Question

Which R version is needed for tximport package?

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harelarik ▴ 60

@harelarik-13564

Last seen 3.1 years ago

Israel

Hi,

I have tried to install tximport, but received the message: "package ‘tximport’ is not available (for R version 3.2.3)".

System data: Ubuntu 16.04.6 LTS, With R version 3.2.3

I have searched in the following 3 but I could not find which R versions can be used with this package (though I might have missed it):

https://www.rdocumentation.org/packages/tximport/versions/1.0.3/topics/tximport
The DESCRIPTION files in the tximport package I have downloaded from: https://bioc.ism.ac.jp/packages/3.5/bioc/html/tximport.html [from 2017], and from https://bioc.ism.ac.jp/packages/3.4/bioc/html/tximport.html [from 2017]
https://bioconductor.riken.jp/packages/3.4/bioc/manuals/tximport/man/tximport.pdf

Is there a tximport version that is supported by R.3.x or must I install R.4.x? If there is tximport for R.x, which R version exactly? where can I download it from?

Thank you very much,

Airk

tximport package R version install tximport • 4.4k views

ADD COMMENT • link 4.2 years ago harelarik ▴ 60

score 1 · Answer 1 · 2020-08-26

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Mike Smith ★ 6.6k

@mike-smith

Last seen 32 minutes ago

EMBL Heidelberg

You can find how long a package has been in Bioconductor from the "Since" section on the package landing page. For tximport that's at https://bioconductor.org/packages/release/bioc/html/tximport.html#since

Based on that you should be able to get a version of the package if you use R-3.3 and Bioconductor 3.3.

However you should bear in mind that the version of tximport you will install if you use R-3.3 will be the version from 4.5 years ago. It may not have many of the features available in the current version, and might be difficult to get support for if you run into problems. For this reason I would recommend using the latest version of R and Bioconductor if possible.

ADD COMMENT • link 4.2 years ago Mike Smith ★ 6.6k

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Thank you very much Mike!

Do you have any experience with R Vers 4. on Ubuntu 16.04? Our sys admin thinks it may cause some system failure.

ADD REPLY • link 4.2 years ago harelarik ▴ 60

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I am using R 4.0.2 on Ubuntu Server 16.04. I have no issues to report.

ADD REPLY • link 4.2 years ago Kevin Blighe ★ 4.0k

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Thank you very much.

ADD REPLY • link 4.2 years ago harelarik ▴ 60

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DESeq2 gave me some hard time, until I have used suggestion in comment 4 of this link: https://www.biostars.org/p/439453/

ADD REPLY • link 4.2 years ago harelarik ▴ 60

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The problem here would seem to be that you (or your system administrator) updated R from a version < 4.0.0 to R version 4.0.0 or higher, but the packages installed in the library were not updated.

I would suggest either updating the packages whenever updating R (see https://bioconductor.org/install/#update-bioconductor-packages section 'recompiling installed Bioconductor packages', though actually the type = "source" is only required for Linux installations), or (better, from my perspective), having an R-version-specific library where packages are installed (see 'Managing Multiple Versions of R' in https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html). In either case, updating R requires the effort of updating R itself, and of updating or re-installing packages. This is costly at the time, but saves effort and confusion in the long run.

ADD REPLY • link 4.2 years ago Martin Morgan 25k

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Thank you. I have recompiled all the existing packages pkgs <- rownames(installed.packages()) BiocManager::install(pkgs, type = "source", checkBuilt = TRUE)

Than installed DESeq2. It is working!

ADD REPLY • link 4.2 years ago harelarik ▴ 60

score 0 · Answer 2 · 2020-08-26

Installed R 4.0.2 on Ubuntu 16.04 LTS based on https://cran.r-project.org/bin/linux/ubuntu/ Installed BioC based on: https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html

sessionInfo() R version 4.0.2 (2020-06-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.6 LTS

tools:::.BioCversionassociatedwithR_version() [1] ‘3.11’

Available packages for this BioC 3.11 version are found in: https://bioc.ism.ac.jp/packages/3.11/ (if "Software" is clicked than it is possible to search all software in the right table) tximport is available

Installed with:

BiocManager::install("tximport")