can't load package in Rstudio

[asifzubair]

I followed the installation instructions and was able to load immunedeconv from the command line into R. However, I wanted to use the package in Rstudio because I want to explore it in an Rmarkdown.

To do that, I did the following:

(base) azubair@D191200:~/projects$ conda activate immunedeconv
(immunedeconv) azubair@D191200:~/projects/decon$ conda install --override -c grst -c bioconda -c conda-forge/label/cf201901 r-immunedeconv
(immunedeconv) azubair@D191200:~/projects/decon$ rstudio

However, when I load the package in Rstudio, I get the following error:

> library(immunedeconv)
Error: package or namespace load failed for ‘immunedeconv’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/azubair/anaconda3/envs/immunedeconv/lib/R/library/RCurl/libs/RCurl.so':
  /home/azubair/anaconda3/envs/immunedeconv/lib/R/library/RCurl/libs/../../../../libcurl.so.4: undefined symbol: SSLv2_client_method

I think it is having some problems with RCurl.

If it helps, when I start Rstudio, I got the following message:

Error in tools::startDynamicHelp() : internet routines cannot be loaded

It could be a problem with my local installation of RStudio, but I wanted to ask if you folks have used immunedeconv within RStudio and if so what was your workflow.

> devtools::session_info()
─ Session info ────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.4.1 (2017-06-30)
 os       Ubuntu 16.04.6 LTS          
 system   x86_64, linux-gnu           
 ui       RStudio                     
 language en_US                       
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       SystemV/CST6CDT             
 date     2019-07-30                  

[mlist]

Hi Asif, I'm speculating here but it sounds like you do not have the ubuntu libraries for curl installed. Could that be? Best, Markus Asif Zubair <[email protected]> schrieb am Di., 30. Juli 2019, 21:33:

…

I followed the installation instructions and was able to load immunedeconv from the command line into R. However, I wanted to use the package in Rstudio because I want to explore it in an Rmarkdown. To do that, I did the following: (base) ***@***.***:~/projects$ conda activate immunedeconv (immunedeconv) ***@***.***:~/projects/decon$ conda install --override -c grst -c bioconda -c conda-forge/label/cf201901 r-immunedeconv (immunedeconv) ***@***.***:~/projects/decon$ rstudio However, when I load the package in Rstudio, I get the following error: > library(immunedeconv) Error: package or namespace load failed for ‘immunedeconv’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/home/azubair/anaconda3/envs/immunedeconv/lib/R/library/RCurl/libs/RCurl.so': /home/azubair/anaconda3/envs/immunedeconv/lib/R/library/RCurl/libs/../../../../libcurl.so.4: undefined symbol: SSLv2_client_method I think it is having some problems with RCurl. If it helps, when I start Rstudio, I got the following message: Error in tools::startDynamicHelp() : internet routines cannot be loaded It could be a problem with my local installation of RStudio, but I wanted to ask if you folks have used immunedeconv within RStudio and if so what was your workflow. > devtools::session_info() ─ Session info ──────────────────────────────────────────────────────────── setting value version R version 3.4.1 (2017-06-30) os Ubuntu 16.04.6 LTS system x86_64, linux-gnu ui RStudio language en_US collate en_US.UTF-8 ctype en_US.UTF-8 tz SystemV/CST6CDT date 2019-07-30 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#17>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAKWBXLXMHGUFSGUY7DUEWDQCCCO3ANCNFSM4IH7ELBQ> .

[asifzubair]

Ah, it does seem to be a problem with RCurl. Inside the conda environment, I can load it at the command line R but NOT in RStudio.

> library(RCurl)
Loading required package: bitops
Error: package or namespace load failed for ‘RCurl’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/azubair/anaconda3/envs/immunedeconv/lib/R/library/RCurl/libs/RCurl.so':
  /home/azubair/anaconda3/envs/immunedeconv/lib/R/library/RCurl/libs/../../../../libcurl.so.4: undefined symbol: SSLv2_client_method

Maybe I should post this either on RCurl or RStudio forum ?

EDIT: Still haven't solved my problem but this issue seems related - rstudio/rstudio#4123

[mlist]

Sounds to me like Rstudio and R command line rely on different R installations. Are you sure you installed libssl: sudo apt install libssl-dev Best, Markus

…

On Wed, Jul 31, 2019 at 7:57 PM Asif Zubair ***@***.***> wrote: Ah, it does seem to be a problem with RCurl. Inside the conda environment, I can load it at the command line R but NOT in RStudio. > library(RCurl) Loading required package: bitops Error: package or namespace load failed for ‘RCurl’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/home/azubair/anaconda3/envs/immunedeconv/lib/R/library/RCurl/libs/RCurl.so': /home/azubair/anaconda3/envs/immunedeconv/lib/R/library/RCurl/libs/../../../../libcurl.so.4: undefined symbol: SSLv2_client_method Maybe I should post this either on RCurl or RStudio forum ? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#17>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAKWBXJHXGMQML7N6WE5B4TQCHG7DANCNFSM4IH7ELBQ> .

