-1ubuntu3.18.04.1) ...
Processing triggers for mime-support (3.60ubuntu1) ...
Processing triggers for hicolor-icon-theme (0.17-2) ...
Errors were encountered while processing:
rstudio-0.99.903-i386.deb
As you can see, each error is in a different folder. I have tried sudo apt-get autoremove and sudo apt-get autoremove rstudio, and even forced the removal of a conflicting package (rstudio:i386) and later reinstall, without success. rstudio appears as not having been installed at all.
sudo apt-get autoremove rstudio
Reading package lists... Done
Building dependency tree
Reading state information... Done
Package 'rstudio' is not installed, so not removed
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Aurele's topic was not solved in the end. Would anyone have an idea of what is happening? Thanks!
Related
first of all please bear with me as my English is still improving. So, yesterday i was trying to install DaVinci Resolve 16 on my newly installed Pop Os using an AMD RX 570 but i came across a problem related to openCL. So, i did some research and i found this command:
sudo apt install mesa-opencl-icd
Once, I did that and started DaVinci it crashed on startup with error "DaVinci Resolve quit unexpectedly "
Again I came to google for help and i found that i need to install amdgpu-pro drivers to get my gpu openCL support and i followed these instructions:
* you need to edit the "amdgpu-pro-install"-file.
* Change the string "ubuntu" to debian or debianlinux or so.
* The string "ubuntu" you can find in function os_release()
* With Linux Mint i need to change it to "linuxmint" and installation will be fine
so I followed the instructions and now it is giving me these errors:
Errors were encountered while processing:
amdgpu-dkms
amdgpu
amdgpu-pro-rocr-opencl
amdgpu-pro
amdgpu-pro-lib32
E: Sub-process /usr/bin/dpkg returned an error code (1)
and now i can't install or uninstall any pkg or deb file
-> sudo apt-get autoremove
Reading package lists... Done
Building dependency tree
Reading state information... Done
0 to upgrade, 0 to newly install, 0 to remove and 0 not to upgrade.
5 not fully installed or removed.
After this operation, 0 B of additional disk space will be used.
Setting up amdgpu-dkms (1:5.6.20.906316-1188099) ...
Removing old amdgpu-5.6.20.906316-1188099 DKMS files...
------------------------------
Deleting module version: 5.6.20.906316-1188099
completely from the DKMS tree.
------------------------------
Done.
Loading new amdgpu-5.6.20.906316-1188099 DKMS files...
Building for 5.8.0-7630-generic
Building for architecture amd64
Building initial module for 5.8.0-7630-generic
ERROR (dkms apport): kernel package linux-headers-5.8.0-7630-generic is not supported
Error! Bad return status for module build on kernel: 5.8.0-7630-generic (amd64)
Consult /var/lib/dkms/amdgpu/5.6.20.906316-1188099/build/make.log for more information.
dpkg: error processing package amdgpu-dkms (--configure):
installed amdgpu-dkms package post-installation script subprocess returned error exit status 10
dpkg: dependency problems prevent configuration of amdgpu:
amdgpu depends on amdgpu-dkms (= 1:5.6.20.906316-1188099); however:
Package amdgpu-dkms is not configured yet.
dpkg: error processing package amdgpu (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of amdgpu-pro-rocr-opencl:
amdgpu-pro-rocr-opencl depends on amdgpu-dkms (= 1:5.6.20.906316-1188099); however:
Package amdgpu-dkms is not configured yet.
dpkg: error processing package amdgpu-pro-rocr-opencl (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of amdgpu-pro:
amdgpu-pro depends on amdgpu (= 20.45-1188099); however:
Package amdgpu is not configured yet.
dpkg: error processing package amdgpu-pro (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of amdgpu-pro-lib32:
amdgpu-pro-lib32 depends on amdgpu (= 20.45-1188099) | amdgpu-hwe (= 20.45-1188099No apport report written because the error message indicates it's a follow-up error from a previous failure.
No apport report written because the error message indicates it's a follow-up error from a previous failure.
No apport report written because MaxReports has already been reached
No apport report written because MaxReports has already been reached
); however:
Package amdgpu is not configured yet.
Package amdgpu-hwe is not installed.
amdgpu-pro-lib32 depends on amdgpu-pro (= 20.45-1188099) | amdgpu-pro-hwe (= 20.45-1188099); however:
Package amdgpu-pro is not configured yet.
Package amdgpu-pro-hwe is not installed.
dpkg: error processing package amdgpu-pro-lib32 (--configure):
dependency problems - leaving unconfigured
Errors were encountered while processing:
amdgpu-dkms
amdgpu
amdgpu-pro-rocr-opencl
amdgpu-pro
amdgpu-pro-lib32
E: Sub-process /usr/bin/dpkg returned an error code (1)
You should be able to uninstall amdgpu(-pro) drivers by running /usr/bin/amdgpu(-pro)-uninstall script.
