Very small bug in DESeq2
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Entering edit mode
arfranco ▴ 130
@arfranco-8341
Last seen 19 hours ago
European Union

I am trying to teach my students the using of DESeq2, and they are repeating the instructions contained into the vignette

And they have found a very small bug. This bug does not appear when the "old" DESeq is installed into your system. But since DESeq2 is recommended, I insisted my students to not install DESeq.

This code has been extracted from the vignette itself

> library(DESeq2)
> library(pasilla)
> library(Biobase)
> data("pasillaGenes")
Warning: namespace ‘DESeq’ is not available and has been replaced
by .GlobalEnv when processing object ‘pasillaGenes’
Error in .requirePackage(package) :
unable to find required package ‘DESeq’
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
there is no package called ‘DESeq

As you can see, in the code example, DESeq is called instead DESeq2. It is clear to me that this error is caused because I have not installed the "old"  DESeq, and that a fix is got if you install it.

But.. Should we install DESeq only for this purpose ?

software error • 2.1k views
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The vignette uses the pasilla data package which requires DESeq (original package). When you install pasilla using biocLite(), everything you need should be installed.

How did you install pasilla?

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Entering edit mode
arfranco ▴ 130
@arfranco-8341
Last seen 19 hours ago
European Union

I am actually sorry to disturb you. I know the reason and the answer to this problem, and I am not happy at the time of writing these messages

I simply wrote this message because my students got very much confused

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Not a problem. I just want to make sure that things are clear.

I see that installing pasilla does not install DESeq as I thought. Maybe we should make a version of the pasilla count matrix and sample table that doesn't depend on loading DESeq.

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Apparently, I can fix this already by removing the CountDataSet and just using count tables and sample tables. I'll try to fix this before the release.

Thanks for the note.

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I just made the change in devel so that the vignette doesn't require DESeq package:

https://github.com/Bioconductor-mirror/DESeq2/commit/8cd4003ff0c2df72aaaf1986974c73111ae0759d

This will be out in Bioc release in a week or so.

Thanks again for your suggestion on improving the vignette.

0
Entering edit mode
arfranco ▴ 130
@arfranco-8341
Last seen 19 hours ago
European Union
I installed the pasilla package with a direct install.package('pasilla') command after defining the bioclite repository with the R command setRepositories() I don't have DESeq package installed, and I know this is actually the problem This is a minor problem, though. It simply represented a serious blockage to my students that are not very much used into the R world
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All Bioconductor packages should always be installed with biocLite(). Deviations from this rule leads to heartbreak.

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Well, look at this code

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help
> biocLite("pasilla")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Installing package(s) ‘pasilla’
installing the source package ‘pasilla’

trying URL 'https://bioconductor.org/packages/3.3/data/experiment/src/contrib/pasilla_0.12.0.tar.gz'
Content type 'application/x-gzip' length 3872945 bytes (3.7 MB)

* installing *source* package 'pasilla' ...
** data
** inst
** help
*** installing help indices
** building package indices
Warning: namespace 'DESeq' is not available and has been replaced
by .GlobalEnv when processing object 'pasillaGenes'
** installing vignettes
** testing if installed package can be loaded
* DONE (pasilla)

‘C:\Users\Antonio\AppData\Local\Temp\RtmpisLwWw\downloaded_packages’

After a biocLite installation of pasilla in my home computer (windows 10), the DESeq package is not installed either