I need to install the package "wkhtmltopdf" on RHEL 7 on IBM power Ecosystem ppc64le.
I tried installing a normal package but it give error
"-bash: ./wkhtmltopdf: cannot execute binary file"
I found build script on github for the IBM powerbox on the link:
wkhtmltopdf_rhel_7.4.sh
It tries to git clone -reccursively, which isnt allowed on our sever due to security policies.
I understand wkhtml needs qtbase so have downloaded both the individual packages (wkhtml & qtbase5.11) reading & navigating through the script on provided link.
Now, I'm stuck about setting up QT.
What next?
wkhtmltopdf-0.12.1 exists for ppc64le as an EPEL package (https://dl.fedoraproject.org/pub/epel/7/ppc64le/Packages/w/)
Related
I have a package that I developed to enable my team (and perhaps other interested users) to install and use a particular R package (RQDA) that was archived on CRAN. I have hosted this package on GitHub and am trying to set up GitHub Actions so that I have a CI workflow in place.
Whenever I run R CMD check locally everything is fine, but when I push to GitHub the build fails. This is because, by default, Actions tries to install that same (archived) package. Expectedly, this fails.
So, my question is this: is there a way I can disable the check for a specific package dependency? There are no plans to ever send this package to CRAN, so I am happy to bypass their package policy in this instance.
2 possible ways:
Upload the source for RQDA to a Github repo, or other publicly accessible location, and put a Remotes: line in your DESCRIPTION file
Save the package to cloud storage, eg an S3 bucket or Azure storage container, and download it from there as a separate workflow step prior to checking
This is how I was able to deal with the problem:
The changes made were entirely in the workflow file at ./.github/workflows/. One of the jobs there is for installing R package dependencies for the project:
- name: Install dependencies
run: |
remotes::install_deps(dependencies = TRUE)
remotes::install_cran("rcmdcheck")
shell: Rscript {0}
The first thing I did was to change the dependencies argument to NA so that only packages listed in Depends and Imports are installed. (The RQDA dependency that was giving me trouble is under Suggests).
There was still an error but this time with some guidance that involved going to the job Check and setting the environment variable _R_CHECK_FORCE_SUGGESTS_ to false.
The check now works as expected.
I am using R again after some time and need to install various packages (e.g. lumi, GENAVi, ideal, limma) and for some the installation works for some not. I receive failure notifications indicating that I the library paths are not writable or that access is denied.
installation of lumi with bioconductor fails
thus, lumi appears to be not existing
My PC uses windows 10, recently updated, and R 4.1.1
I tried the following steps (based on older forum entries):
I ran R Studio with administrator permissions
I gave R full permission through the firewall of my antivirus program
I gave R permission through the windows security settings
I reinstalled R on another harddrive (E:/) where it should have full permission for all paths.
I added a path in the xxx
I ran R inside a new environment in the “Conda” software, but the permission problems persisted.
(Outside of Conda) I installed the lumi package out of a zip file (instead of a Bioconductor download). Still didnt work...
So I now don’t know what to do anymore and barely find new ideas for solving the problem.
I appreciate your help
I gave the following command
library(reticulate)
py_install("pandas")
I am getting an error while installing python packages in RStudio :
Solving environment: ...working... failed
CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://repo.anaconda.com/pkgs/main/noarch/repodata.json.bz2>
Elapsed: -
An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.
If your current network has https://www.anaconda.com blocked, please file
a support request with your network engineering team.
SSLError(MaxRetryError('HTTPSConnectionPool(host=\'repo.anaconda.com\', port=443): Max retries exceeded with url: /pkgs/main/noarch/repodata.json.bz2 (Caused by SSLError("Can\'t connect to HTTPS URL because the SSL module is not available."))'))
Error: Error 1 occurred creating conda environment r-reticulate
Please help in resolving this error.
Solved a similar error arising from install_tensorflow():
SSLError("Can't connect to HTTPS URL because the SSL module is not available."))'))
by adding the path of the openssl.exe to the %PATH% environment variable of Windows. In my pc, the path is like this (replace "[username]" by yours):
C:\Users\[username]\Anaconda3\pkgs\openssl-1.1.1b-he774522_1\Library\bin
If somehow your openssl is an old version (as discussed here: https://github.com/conda/conda/issues/8046), you can install an up-to-date version following the guides below:
https://jchornsey.wordpress.com/2015/03/17/installing-openssl-in-windows-8-1/
https://www.cloudinsidr.com/content/how-to-install-the-most-recent-version-of-openssl-on-windows-10-in-64-bit/
As these guides explain, "the official OpenSSL website offers Linux sources only." For Windows binaries, you can obtain from https://slproweb.com/products/Win32OpenSSL.html provided by Shining Light Productions. The github issue discussion mentions that this link is listed on the OpenSSL wiki (https://wiki.openssl.org/index.php/Binaries -- I went there two days ago to confirm but today that page does not load, perhaps due to the Easter holidays).
