"Unknown package from github" -"Line malformed"

[slendsa]

Hi, I tried to install your package on Rstudio with R version 3.6.0 with the code you provided in the tutorial (I installed devtools as well); However, the installation process failed with the following errror:

"install_github("nhanhocu/metamicrobiomeR") Error: Failed to install 'unknown package' from GitHub: Line starting ': an R package for a ...' is malformed!"

Is your package compatible with R 3.6.0?

[VGalata]

I could install it using R 3.6.0 through conda.

Edit: I installed r-base==3.6.0 and devtools and then installed metamicrobiomeR in an R-session using install_github().

[slendsa]

Hi VGalata, thanks for your quick reply.

I am still stucked. I installed similar package along the same methods and I didn't have any problem. However, although the R version indicated at the beginning of the console is 3.6.0, I saw that the recent packages I installed were compiled with the R version 3.6.1. So maybe my R version was upgraded to R 3.6.1 and it's not compatible with your package ?

Please see below a print of the screen :

"> devtools::install_github("nhanhocu/metamicrobiomeR") Error: Failed to install 'unknown package' from GitHub: Line starting ': an R package for a ...' is malformed!

devtools::install_github("jtclaypool/microbiome") Downloading GitHub repo jtclaypool/microbiome@master These packages have more recent versions available. Which would you like to update?

1: All
2: CRAN packages only
3: None
4: ggplot2 (3.1.1 -> 3.2.0 ) [CRAN] 5: digest (0.6.19 -> 0.6.20) [CRAN] 6: pillar (1.4.1 -> 1.4.2 ) [CRAN] 7: vctrs (0.1.0 -> 0.2.0 ) [CRAN] 8: mime (0.6 -> 0.7 ) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 3 Installing 16 packages: Hmisc, reshape, Formula, latticeExtra, acepack, htmlTable, viridis, htmltools, base64enc, knitr, checkmate, htmlwidgets, evaluate, highr, markdown, xfun trying URL 'https://cran.cnr.berkeley.edu/bin/windows/contrib/3.6/Hmisc_4.2-0.zip' Content type 'application/zip' length 3122278 bytes (3.0 MB) ..."

It doesn't work either when I do it manually: downloading the zip file of your package and install it locally.

[VGalata]

Hi @slendsa,

I am not one of the maintainers of metamicrobioR. I am only trying it out it for my own analyses. :)

Regarding you problem: I would create a conda environment and install the package there. Maybe some of your packages (or their versions) are not compatible with metamicrobiomeR. For me, using conda (version 4.7.5) worked without any problems.

Installing MiniConda:

# get miniconda (for linux)
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
# install (follow the instructions)
bash Miniconda3-latest-Linux-x86_64.sh

Requirements (requirements.yml):

channels:
    - r
dependencies:
    - r-base==3.6.0
    - r-devtools==2.0.2

Creating the environment:

conda env create --name myenv -f requirements.yml
conda activate myenv
R

In the R session:

library(devtools)
devtools::install_github("nhanhocu/metamicrobiomeR", upgrade=FALSE)

[slendsa]

Hi VGalata,

Thanks a lot for your help! I will try your script on my linux computer and hope it will help. I keep you in touch and I hope I will be able to try this interesting package as well. Thanks for sharing your expertise!

[nhanhocu]

Hi, If you still have the above problem, please try our new version on R cran. Thanks, Nhan

[slendsa]

Hi nhanhocu,

Thanks for the notification. I just installed your new version of the package on R without anymore problem. It works now. Thanks for sharing your updates. Cheers, slendsa