PackageInstallations_Troubleshoots.qmd

---
title: "Troubleshooting tips for installing miaverse packages"
output: html_document
---

```{r}
#| label = "setup",
#| include = FALSE
knitr::opts_chunk$set(echo = TRUE)
```


First of all, please ensure that you have an up-to-date version of R
(this note is based on R 4.3.1).

## Mac M1 user

When attempting to install miaverse packages, you may encounter
installation failures related to the 'scuttle' and 'scatter'
dependencies, which require a gcc compiler for installation. The error
message might resemble the following:

```
ld: warning: directory not found for option
'-L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0'
ld: warning: directory not found for option '-L/opt/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see
invocation)
```

This error indicates that R is unable to locate the 'libgfortran'
during the package compilation process. If you encounter this error,
you can use the following workaround:

1. Install 2 essentials tools in order to compile R for macOS as
described in [Mac-r-project](https://mac.r-project.org/tools/)

- install the xcode: 
	- sudo xcode-select --install
- GNU Fortran compiler*
	- download from
	[here](https://mac.r-project.org/tools/gfortran-12.2-universal.pkg)
	*you can also install from package manager for example homebrew,
	but it is not reccomended.
	
2. Locate the gfortran using `which gfortran` to find the version of
gfortran that is stored in your ~/.bashrc or ~/bash_profile. Make sure
it pointing to the gfortran that you want to use. For example if you
have both homebrew and mac-r project gfortran, you may want to add the
mac-r project gfortran to your $PATH variable.
    
- add `export PATH="/opt/gfortran/bin:$PATH"` to your ~/.bash_profile
or ~/.bashrc, followed by `source ~/.bash_profile` in your terminal

3. Modify your `/Library/Frameworks/R.framework/Resources/etc/Makeconf`
	
	from: 
	
	```
	FLIBS =  -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0     /11.0.0 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lm
	```
	to*:
	
	```
	FLIBS =  -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0       -L/opt/gfortran/lib -lgfortran -lm -lquadmath
	```
*note that the path is depend on your installations site, sometimes it
is located in `/usr/local/gfortran/lib` so you have to change
`/opt/gfortran/lib` accordingly in the lines above.

After all of those steps, you can follow the installations based on
Bioconductor page. For example for mia package:

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

BiocManager::install("mia")
```

If the installations prompt to compile from source, you can answer yes,
and hopefully it can be successfully compiled. Good Luck!

Follow-up reading:

- https://support.bioconductor.org/p/9138121/ 
- https://medium.com/biosyntax/following-up-library-dependency-when-compiling-r-packages-89f191b9f227


Session info at the time of writing

```
sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Helsinki
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] compiler_4.3.1    bookdown_0.36     fastmap_1.1.1     cli_3.6.1        
 [5] htmltools_0.5.6.1 tools_4.3.1       rstudioapi_0.15.0 yaml_2.3.7       
 [9] rmarkdown_2.25    knitr_1.44        xfun_0.40         digest_0.6.33    
[13] rlang_1.1.1       evaluate_0.22 
```


## Linux user


For Ubuntu package please see [here](https://packages.ubuntu.com/)