The guides also explain that "If you’re not developing software, you don’t need the full versions; the “Light” version is intended for end-users.
Installing Python from RStudio seems interesting. One way to go is use reticulatepackage in R which provides R interface to Python and use Python within R.
Python packages are generally installed either using pip or 'conda' if anaconda is being used.
Then to use it in R, mention the proper path where python is installed in the system.
library(reticulate)
use_python("/usr/local/bin/python")
Reticulate also provides a way to install package using py_install() function.
library(reticulate)
py_install("pandas")
Please look for more details about reticulatepackage here and about installing packages here.
I'm working in RStudio and am attempting to install the dplyr package. I have installed various other packages without problem but have hit a problem with this.
It seems there are various parts to the install, some of these worked but the problem happens when I get 'the dependency BH'. This is the error:
>Installing package into ‘\\xxxxxxxx.local/Desktops/jagnew/My Documents/R/win-library/3.3’
(as ‘lib’ is unspecified)
also installing the dependency ‘BH’
>trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/BH_1.62.0-1.zip'
Content type 'application/zip' length 16150075 bytes (15.4 MB)
downloaded 15.4 MB
>trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/dplyr_0.5.0.zip'
Content type 'application/zip' length 2556205 bytes (2.4 MB)
downloaded 2.4 MB
>Error in install.packages : cannot open file '\\xxxxxxx.local/Desktops/jagnew/My Documents/R/win-library/3.3/file142032c9327b/BH/include/boost/function/detail/gen_maybe_include.pl': Permission denied
I have changed the directory/libpath as it did not appear that the file was downloading to the correct folder. file142032c9327b is now in the correct path, but path specified in the error is only correct up to /boost, there is no function folder here..?
I'm not sure if this missing folder is the issue, as the error says 'Permission denied', but it seems odd.
I had the same issue. Tried doing the following and worked for me:
Run the RStudio as administrator
Under the Packages tab, click Install and change Install to Library option to C:/Program...../R/../library and select the desired package to install.
Hope it works.
I had the same problem. R gave me an error message whenever I tried to install a new, or update an existing package. I don't remember what the message said exactly, but it was saying "Cannot open file (...) access denied". I tried all the following. Not sure what exactly fixed the problem, but now I can update and/or install new packages:
Open R/RStudio as administrator;
Change the R library folder (where packages are installed) security settings, and grant full access to my computer user account. Link1, link2;
(I think this was what fixed the problem) Follow instructions on this link. It prompted me to install another package, "devtools". Then it worked.
Well, I think my problem was a special case, but it might benefit someone. I had the Windows Defender Ransomware Protection set to ON. That was blocking rsession.exe by default. Allowing rsession.exe solved the problem.
TL;DR
The "Documents" (or "My Documents") directory is a special location in Windows. I don't know if the system itself processes its permissions differently or if antiviruses target operations inside this directory more strictly, but many R users have issues installing packages in the personal library inside this folder (even if running R as administrator). Other answers haven't worked.
For me, what solved the problem was to put the personal library directly under X:\\Users\username\ instead of under Documents, which is the R default on Windows. To make it permanent, I set a user environment variable R_USER to %USERPROFILE%. Here is a nice guide of how to set environment variables in Windows.
Note: after this change, you may need to move your .Rprofile, .Renviron, etc. files from Documents to the user profile directory.
Details
The default location for R's user "home" directory on Windows is X:\\Users\username\Documents. This is because there is no concept of HOME in Windows, just of a "personal" directory (Documents): https://cran.r-project.org/bin/windows/base/rw-FAQ.html#What-are-HOME-and-working-directories_003f
Therefore, by default, the personal library location is under X:\\Users\username\Documents\R\win-library\X.Y\. You can get the exact location on your machine with this command in the R console:
Sys.getenv('R_LIBS_USER')
I was getting this same cannot open file error when trying to install or update packages, even when running as administrator. I suspected of directory permissions, checked it within the directories' "properties" without luck. Removed the whole R\win-library tree and recreated it and nothing... Finally, I tried to move the personal library location to my users' directory:
.libPaths('X://Users/username/R/win-library/X.Y/')
And it worked!
Warning in install.packages :
cannot create file '/usr/local/Cellar/r/3.6.2/lib/R/doc/html/packages.html', reason 'Permission denied'
Warning in install.packages :
cannot update HTML package index
I had the same permission issue when trying to download a pkg--ISLR. Fixed it after following the above answers.
