Question

CellCODE not installing

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christopher.clarskon15 ▴ 20

@christopherclarskon15-9965

Last seen 8.7 years ago

Hi,

I am new to R and have check stack overflow for answers but can not find any that sort my installation problem. I am simply trying to install the CellCODE package that I downloaded from http://www.pitt.edu/~mchikina/CellCODE/.

With "install.packages(pkgs="CellCODE",repos=NULL)" I get:

Error in install.packages : type == "both" cannot be used with 'repos = NULL'

Without specifying repos: install.packages(pkgs="CellCODE") I get:

Warning in install.packages :
package ‘cellCODE’ is not available (for R version 3.2.4)

Downloading via github:

"library(devtools)

install_github("mchikina/CellCODE")"

I get:

ERROR: dependency ‘sva’ is not available for package ‘CellCODE’

I'm pretty sure that I have tried everything at the following link: http://stackoverflow.com/questions/25721884/how-should-i-deal-with-package-xxx-is-not-available-for-r-version-x-y-z-wa

But nothing seems to work??

differential gene expression microarray • 2.6k views

ADD COMMENT • link 8.7 years ago christopher.clarskon15 ▴ 20

score 1 · Answer 1 · 2016-03-22

1

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Martin Morgan 25k

@martin-morgan-1513

Last seen 4 months ago

United States

CellCODE is not a Bioconductor package, so this isn't the appropriate forum. But the problem is that your getOption("pkgType") returns "both", and this is used for the the type= argument to install.packages. Instead, provide the argument "source", like install.packages("CellCODE_0.99.0.tar.gz", repos=NULL, type="source"). I updated the answer to reflect the file (CellCODE_0.99.0.tar.gz, rather than CellCODE) downloaded from the package web page.

ADD COMMENT • link 8.7 years ago Martin Morgan 25k

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Oh thank you very much that made a difference but now it is returning the following error:

"Warning: invalid package ‘CellCODE’
Error: ERROR: no packages specified
Warning in install.packages :
installation of package ‘CellCODE’ had non-zero exit status"

ADD REPLY • link 8.7 years ago christopher.clarskon15 ▴ 20

0

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That's not enough of the output to be helpful. EDIT your reply to provide more context.

ADD REPLY • link 8.7 years ago Martin Morgan 25k

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"Warning: invalid package ‘CellCODE’
Error: ERROR: no packages specified
Warning in install.packages :
installation of package ‘CellCODE’ had non-zero exit status"

ADD REPLY • link 8.7 years ago christopher.clarskon15 ▴ 20

0

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This kind of error comes up when the package name or path is not specified correctly, like

> install.packages("CellCODE", repos=NULL, type="source")
Installing package into '/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.3'
(as 'lib' is unspecified)
Bioconductor version 3.3 (BiocInstaller 1.21.3), ?biocLite for help
Warning: invalid package 'CellCODE'
Error: ERROR: no packages specified
Warning message:
In install.packages("CellCODE", repos = NULL, type = "source") :
  installation of package 'CellCODE' had non-zero exit status

versus

> install.packages("CellCODE_0.99.0.tar.gz", repos=NULL, type="source")
Installing package into '/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.3'
(as 'lib' is unspecified)
Bioconductor version 3.3 (BiocInstaller 1.21.3), ?biocLite for help
* installing *source* package 'CellCODE' ...
** R
** data
...

ADD REPLY • link 8.7 years ago Martin Morgan 25k

score 0 · Answer 2 · 2016-03-22

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christopher.clarskon15 ▴ 20

@christopherclarskon15-9965

Last seen 8.7 years ago

http://stackoverflow.com/questions/27893230/installation-of-package-file-path-had-non-zero-exit-status-in-r

http://stackoverflow.com/questions/26169358/how-to-install-tar-gz-r-package-with-non-zero-exit-status

ADD COMMENT • link 8.7 years ago christopher.clarskon15 ▴ 20

0

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You were asked to show your actual output, not link to other irrelevant posts. BTW, the link you post above for the package does not exist. I'd go back to trying install_github(), but first install sva with

install.packages("sva")

Repeat as necessary for any other packages that install_github() complains about.

ADD REPLY • link 8.7 years ago Dan Tenenbaum ★ 8.2k