update documentation for R package management with conda #393
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| A lot of bioconda and bioconductor packages are not in sync with their dependencies, therefore you may need to create a separate environment for each of those packages to avoid conflicts. | ||
| A lot of bioconda and bioconductor packages are not in sync with their dependencies, therefore you may need to create a separate environment for each of those packages to avoid conflicts. |
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For bioconda I'm not sure, but with bioconductor this is because there are 2 releases per year, so dependencies can become somewhat older at some point. I would rather say here: start with installing the bioconductor (and bioconda?) packages and let conda figure out the dependencies.
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I did not change the content of this remark, I just made it a propper .. note:: . I am not sure what the reason was behind this remark. Do you know @moravveji?
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I don't know where this comment comes from, but it is a very relevant one. So, I'd keep it.
…in r_package_management.rst
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It seems I completely missed this new review request, sorry. I don't know if this is still relevant, but looks good to me in any case |
| @@ -105,17 +88,19 @@ If the result is blank, or reports that conda can not be found, modify | |||
| the \`PATH\` environment variable appropriately by adding miniconda's bin | |||
| directory to PATH. | |||
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| Creating a new conda environment is straightforward:: | |||
| The next step is to create a new conda environment which can be done as follows:: | |||
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some users are dummies. For such, we have to also mention that they need to pick a specific R version in advance, and substitute that below when <version>. Can you please include a sentence to cover this?
| $ conda create -n science -c r r-essentials r-rodbc | ||
| This command creates a new conda environment called "science", and installs your prefered R | ||
| version from the conda-forge channel as well as the r-essentials bundle which includes number | ||
| of commonly used R packages such as ggplot2, glmnet, dplyr, tidyr, and shiny. |
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following our style for the vsc pages, please change the typesetting for the package names by sandwiching them with opening/closing double-backticks; so that instead of ggplot2, we eventually render ggplot2.
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| A lot of bioconda and bioconductor packages are not in sync with their dependencies, therefore you may need to create a separate environment for each of those packages to avoid conflicts. | ||
| A lot of bioconda and bioconductor packages are not in sync with their dependencies, therefore you may need to create a separate environment for each of those packages to avoid conflicts. |
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I don't know where this comment comes from, but it is a very relevant one. So, I'd keep it.
| @@ -133,7 +118,7 @@ Here, science is the name of the environment you want to work in. | |||
| Install an additional package | |||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |||
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| To install an additional package, e.g., \`pandas`, first ensure that the | |||
| To install an additional package, e.g., \`rodbc`, first ensure that the | |||
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instead of `rodbc, you need to put rodbc` in between opening/closing double-backticks.
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