Error in install.packages(missing.packages)

[wangyy99]

Hello, I encountered some problems when using phyloFlash, I need to ask you how to solve it. as follows:

When comparing and analyzing multiple samples, phyloFlash_compare.pl --csv test1.phyloFlash.NTUabundance.csv, test2.phyloFlash.NTUabundance.csv --task heatmap --level 4 --out test_comparison --outfmt png was used Run, and then the following error appears：

Additional packages required: optparse ggdendro Installing packages into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) Warning in install.packages(missing.packages) : 'lib = "/usr/local/lib/R/site-library"' is not writable Error in install.packages(missing.packages) : unable to install packages Calls: check_libraries -> install.packages

does the software need to install R language? I need your help very much, I will not appreciate it.

[kbseah]

Hello @wangyy99 ,

Yes you will need some R libraries to produce the plot. The error message says that you don't have write permissions for the default location where R attempts to install packages.

Could you try to install the packages manually? Start R, and use the following command to install the necessary packages:

install.packages(c("ggdendro","gtable","reshape2","ggplot2","optparse"))

Then re-run phyloFlash_compare.pl and check that it works.

If you have set up phyloFlash in a Conda environment, and wish to have the R packages only in that environment, you can use Conda to install them instead:

conda install -c conda-forge r-ggendro r-optparse r-gtable r-reshape2 r-ggplot2

The -c conda-forge option searches for these packages in the conda-forge channel first. The command above assumes that you have already activated the environment that you want to install the packages to.

[wangyy99]

Hello@kbseah I‘m very grateful for your detailed explanation, I will try it.Thanks.

[kbseah]

@HRGV i think we can close this issue now