Did you try to install the amdgpu drivers with the different kernel as advised here?
So here is the error i am getting from the console. I understand that hydromad package is not on cran but I have added it as secondary repos in packages(Tools options in R studio) and in .R profile file. Still I am getting this error
****Preparing to deploy application...DONE
Uploading bundle for application: 2120925...DONE
Deploying bundle: 3058356 for application: 2120925 ...
Waiting for task: 720810692
building: Parsing manifest
building: Building image: 3408182
building: Installing system dependencies
building: Fetching packages
error: Building package: hydromad
########################## Begin Task Log ################################
[2020-04-24T06:51:09.225825780+0000] Execute script: packages/build/sys.sh
+ set -e
+ apt-get update -qq
+ apt-get install -y libapparmor-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
libapparmor-dev
0 upgraded, 1 newly installed, 0 to remove and 114 not upgraded.
Need to get 67.8 kB of archives.
After this operation, 229 kB of additional disk space will be used.
Get:1 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libapparmor-dev amd64 2.10.95-0ubuntu2.11 [67.8 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 67.8 kB in 0s (0 B/s)
Selecting previously unselected package libapparmor-dev:amd64.
(Reading database ... 119718 files and directories currently installed.)
Preparing to unpack .../libapparmor-dev_2.10.95-0ubuntu2.11_amd64.deb ...
Unpacking libapparmor-dev:amd64 (2.10.95-0ubuntu2.11) ...
Processing triggers for man-db (2.7.5-1) ...
Setting up libapparmor-dev:amd64 (2.10.95-0ubuntu2.11) ...
########################### End Task Log #################################
Error: Unhandled Exception: Child Task 720810693 failed: Error building image: Error fetching hydromad (0.9-26) source. <CRANPackageSource repo='http://cran.rstudio.org'> unable to satisfy package: hydromad (0.9-26)
In addition: Warning message:
In FUN(X[[i]], ...) :
Package 'hydromad 0.9-26' was installed from sources; Packrat will assume this package is available from a CRAN-like repository during future restores
Execution halted****
Can anyone help me resolve this error? Will be grateful
Welcome to StackOverflow! Your question is quite specific, so I would recommend to use a more specialized resource. The good news is that package hydromad has its own forum
I'm trying to install jupyter_nbextensions_configurator on windows10 for python3.7 using conda.
An error occurred while installing the package.
I have already tried to reinstall anaconda,but the problem still occurs.
ERROR conda.core.link:_execute(700): An error occurred while installing package 'conda-forge::jupyter_nbextensions_configurator-0.4.1-py37_0'.
Rolling back transaction: done
LinkError: post-link script failed for package conda-forge::jupyter_nbextensions_configurator-0.4.1-py37_0
location of failed script: C:\Users\Cesare\Anaconda3\Scripts\.jupyter_nbextensions_configurator-post-link.bat
I want to know how to install it successfully.
I too was facing the same problem. Here's the output when I tried cloning the base environment [Running as Administrator]:
(base) PS C:\WINDOWS\system32> conda create --name django --clone base
WARNING: A conda environment already exists at 'C:\Users\Tanishk\anaconda3\envs\django'
Remove existing environment (y/[n])? y
Source: C:\Users\Tanishk\anaconda3
Destination: C:\Users\Tanishk\anaconda3\envs\django
The following packages cannot be cloned out of the root environment:
- conda-forge/win-64::conda-4.9.2-py38haa244fe_0
- defaults/win-64::conda-build-3.20.5-py38_1
- defaults/win-64::conda-env-2.6.0-1
Packages: 305
Files: 2077
Preparing transaction: done
Executing transaction: done
ERROR conda.core.link:_execute(698): An error occurred while installing package 'defaults::openssl-1.1.1h-he774522_0'.
Rolling back transaction: done
CondaError: Cannot link a source that does not exist. C:\Users\Tanishk\anaconda3\pkgs\openssl-1.1.1h-he774522_0\Library\bin\openssl.exe
Running `conda clean --packages` may resolve your problem.
()
You will notice the package giving me problem is different than yours, but the ERROR remains the same (ERROR conda.core.link).
Here's how I solved it:
Google the package mentioned in the ERROR. In my case it was openssl-1.1.1h-he774522_0
Open the result from Anaconda Files (should likely be the first search result):
anaconda / packages / openssl 1 - Files :: Anaconda Cloud
Ctrl+F to find the package in the list.
Download the compressed package to your local Downloads folder.
