nolanlab/spade — Issue #15: Unable to load SPADE
Author: cblish
Created: 2011-11-21 23:59:57+00:00
State: open

For some reason, can't seem to get SPADE loaded on a MAC OS X, despite following instructions today (11/21/11). We see last update is 4 days ago by esimmons. Below is the R code and where we are getting stuck. WE have tried a number of variations on the file names (removing the period, adding tilda, removing asterisks, resetting directory, using instructions in Issue 6etc.), in hopes that the directory will read. Nothing has worked. We'd greatly appreciate any help.

[Workspace restored from /Users/catherine/.RData]
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> source("http://bioconductor.org/biocLite.R")
BioC_mirror = http://bioconductor.org
Change using chooseBioCmirror().
> biocLite(c("igraph","flowCore"))
Using R version 2.13.1, biocinstall version 2.8.4.
Installing Bioconductor version 2.8 packages:
[1] "igraph" "flowCore"
Please wait...

Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13
trying URL 'http://cran.fhcrc.org/bin/macosx/leopard/contrib/2.13/igraph_0.5.5-3.tgz'
Content type 'application/x-gzip' length 6798880 bytes (6.5 Mb)
opened URL
==================================================
downloaded 6.5 Mb

trying URL 'http://bioconductor.org/packages/2.8/bioc/bin/macosx/leopard/contrib/2.13/flowCore_1.18.0.tgz'
Content type 'application/x-gzip' length 10996284 bytes (10.5 Mb)
opened URL
==================================================
downloaded 10.5 Mb

The downloaded packages are in
/var/folders/lA/lAgSLBR62RWRtU+1Ytx9pU+++TM/-Tmp-//Rtmp50PX4s/downloaded_packages
> install.packages("./**spade_0.3.3.tgz**",repos=NULL)
tar: Error opening archive: Failed to open './**spade_0.3.3.tgz**': No such file or directory
Warning messages:
1: 'tar' returned non-zero exit code 1
2: In file.rename(file.path(tmpDir, pkgname), instPath) :
cannot rename file '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/file274c9178/**spade' to '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/**spade', reason 'No such file or directory'
3: unable to move temporary installation '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/file274c9178/**spade' to '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/**spade'
> install.packages("./**spade_0.3.3.tgz**",repos=NULL)
tar: Error opening archive: Failed to open './**spade_0.3.3.tgz**': No such file or directory
Warning messages:
1: 'tar' returned non-zero exit code 1
2: In file.rename(file.path(tmpDir, pkgname), instPath) :
cannot rename file '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/file13e27170/**spade' to '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/**spade', reason 'No such file or directory'
3: unable to move temporary installation '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/file13e27170/**spade' to '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/**spade'
> install.packages(".spade_0.3.3.tgz",repos=NULL)
tar: Error opening archive: Failed to open '.spade_0.3.3.tgz': No such file or directory
Warning messages:
1: 'tar' returned non-zero exit code 1
2: In file.rename(file.path(tmpDir, pkgname), instPath) :
cannot rename file '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/file77857a42/.spade' to '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/.spade', reason 'No such file or directory'
3: unable to move temporary installation '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/file77857a42/.spade' to '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/.spade'