Error installing UniprotR in R 4.3.1

[Tomas-Pe]

Hello,

I'm trying to install UniprotR in R 4.3.1, and I'm having an error: Also, I see that yesterday a new doc of UniprotR was released in CRAN , corresponding to the version 2.3.0, but here I see that here in GitHub the last version of UniprotR is 2.2.0

R version: 4.3.1 OS: Ubuntu 20.04 Rstudio version: 2022.12.0 Build 353

Console output:

> install.packages("UniprotR")
Installing package into ‘/home/megatron/R/x86_64-pc-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)
Warning in install.packages :
  dependency ‘GenomicAlignments’ is not available
also installing the dependencies ‘nloptr’, ‘pbkrtest’, ‘lme4’, ‘car’, ‘rstatix’, ‘ggpubr’, ‘alakazam’

trying URL 'https://cloud.r-project.org/src/contrib/nloptr_2.0.3.tar.gz'
Content type 'application/x-gzip' length 2219877 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

trying URL 'https://cloud.r-project.org/src/contrib/pbkrtest_0.5.2.tar.gz'
Content type 'application/x-gzip' length 75295 bytes (73 KB)
==================================================
downloaded 73 KB

trying URL 'https://cloud.r-project.org/src/contrib/lme4_1.1-34.tar.gz'
Content type 'application/x-gzip' length 2948976 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

trying URL 'https://cloud.r-project.org/src/contrib/car_3.1-2.tar.gz'
Content type 'application/x-gzip' length 579829 bytes (566 KB)
==================================================
downloaded 566 KB

trying URL 'https://cloud.r-project.org/src/contrib/rstatix_0.7.2.tar.gz'
Content type 'application/x-gzip' length 405256 bytes (395 KB)
==================================================
downloaded 395 KB

trying URL 'https://cloud.r-project.org/src/contrib/ggpubr_0.6.0.tar.gz'
Content type 'application/x-gzip' length 1941659 bytes (1.9 MB)
==================================================
downloaded 1.9 MB

trying URL 'https://cloud.r-project.org/src/contrib/alakazam_1.2.1.tar.gz'
Content type 'application/x-gzip' length 2075971 bytes (2.0 MB)
==================================================
downloaded 2.0 MB

trying URL 'https://cloud.r-project.org/src/contrib/UniprotR_2.3.0.tar.gz'
Content type 'application/x-gzip' length 30134 bytes (29 KB)
==================================================
downloaded 29 KB

* installing *source* package ‘nloptr’ ...
** package ‘nloptr’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ -std=gnu++17 accepts -g... yes
checking for g++ -std=gnu++17 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... g++ -std=gnu++17 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++ -std=gnu++17 accepts -g... (cached) yes
checking for g++ -std=gnu++17 option to enable C++11 features... (cached) none needed
checking for pkg-config... /usr/bin/pkg-config
checking if pkg-config knows NLopt... no
checking for cmake... no

------------------ CMAKE NOT FOUND --------------------

CMake was not found on the PATH. Please install CMake:

 - sudo yum install cmake          (Fedora/CentOS; inside a terminal)
 - sudo apt install cmake          (Debian/Ubuntu; inside a terminal).
 - sudo pacman -S cmake            (Arch Linux; inside a terminal).
 - sudo brew install cmake         (MacOS; inside a terminal with Homebrew)
 - sudo port install cmake         (MacOS; inside a terminal with MacPorts)

Alternatively install CMake from: <https://cmake.org/>

-------------------------------------------------------

ERROR: configuration failed for package ‘nloptr’
* removing ‘/home/megatron/R/x86_64-pc-linux-gnu-library/4.3/nloptr’
Warning in install.packages :
  installation of package ‘nloptr’ had non-zero exit status
ERROR: dependency ‘GenomicAlignments’ is not available for package ‘alakazam’
* removing ‘/home/megatron/R/x86_64-pc-linux-gnu-library/4.3/alakazam’
Warning in install.packages :
  installation of package ‘alakazam’ had non-zero exit status
ERROR: dependency ‘nloptr’ is not available for package ‘lme4’
* removing ‘/home/megatron/R/x86_64-pc-linux-gnu-library/4.3/lme4’
Warning in install.packages :
  installation of package ‘lme4’ had non-zero exit status
ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’
* removing ‘/home/megatron/R/x86_64-pc-linux-gnu-library/4.3/pbkrtest’
Warning in install.packages :
  installation of package ‘pbkrtest’ had non-zero exit status
ERROR: dependencies ‘pbkrtest’, ‘lme4’ are not available for package ‘car’
* removing ‘/home/megatron/R/x86_64-pc-linux-gnu-library/4.3/car’
Warning in install.packages :
  installation of package ‘car’ had non-zero exit status
ERROR: dependency ‘car’ is not available for package ‘rstatix’
* removing ‘/home/megatron/R/x86_64-pc-linux-gnu-library/4.3/rstatix’
Warning in install.packages :
  installation of package ‘rstatix’ had non-zero exit status
ERROR: dependency ‘rstatix’ is not available for package ‘ggpubr’
* removing ‘/home/megatron/R/x86_64-pc-linux-gnu-library/4.3/ggpubr’
Warning in install.packages :
  installation of package ‘ggpubr’ had non-zero exit status
ERROR: dependencies ‘ggpubr’, ‘alakazam’ are not available for package ‘UniprotR’
* removing ‘/home/megatron/R/x86_64-pc-linux-gnu-library/4.3/UniprotR’
Warning in install.packages :
  installation of package ‘UniprotR’ had non-zero exit status

[AliYoussef96]

Hi @Tomas-Pe,

I believe this can be fixed by installing first GenomicAlignments;

if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")

BiocManager::install("GenomicAlignments")

Also due to dependency "alakazam" version 1.1.0 while UniprotR requires alakazam version 1.0.0. This can be solved now by installing alakazam before installing UniprotR using

install.packages("https://cran.r-project.org/src/contrib/Archive/alakazam/alakazam_1.0.0.tar.gz", repo=NULL, type="source")

For the GitHub version we are working on updating it.

[AliYoussef96]

The last version of UniprotR 2.3.0, available now on GitHub.