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Question: Error when installing package gageData
0
gravatar for colaneri
8 months ago by
colaneri30
United States
colaneri30 wrote:

Hi I am trying to install the gage data package from bioconductor:

 

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

However I got this error during installation (see below). I have not idea how to solve this problem. Any suggestion?

ALe

##############################################################################

Pathview is an open source software package distributed under GNU General

Public License version 3 (GPLv3). Details of GPLv3 is available at

http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to

formally cite the original Pathview paper (not just mention it) in publications

or products. For details, do citation("pathview") within R.

 

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG

license agreement (details at http://www.kegg.jp/kegg/legal.html).

##############################################################################

Error in library("gageData") : there is no package called ‘gageData’

Execution halted

 

The downloaded source packages are in

‘/private/var/folders/83/rzpdd5ts59xddl4ql9_jv1zw0000gp/T/Rtmpcy1kZi/downloaded_packages’

Warning messages:

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

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

2: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :

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

3: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :

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

4: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :

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

5: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :

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

 

 

ADD COMMENTlink modified 8 months ago • written 8 months ago by colaneri30
0
gravatar for Luo Weijun
8 months ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:

This is not a gageData specific problem, the installation of other packages failed too in your output.

Your code is not consistent with the output either. You code only install gageData, but output shows that other packages were also being installed, and pathview package was loaded somehow.

ADD COMMENTlink written 8 months ago by Luo Weijun1.4k
0
gravatar for colaneri
8 months ago by
colaneri30
United States
colaneri30 wrote:

Dear Luo

Thanks for the answer, I have also noticed what you are saying but unfortunately that is what got after running the installation of gageData this is what I got once I run:

biocLite("gageData")

I did install other packages (like gage in self) today and I have not problem. Any idea?

 

 

ADD COMMENTlink written 8 months ago by colaneri30
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