Rocker R-ver

https://rocker-project.org/images/versioned/r-ver.html
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Rocker R-ver is an alternative Docker image to r-base, emphasizing reproducibility for R...
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### Use setup_R.sh to Configure CRAN Mirror

Source: https://rocker-project.org/images/versioned/r-ver.html

Utilize the included setup_R.sh script in the rocker/r-ver image to configure a CRAN mirror, supporting binary installations from Posit Public Package Manager (P3M) and adapting to non-amd64 platforms.

```dockerfile
FROM rocker/r-ver:4
RUN /rocker_scripts/setup_R.sh https://packagemanager.posit.co/cran/__linux__/jammy/2023-01-29
```

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

### Configure P3M and CRAN Simultaneously in Dockerfile

Source: https://rocker-project.org/images/versioned/r-ver.html

Set up both Posit Public Package Manager (P3M) and CRAN as repositories in Rprofile.site within a Dockerfile. This ensures binary installations and successful package checks.

```dockerfile
FROM rocker/r-ver:4
RUN echo 'options(repos = c(P3M = "https://packagemanager.posit.co/cran/__linux__/jammy/latest", CRAN = "https://cloud.r-project.org"))' >>"${R_HOME}/etc/Rprofile.site"
```

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### Switch BLAS to libblas

Source: https://rocker-project.org/images/versioned/r-ver.html

Configure the system to use the reference BLAS implementation (libblas) instead of OpenBLAS. This is done using the update-alternatives command in the terminal.

```bash
ARCH=$(uname -m)
update-alternatives --set "libblas.so.3-${ARCH}-linux-gnu" "/usr/lib/${ARCH}-linux-gnu/blas/libblas.so.3"
update-alternatives --set "liblapack.so.3-${ARCH}-linux-gnu" "/usr/lib/${ARCH}-linux-gnu/lapack/liblapack.so.3"
```

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

### Check Current BLAS Implementation in R

Source: https://rocker-project.org/images/versioned/r-ver.html

Display R session information, including the currently used BLAS library. This helps diagnose potential segfaults when using Python packages like numpy with R.

```r
sessionInfo()
#> R version 4.2.0 (2022-04-22)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 20.04.4 LTS
#>
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
```

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

### Switch BLAS to OpenBLAS

Source: https://rocker-project.org/images/versioned/r-ver.html

Revert the BLAS implementation back to OpenBLAS using the update-alternatives command. This command sets the symbolic links for libblas and liblapack to point to the OpenBLAS libraries.

```bash
ARCH=$(uname -m)
update-alternatives --set "libblas.so.3-${ARCH}-linux-gnu" "/usr/lib/${ARCH}-linux-gnu/openblas-pthread/libblas.so.3"
update-alternatives --set "liblapack.so.3-${ARCH}-linux-gnu" "/usr/lib/${ARCH}-linux-gnu/openblas-pthread/liblapack.so.3"
```

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

### Set Default CRAN Mirror in Dockerfile

Source: https://rocker-project.org/images/versioned/r-ver.html

Configure the default CRAN mirror for R by adding an options setting to Rprofile.site within a Dockerfile. This ensures R uses the specified repository upon container startup.

```dockerfile
FROM rocker/r-ver:4
RUN echo 'options(repos = c(CRAN = "https://cloud.r-project.org"))' >>"${R_HOME}/etc/Rprofile.site"
```

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

### Set Default CRAN Mirror as Non-Root User

Source: https://rocker-project.org/images/versioned/r-ver.html

Modify the default CRAN mirror from within a running container as a non-root user. This command pipes the options setting to the Rprofile.site file using sudo.

```bash
echo 'options(repos = c(CRAN = "https://cloud.r-project.org"))' | sudo sh -c 'cat - >>"${R_HOME}/etc/Rprofile.site"'
```

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### Temporarily Change CRAN Mirror in R Session

Source: https://rocker-project.org/images/versioned/r-ver.html

Adjust the CRAN mirror for the current R session using the options() function. This is useful for development tasks like package checking with devtools::check() to avoid '404 Not Found' errors.

```r
options(repos = c(CRAN = "https://cloud.r-project.org"))
devtools::check()
```
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