Older source of biocFileCache package
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@081606a2
Last seen 9 weeks ago
Germany

Dear all,

can anyone provide me an older source of biocFileCache (ideally 1.2.0)? This is due to the fact that our institution HPC cluster runs with R 3.3.3. The oldest package version I have is 1.10.0, which is not compatible with this R version.

Best

Julian

biomaRt • 242 views
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Mike Smith ★ 5.9k
@mike-smith
Last seen 1 hour ago
EMBL Heidelberg

You can find the source tarball for 1.2.3 on https://bioconductor.org/packages/3.6/bioc/html/BiocFileCache.html It doesn't look like the archive of 1.2.0 is available.

You could also check out the git repo from https://github.com/Bioconductor/BiocFileCache/tree/RELEASE_3_6 and maybe roll back 3 commits.

However I think you might be better persuading your hpc admins to update R, or trying to run a Docker container. R 3.3 and associated packages is so old now, you're surely missing out on many new features & packages.

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Chiming in here because Martin Morgan recently told me on Slack that you can get any archived version (Bioc >=3.6) via:

https://bioconductor.org/packages/{BIOC_VERSION}/bioc/src/contrib/Archive/{PACKAGE}/{PACKAGE}_{VERSION}.tar.gz


Here, BiocFileCache 1.2.0 is available:

https://bioconductor.org/packages/3.6/bioc/src/contrib/Archive/BiocFileCache/BiocFileCache_1.2.0.tar.gz

Seconding the suggestion of updating R, or at best see whether Singularity is available so you can containerize your analysis. Alternatively, use conda which can install software without root permissions. Still, most HPCs have module systems in place so it should be easy enough for your admin (if not already available) to get a recent R version going.

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Cool, nice to know the direct links work even if the archive page at https://bioconductor.org/packages/3.6/bioc/src/contrib/Archive/BiocFileCache/ gives me an error.
{"extraction_info": {"found_math": true, "script_math_tex": 0, "script_math_asciimath": 0, "math_annotations": 0, "math_alttext": 0, "mathml": 0, "mathjax_tag": 0, "mathjax_inline_tex": 0, "mathjax_display_tex": 0, "mathjax_asciimath": 1, "img_math": 0, "codecogs_latex": 0, "wp_latex": 0, "mimetex.cgi": 0, "/images/math/codecogs": 0, "mathtex.cgi": 0, "katex": 0, "math-container": 0, "wp-katex-eq": 0, "align": 0, "equation": 0, "x-ck12": 0, "texerror": 0, "math_score": 0.21961696445941925, "perplexity": 4624.261031231485}, "config": {"markdown_headings": true, "markdown_code": true, "boilerplate_config": {"ratio_threshold": 0.18, "absolute_threshold": 10, "end_threshold": 15, "enable": true}, "remove_buttons": true, "remove_image_figures": true, "remove_link_clusters": true, "table_config": {"min_rows": 2, "min_cols": 3, "format": "plain"}, "remove_chinese": true, "remove_edit_buttons": true, "extract_latex": true}, "warc_path": "s3://commoncrawl/crawl-data/CC-MAIN-2023-06/segments/1674764500619.96/warc/CC-MAIN-20230207134453-20230207164453-00835.warc.gz"}