-- Dr. Markus List Head of the Research Group on Big Data in BioMedicine Chair of Experimental Bioinformatics TUM School of Life Sciences Weihenstephan Technical University of Munich (TUM) Freising-Weihenstephan, Germany e-mail: [email protected] tel: +49 8161 71 2761 www: http://biomedical-big-data.de orcid: https://orcid.org/0000-0002-0941-4168 twitter: @itisalist <https://twitter.com/itisalist>

[grst]

I suppose the conda and system libraries are getting mixed. Try to `conda install rstudio` within the env and start rstudio from the command line. There might be a way to use the system rstudio with the conda env but I don't know how to do that properly. Cheers, Gregor

…

On Fri, Aug 2, 2019, 13:49 Markus List ***@***.***> wrote: Sounds to me like Rstudio and R command line rely on different R installations. Are you sure you installed libssl: sudo apt install libssl-dev Best, Markus On Wed, Jul 31, 2019 at 7:57 PM Asif Zubair ***@***.***> wrote: > Ah, it does seem to be a problem with RCurl. Inside the conda > environment, I can load it at the command line R but NOT in RStudio. > > > library(RCurl) > > Loading required package: bitops > > Error: package or namespace load failed for ‘RCurl’ in dyn.load(file, DLLpath = DLLpath, ...): > > unable to load shared object '/home/azubair/anaconda3/envs/immunedeconv/lib/R/library/RCurl/libs/RCurl.so': > > /home/azubair/anaconda3/envs/immunedeconv/lib/R/library/RCurl/libs/../../../../libcurl.so.4: undefined symbol: SSLv2_client_method > > > Maybe I should post this either on RCurl or RStudio forum ? > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > < #17 >, > or mute the thread > < https://github.com/notifications/unsubscribe-auth/AAKWBXJHXGMQML7N6WE5B4TQCHG7DANCNFSM4IH7ELBQ > > . > -- Dr. Markus List Head of the Research Group on Big Data in BioMedicine Chair of Experimental Bioinformatics TUM School of Life Sciences Weihenstephan Technical University of Munich (TUM) Freising-Weihenstephan, Germany e-mail: ***@***.*** tel: +49 8161 71 2761 www: http://biomedical-big-data.de orcid: https://orcid.org/0000-0002-0941-4168 twitter: @itisalist <https://twitter.com/itisalist> — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#17>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABVZRV7O7KNIVBNV5FKKJHTQCPRIFANCNFSM4IH7ELBQ> .

[asifzubair]

I did try doing a conda install rstudio inside the environment but then it has conflicts with a number of packages that were installed along with immunedeconv already

[grst]

I see. Should be fixed when the package gets accepted to bioconda (#2)

Until then, you'll have to install the package manually to use it with rstudio (see README)

[grst]

Ah, one more thing you could try is to use

conda install --override -c conda-forge/label/cf201901 rstudio

[asifzubair]

Great, will try to to do that! Thank you.

And thank you for the bioconda heads up, that will be very useful.

[asifzubair]

Sorry @grst , I don't think the channel specification works:

(immunedeconv) azubair@D191200:~/projects/splattercon$ conda install --override -c conda-forge/label/cf201901 rstudio
Collecting package metadata (repodata.json): done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - rstudio

Current channels:

  - https://conda.anaconda.org/conda-forge/label/cf201901/linux-64
  - https://conda.anaconda.org/conda-forge/label/cf201901/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

[grst]

Ok, hope I'll get the bioconda package through soon. Would be great if you could test that once it's published! Best, Gregor

…

On Tue, Aug 13, 2019, 01:39 Asif Zubair ***@***.***> wrote: Sorry @grst <https://github.com/grst> , I don't think the channel specification works: (immunedeconv) ***@***.***:~/projects/splattercon$ conda install --override -c conda-forge/label/cf201901 rstudio Collecting package metadata (repodata.json): done Solving environment: failed PackagesNotFoundError: The following packages are not available from current channels: - rstudio Current channels: - https://conda.anaconda.org/conda-forge/label/cf201901/linux-64 - https://conda.anaconda.org/conda-forge/label/cf201901/noarch To search for alternate channels that may provide the conda package you're looking for, navigate to https://anaconda.org and use the search bar at the top of the page. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#17>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABVZRV6DOSAOVOHSCEHC7ZDQEG37TANCNFSM4IH7ELBQ> .

[asifzubair]

Yes, will do! thanks!

[grst]

Bioconda package is available now.
I also update installation instructions in the readme.

[asifzubair]

awesome, will check it out asap and report back! thanks!

[asifzubair]

hi @grst . just a quick question - would it be possible to change the signature matrix used by different methods in this package? I see that in the function signature at least this argument is not exposed. please let me know. thanks!

[grst]

Not atm - See #15.

Did the installation with conda work out for you now?

[asifzubair]

Yes, the installation worked! But I am still having problems with rstudio. In the end, I just installed using remotes. Hope everything still works! Gonna close this for now.

[grst]

Ok, thanks for testing!
Glad it at least worked out with remotes in the end.