[Bioc-devel] python or python3 support in Linux

Jennifer Wokaty Jenn||er@Wok@ty @end|ng |rom @ph@cuny@edu
Thu Sep 30 17:19:45 CEST 2021

Hi Zheng,

The builders all have Python installed, but how you access it depends on the OS: for Mac and Linux, use `python3` and for Windows, use `python`. The issue we see in Rbowtie2's build error is related to the lines

432     invisible(.callbinary(lang = "python",
433                           bin1 = "bowtie2-build",
434                           args1 = paste(argvs,collapse = " ")))

505     .callbinary(lang = "python", bin1 = "bowtie2-build", args1 = "-h")

You should check for the the OS to determine how you should call Python, for example using `.Platform$OS.type`. The reason it isn't also failing on Mac is that `python` exists, but it's Python 2, which we no longer support and will likely be removed in the future.

Jennifer Wokaty (they/them)
Bioconductor Core Team

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Zheng Wei via Bioc-devel <bioc-devel using r-project.org>
Sent: Wednesday, September 29, 2021 7:41 PM
To: bioc-devel
Subject: [Bioc-devel] python or python3 support in Linux

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Dear all,

I have tested python (Rbowtie2 version 1.15.3) and python3 (Rbowtie2 version 1.15.4). Both of the building results are the same:

The python or python3 can not be found in Linux Server. Both versions of python works in Windows and Mac. 

Could anyone check the Linux server?

Zheng Wei
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