I?m having trouble installing the SPOT R package for microarray image analysis.
I?m awaiting a response from the packager developer, but wanted to see if anyone
here has successfully used CSIRO?s SPOT software.
I?ve been following the developer?s "Spot Installation Instructions for
Linux and Unix"
<http://www.hca-vision.com/Spot_Documentation/Spot_Install_UNIX.pdf>:
- Downloaded the Spot package (Spot_3.2_x86_64.tar) to my hard disk.
- Started R:
R version 3.2.1 (2015-06-18) -- "World-Famous Astronaut"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)
?
- As instructed, executed the command:
>install.packages("Spot_3.2_x86_64.tar.gz", CRAN = NULL)
This produced:
Warning in install.packages :
package ?Spot_3.2_x86_64.tar.gz? is not available (for R version 3.2.1)
Presuming that R was looking for the package in a repository and not my hard
disk, I modified the command:
> install.packages("~/Downloads/Spot_3.2_x86_64.tar.gz", repos
= NULL, type = "source")
This produced:
* installing *source* package ?Spot? ...
ERROR: a 'NAMESPACE' file is required
* removing
?/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Spot?
Warning in install.packages :
installation of package ?/Users/wmorgan/Downloads/Spot_3.2_x86_64.tar.gz?
had non-zero exit status
(I also tried type = ?mac.binary? or ?mac.binary.maverick?, but this only
produced an error message that it's is not a mac binary file.)
William R. Morgan, Ph.D.
The College of Wooster
Department of Biology
Wooster, OH 44691
On 21/07/2015 11:43 AM, William Morgan wrote:> I?m having trouble installing the SPOT R package for microarray image analysis. I?m awaiting a response from the packager developer, but wanted to see if anyone here has successfully used CSIRO?s SPOT software. > > I?ve been following the developer?s "Spot Installation Instructions for Linux and Unix" <http://www.hca-vision.com/Spot_Documentation/Spot_Install_UNIX.pdf>: > > - Downloaded the Spot package (Spot_3.2_x86_64.tar) to my hard disk. > > - Started R: > > R version 3.2.1 (2015-06-18) -- "World-Famous Astronaut" > Copyright (C) 2015 The R Foundation for Statistical Computing > Platform: x86_64-apple-darwin13.4.0 (64-bit) > ? > > - As instructed, executed the command: > >install.packages("Spot_3.2_x86_64.tar.gz", CRAN = NULL) > > This produced: > Warning in install.packages : > package ?Spot_3.2_x86_64.tar.gz? is not available (for R version 3.2.1) > > Presuming that R was looking for the package in a repository and not my hard disk, I modified the command: > > install.packages("~/Downloads/Spot_3.2_x86_64.tar.gz", repos = NULL, type = "source") > > This produced: > * installing *source* package ?Spot? ... > ERROR: a 'NAMESPACE' file is required > * removing ?/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Spot? > Warning in install.packages : > installation of package ?/Users/wmorgan/Downloads/Spot_3.2_x86_64.tar.gz? had non-zero exit statusNAMESPACE files have been required in R since R 3.0.0. If that package doesn't have one, it sounds as though it hasn't been actively maintained. Will definitely be a case of "some assembly required", not to mention the usual "use at your own risk". Duncan Murdoch> > (I also tried type = ?mac.binary? or ?mac.binary.maverick?, but this only produced an error message that it's is not a mac binary file.) > > > William R. Morgan, Ph.D. > The College of Wooster > Department of Biology > Wooster, OH 44691 > > > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >
On Jul 21, 2015, at 8:43 AM, William Morgan wrote:> I?m having trouble installing the SPOT R package for microarray image analysis. I?m awaiting a response from the packager developer, but wanted to see if anyone here has successfully used CSIRO?s SPOT software. > > I?ve been following the developer?s "Spot Installation Instructions for Linux and Unix" <http://www.hca-vision.com/Spot_Documentation/Spot_Install_UNIX.pdf>: > > - Downloaded the Spot package (Spot_3.2_x86_64.tar) to my hard disk. > > - Started R: > > R version 3.2.1 (2015-06-18) -- "World-Famous Astronaut" > Copyright (C) 2015 The R Foundation for Statistical Computing > Platform: x86_64-apple-darwin13.4.0 (64-bit) > ? > > - As instructed, executed the command: >> install.packages("Spot_3.2_x86_64.tar.gz", CRAN = NULL) > > This produced: > Warning in install.packages : > package ?Spot_3.2_x86_64.tar.gz? is not available (for R version 3.2.1) > > Presuming that R was looking for the package in a repository and not my hard disk, I modified the command: >> install.packages("~/Downloads/Spot_3.2_x86_64.tar.gz", repos = NULL, type = "source") > > This produced: > * installing *source* package ?Spot? ... > ERROR: a 'NAMESPACE' file is requiredIf your package does not have a NAMESPACE (which was acceptable several R versions ago) then you either need to revert to an older R from the same era as this was written, or you need to edit the source of the package to create a NAMESPACE. -- David.> * removing ?/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Spot? > Warning in install.packages : > installation of package ?/Users/wmorgan/Downloads/Spot_3.2_x86_64.tar.gz? had non-zero exit status > > (I also tried type = ?mac.binary? or ?mac.binary.maverick?, but this only produced an error message that it's is not a mac binary file.) > >David Winsemius Alameda, CA, USA