Backup the contents of the installed erroneous package *C:\Users\Tanishk\anaconda3\pkgs\openssl-1.1.1h-he774522_0* somewhere.
Copy the contents of the de-compressed downloaded package into the *C:\Users\Tanishk\anaconda3\pkgs\openssl-1.1.1h-he774522_0* folder.
Re-try in Anaconda prompt with whatever you got stuck at.
Note:
After step 7, I got another same error but for a different package this time (vs2015_runtime-14.16.27012-hf0eaf9b_3). I performed the same steps for this package too --> Google -- Download -- Replace old content. And I was able to run things successfully after that.
I suggest to google the package because if you search for the package name on Anaconda itself, it will ask you to login first.
I am having a tough time installing R-packages that are not available in the Anaconda repositories. My attempts so far can be found here How to install R-packages not in the conda repositories?.
Currently, I am trying to build the R-package rafalib for conda by following the instructions from this article under the heading Building a conda R package.
The first part works fine.
conda skeleton cran rafalib
Out:
Tip: install CacheControl to cache the CRAN metadata
Fetching metadata from http://cran.r-project.org/
Writing recipe for rafalib
Done
The build command runs into errors
conda build r-rafalib
Out:
Removing old build environment
Removing old work directory
BUILD START: r-rafalib-1.0.0-r3.2.2_0
Using Anaconda Cloud api site https://api.anaconda.org
Fetching package metadata: ......
Solving package specifications: .
Error: Packages missing in current linux-64 channels:
- r 3.2.2*
- r-rcolorbrewer
I have r 3.2.2-64bit installed via conda and it runs without problems. I also already have r-colorbrewer installed via conda and I can use that package without issues in R. Why am I getting these errors when trying to build a conda package?
I am on Linux (Antergos, an Arch derivative) with kernel 4.4.5-1-ARCH.
UPDATE 2015/04/19
Thanks to this answer, I found out that I could include the dependencies by building them separately in the same directory as the package I want to install. That didn't work for me, but I also read that I can include a channel in the build command with -c, just as when installing. So now I do:
conda build -c r r-rafalib
This gets passed all the dependency problems, but after fetching, extracting and linking packages, it fails. Here is the end of the error message.
Removing old work directory
Source cache directory is: /home/joel/anaconda2/conda-bld/src_cache
Downloading source to cache: rafalib_1.0.0.tar.gz
Downloading http://cran.r-project.org/src/contrib/rafalib_1.0.0.tar.gz
rafalib_1.0.0. 100% |#######################| Time: 0:00:00 4.87 MB/s
Success
Extracting download
Package: r-rafalib-1.0.0-r3.2.2_0
source tree in: /home/joel/anaconda2/conda-bld/work/rafalib
+ mv DESCRIPTION DESCRIPTION.old
+ grep -v '^Priority: ' DESCRIPTION.old
+ /home/joel/anaconda2/envs/_build/bin/R CMD INSTALL --build .
sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook
Command failed: /bin/bash -x -e /home/joel/drafts/r-rafalib/build.sh
The error sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook is the same as I encounter when using install.packages() as reported here.
There is some related discussion in this thread. I have tried to get around this error by installing different versions of ncurses, including this patched version, and I have tried to link the readline libraries, as suggested here, but I keep running into the same error. I'm quite lost at this point and any help to solve this would be greatly appreciated.
Although I started out with a different problem, the final solution turned out to be the same as I posted elsewhere How to install R-packages not in the conda repositories?. I am adding it here for completeness.
In the end, I got around the rl_event_hookproblems by following the approach recommended here and symlinking anaconda's libreadline to the system one:
mv ~/anaconda3/lib/libreadline.s.6.2 ~/anaconda3/lib/libreadline.s.6.2.bak
ln -s /usr/lib/libreadline.so.6.3 ~/anaconda3/lib/libreadline.s.6.2
I am still having troubles installing some dependency heavy R-packages due to failure to load shared objects when using install.packages() from withing R. However, simpler packages work fine and I can get most of the dependency heavy packages from anacondas R-repositories.
I am getting the following error when I try to run
sudo apt-get upgrade
I am not sure what is the issue. Please guide me. Thanks
Preparing to unpack .../nginx_1.8.0-1~jessie_amd64.deb ...
Unpacking nginx (1.8.0-1~jessie) over (1.6.2-5) ...
dpkg: error processing archive /var/cache/apt/archives/nginx_1.8.0-1~jessie_amd64.deb (--unpack):
trying to overwrite '/usr/sbin/nginx', which is also in package nginx-full 1.6.2-5
dpkg-deb: error: subprocess paste was killed by signal (Broken pipe)
Errors were encountered while processing:
/var/cache/apt/archives/nginx_1.8.0-1~jessie_amd64.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)