In case, some are new to R studio like me. These were my steps to install a pkg.
Click Terminal next to Console in R studio
Type sudo r, to run r as an administrator
install.packages("ISLR") to install your package
--- Please select a CRAN mirror for use in this session ---
https://cran.rstudio.com/src/contrib/ISLR_1.2.tar.gz
Secure CRAN mirrors
1: 0-Cloud [https] 2: Australia (Canberra) [https]
3: Australia (Melbourne 1) [https] 4: Australia (Melbourne 2) [https]
Pick a number -- a mirror site, then click enter.
Voilà! Package installed.
I had faced also this issue. The one and only solution that helped me was to turn off my firewall. Then I was able to download all packages.
The problem solved for me after running R in admin mode and disabling Antivirus.
Translating #Shubham Yadav's answer to code mode would be something like this: install.packages("your_package", lib = "C:/Program Files/R/R-4.0.3/library")
It's working for me (running RStudio as admin, course).
This procedure worked for me.
Removed existing package with remove.packages()
ran RStudio as an admin
Installed by specifying the libpath: devtools::install_github('https://github.com/Rdatatable/data.table/tree/frollmax', lib=.libPaths()[2])
For me what worked was manually deleting within the library directory the folder that I had problem with updating. And then install.package() again.
I had faced the same issue.
I tried below steps to resolve this issue:
Launch RGui application.
Go to Packages section and select Install Packages.
Select the Package that you want to install from the Packages pop up window.
And click OK, that's it package will get successfully installed.
After following above steps, you can run use your package from RStudio.
I ran into this issue today where rlang couldn't install the newest version and so tidyverse wouldn't work. I tried running as admin, changing install location, running as admin, permitting rstudio through Windows Defender Randsomware Protection, and installing DevTools. The only thing that worked was to uninstall RStudio, reboot, reinstall.
I'm trying to get R to recognize that I have installed Rtools.exe. I've tried installing it in several different locations. However, whenever I restart R and load devtools I get the same error:
> library(devtools)
WARNING: Rtools is required to build R packages, but is not currently installed.
Please download and install Rtools 3.0 from http://cran.r-project.org/bin/windows
/Rtools/ and then run find_rtools().
Naturally, whenever I try the function find_rtools() I get the same error message. I'm done trying to figure this out with help files, as the devtools help doesn't offer much. I've tried installing in several of the locations returned by get_path() but the problem persists.
FYI, currently my R is installed at D:/R.
Has anyone else had this problem, and more importantly, can anyone help me?
I'm sorry if this is a duplicate, and I've tried to include as many relevant details as possible so if you need any clarification please let me know.
Thanks,
Nick
Grab the batch file Rpathset.bat from batchfiles, edit the SET statements in it appropriately and then run R like this from the Windows console:
Rpathset
Rgui
I ran into this issue running a Windows 7 machine without admin rights. I leveraged G. Grothendieck's response, with a few additional steps.
Get Rpathset.bat from https://code.google.com/p/batchfiles/
Edit the Set statements in Rpathset.bat to your paths
Run CMD and change directories to where Rpathset.bat is stored
In the command prompt, run rpathset.bat > mypath.txt
Open mypath.txt with a text editor
Click Windows Start and search for environment
Click Edit environment variables for your account
Click path and then edit
Copy and paste the entire path from mypath.txt into the Windows path (everything after the path statement)
Restart RStudio and check that devtools::find_rtools() is TRUE
This file rtools.r contains the code for find_rtools(). It looks like it is trying to find ls and gcc in your system path (and then does some more checks based on the version) and if that fails it tries to look up SOFTWARE\R-core\Rtools in the the Windows registry.
As Thomas mentioned here, "Rtools is not a package." This is what I did to install Rtools. My RStudio is running R version 3.1.3. So I downloaded Rtools31.exe from https://cran.r-project.org/bin/windows/Rtools/. I executed the exe file, selected all the default options in the Setup Wizard and installed. (I had admin privilege on the computer I was using but I am not sure if that makes any difference.) To check that it was properly installed, you can enter find_rtools() in the R prompt which should return TRUE if Rtools installed properly.
For R 3.0, you probably just need to download Rtools30.exe and follow the same steps above.
I ran into this problem trying to install Rtools33 to use Hadley Wickham's lineprof package. I got that error multiple times. I'm running Windows 7 on a laptop.
I was able to fix the problem by running the Rtools installation file as the windows Admin (i.e. right-click the Rtools33.exe and choose "Run as administrator")
I also made sure to point the path to the R source directory, which I kept in C:\Rtools\ (which contains C:\Rtools\bin\ and C:\Rtools\gcc-4.6.3\).
This solved the problem for me and I am now able to install lineprof from GitHub and make use of it.