Question: Problem when installing DESeq on MAC OS X
0
gravatar for yoonsora
3.5 years ago by
yoonsora0
yoonsora0 wrote:

Hello, I have a question about installing error of DESeq or DESeq2. 

Whenever I tried to install DESeq on my MAC OS X, such messages appeared. (Bold characters are what I typed.)


>source('http://bioconductor.org/biocLite.R')

>biocLite('DESeq')

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.3 (2015-12-10).
Installing package(s) ‘DESeq’
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0100 2122k  100 2122k    0     0  2465k      0 --:--:-- --:--:-- --:--:-- 2465k

The downloaded binary packages are in
    /var/folders/33/tggfm27n35n35mxyk2wn7t940000gn/T//Rtmpdvsm5g/downloaded_packages

>library(DESeq)

Error : Function found when exporting methods from the namespace ‘S4Vectors’ which is not S4 generic: ‘unlist’


Does anyone know why such error happened?? 

My session information is as following.


> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.3 (El Capitan)

locale:
[1] ko_KR.UTF-8/ko_KR.UTF-8/ko_KR.UTF-8/C/ko_KR.UTF-8/ko_KR.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] lattice_0.20-33      locfit_1.5-9.1       doParallel_1.0.10    iterators_1.0.8     
[5] foreach_1.4.3        Biobase_2.30.0       BiocGenerics_0.17.3  BiocInstaller_1.20.1

loaded via a namespace (and not attached):
[1] codetools_0.2-14 XML_3.98-1.3     grid_3.2.3       DBI_0.3.1        xtable_1.8-2    
[6] stats4_3.2.3     RSQLite_1.0.0    tools_3.2.3    


Thank you for your reading.

deseq s4vectors mac os x • 1.0k views
ADD COMMENTlink modified 3.5 years ago by Wolfgang Huber13k • written 3.5 years ago by yoonsora0
Answer: Problem when installing DESeq on MAC OS X
2
gravatar for Wolfgang Huber
3.5 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:

Your installed packages are out of sync, in particular BiocGenerics 0.17.3 is "too new". Best to install R from scratch, then use biocLite to install DESeq and its dependencies.

 

(Bioc release 3.2 goes with BiocGenerics 0.16: http://bioconductor.org/packages/3.2/bioc/html/BiocGenerics.html )

ADD COMMENTlink written 3.5 years ago by Wolfgang Huber13k

Thank you, Dr. Wolfgang Huber!

Now DESeq and DESeq2 packages are available!

ADD REPLYlink written 3.5 years ago by yoonsora0
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