Problems installing ChipPeakAnno with newest version of R and Bioconductor
2
0
Entering edit mode
@rebeccahalbach-9222
Last seen 5.8 years ago
Netherlands

Hi everyone,

I need to use the package ChipPeakAnno, however I fail to install. I am using the latest version of R and Bioconductor. I am not too familiar with using Bioconductor, so please excuse my question.

Thanks a ton,

Rebecca

This is what I get:

> source("https://bioconductor.org/biocLite.R")

Bioconductor version 3.2 (BiocInstaller 1.20.0), ?biocLite for help
> biocLite("ChIPpeakAnno")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.0), R 3.2.2 (2015-08-14).
Installing package(s) ‘ChIPpeakAnno’
also installing the dependencies ‘curl’, ‘httr’, ‘XML’, ‘RCurl’, ‘rtracklayer’, ‘AnnotationHub’, ‘biomaRt’, ‘BSgenome’, ‘GenomicFeatures’, ‘regioneR’, ‘ensembldb’

...

The
downloaded source packages are in    
‘/tmp/RtmpGN4MyX/downloaded_packages’
Es gab 12 Warnungen (Anzeige mit warnings())

> warnings()

Warnmeldungen:

1:In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘curl’ had non-zero exit status

2: In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘XML’ had non-zero exit status

3: In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘RCurl’ had non-zero exit status

4: In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘httr’ had non-zero exit status

5:In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘rtracklayer’ had non-zero exit status

6:In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘biomaRt’ had non-zero exit status

7: In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘AnnotationHub’ had non-zero exit status

8: In install.packages(pkgs = doing, lib = lib, ...) :

installation of package ‘BSgenome’ had non-zero exit status

9: In install.packages(pkgs = doing, lib = lib, ...) :installation of package ‘GenomicFeatures’ had non-zero exit status

10: In install.packages(pkgs = doing, lib = lib, ...) : 
installationof package ‘regioneR’ had non-zero exit status

11:In install.packages(pkgs = doing, lib = lib, ...) : 
installation of package ‘ensembldb’ had non-zero exit status

12: In install.packages(pkgs = doing, lib = lib, ...) : 
installation of package ‘ChIPpeakAnno’ had non-zero exit status

>sessionInfo()

R
version 3.2.2 (2015-08-14)

Platform:
x86_64-pc-linux-gnu (64-bit)

Running
under: Ubuntu 14.04.3 LTS

locale:

 [1]
LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C              
LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8    
LC_MONETARY=de_DE.UTF-8   

 [6]
LC_MESSAGES=de_DE.UTF-8    LC_PAPER=de_DE.UTF-8       LC_NAME=C      
           LC_ADDRESS=C               LC_TELEPHONE=C            

[11]
LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       


attached
base packages:

[1]
stats     graphics  grDevices utils     datasets  methods   base     

other
attached packages:

[1]
BiocInstaller_1.20.0


loaded
via a namespace (and not attached):

[1]
tools_3.2.2

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

Bioconductor
version 3.2 (BiocInstaller 1.20.0), ?biocLite for help
chippeakanno installation • 1.4k views
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0
Entering edit mode
@martin-morgan-1513
Last seen 10 weeks ago
United States

Start by addressing the problems associated with the first package that fails to install. You don't provide the details, but probably you need to get XML and RCurl to install, probably by adding as system administrator the system dependencies libxml2-dev and libcurl-opensll-dev

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0
Entering edit mode
@rebeccahalbach-9222
Last seen 5.8 years ago
Netherlands

Thanks a lot. I tried that and now it works.

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