Question

Very small bug in DESeq2

1

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arfranco ▴ 130

@arfranco-8341

Last seen 9 months 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Warning: namespace ‘DESeq’ is not available and has been replaced
by .GlobalEnv when processing object ‘pasillaGenes’
Loading required package: DESeq
Error in .requirePackage(package) : 
  unable to find required package ‘DESeq’
In addition: Warning message:
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 • 2.6k views

ADD COMMENT • link 7.5 years ago arfranco ▴ 130

0

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Can you post your sessionInfo() please?

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?

ADD REPLY • link 7.5 years ago Michael Love 41k

score 1 · Answer 1 · 2016-10-06

1

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arfranco ▴ 130

@arfranco-8341

Last seen 9 months 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

ADD COMMENT • link 7.5 years ago arfranco ▴ 130

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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.

ADD REPLY • link 7.5 years ago Michael Love 41k

1

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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.

ADD REPLY • link 7.5 years ago Michael Love 41k

1

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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.

ADD REPLY • link 7.5 years ago Michael Love 41k

score 0 · Answer 2 · 2016-10-06

0

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arfranco ▴ 130

@arfranco-8341

Last seen 9 months 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

ADD COMMENT • link 7.5 years ago arfranco ▴ 130

2

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All Bioconductor packages should always be installed with biocLite(). Deviations from this rule leads to heartbreak.

ADD REPLY • link 7.5 years ago Michael Love 41k

1

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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)
downloaded 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)

The downloaded source packages are in
    ‘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

ADD REPLY • link 7.5 years ago arfranco ▴ 130