Installation issues with Rfast

[camcecc]

Hi all, I'm having BIG issues trying to install ggpicrust2. I've addressed many of those (mainly related to the R and RStudio needed upgrade) but I'm clueless about the installation of Rfast and ALDEx2 (which will eventually lead to ggpicrust2, I hope). I'm using Ubuntu18.04, I hope that's not the problem because I'm running late with these results and the last thing I need is to upgrade the OS... thank you in advance!

* installing *source* package ‘Rfast’ ...
** package ‘Rfast’ successfully opened with MD5 sum check
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0’
using C++ compiler: ‘g++ (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0’
using C++17
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/camilla/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include' -I'/home/camilla/R/x86_64-pc-linux-gnu-library/4.3/RcppArmadillo/include' -I'/home/camilla/R/x86_64-pc-linux-gnu-library/4.3/RcppParallel/include'    -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-E8saoI/r-base-4.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Coeff.cpp -o Coeff.o
In file included from ../inst/include/Rfast/templates.h:10:0,
                 from ../inst/include/Rfast/matrix.hpp:14,
                 from ../inst/include/Rfast.h:5,
                 from mn.h:4,
                 from Coeff.cpp:4:
../inst/include/Rfast/parallel.h:20:10: fatal error: execution: No such File or directory 
 #include <execution>
          ^~~~~~~~~~~
compilation terminated.
/usr/lib/R/etc/Makeconf:200: recipe for target 'Coeff.o' failed
make: *** [Coeff.o] Error 1
ERROR: compilation failed for package ‘Rfast’
* removing ‘/home/camilla/R/x86_64-pc-linux-gnu-library/4.3/Rfast’
ERROR: dependency ‘Rfast’ is not available for package ‘ALDEx2’
* removing ‘/home/camilla/R/x86_64-pc-linux-gnu-library/4.3/ALDEx2’
ERROR: dependency ‘ALDEx2’ is not available for package ‘ggpicrust2’
* removing ‘/home/camilla/R/x86_64-pc-linux-gnu-library/4.3/ggpicrust2’

I pacchetti scaricati con il codice sorgente sono in
    ‘/tmp/RtmpBP2aaU/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /usr/lib/R/library
  packages:
    boot, nlme
Warning message:
1: In install.packages(...) :
  installation of package  ‘Rfast’ has non-zero exit status
2: In install.packages(...) :
  installation of package ‘ALDEx2’ has non-zero exit status
3: In install.packages(...) :
  installation of package ‘ggpicrust2’ has non-zero exit status

(sorry if part of the error may be in Italian or sound odd, I've translated it manually)

[cafferychen777]

Dear Camilla,

Thank you for reaching out and sharing the details of the issues you've encountered while trying to install ggpicrust2, along with its dependencies Rfast and ALDEx2. I understand how frustrating it can be to face such challenges, especially under time constraints.

After reviewing the error messages and considering the underlying causes, it appears that the primary issue stems from using Ubuntu 18.04. While Linux systems are generally well-supported for R and its packages, the specific version of Ubuntu you're using, coupled with the dependencies required by ggpicrust2, introduces a complex dependency chain that might not be fully compatible with older Linux distributions. This is partly because the R package ecosystem in Linux can sometimes lag behind, leading to version incompatibility issues.

Given these considerations, I would recommend trying an alternative operating system, such as macOS or Windows, for installing ggpicrust2. These systems tend to have more up-to-date support for R and its related packages, which could alleviate the dependency issues you're encountering. Switching to macOS or Windows might provide a smoother installation process for ggpicrust2 and its dependencies, helping you to avoid the intricate dependency chains and potential version incompatibility issues present on older Linux systems.

I understand that changing operating systems might not be the most convenient option, but it could save you considerable time and effort in troubleshooting these installation issues. Should you decide to continue with Linux, you might consider updating to a more recent version of Ubuntu or another distribution that has more current support for R and its packages, though this approach also has its challenges.

Please let me know if there's anything else I can assist you with or if you have further questions.

Best regards,

Chen Yang

[camcecc]

Thank you for the fast and kind answer, I "solved" the issue by upgrading my OS to Ubuntu 22.04... after that, the installation has been a piece of cake