Hey Henrik.
If I run those commands, they work for me, but only because I already have
digest, etc. installed. In order for it to give an error on my R 2.9.1,
I've removed a few packages (e.g. digest) from my default install
directory (/Users/mrobinson/Library/R/2.9/library/), so that it requires
an installation of those dependencies. The error for me appears to be
related to not finding the digest package. See below.
Does that help?
Mark
-------------------------------
> source("http://www.braju.com/R/hbLite.R";);
> hbLite("R.filesets");
Using repository: http://www.braju.com/R/repos
Identified packages to be processed: utils, R.methodsS3, methods, R.oo,
R.utils, digest, R.filesets
Installing external packages...
Packages: utils, methods, digest
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
Updating packages: utils, methods, digest
01/03. utils: not available.
02/03. methods: not available.
03/03. digest: missing. Installing:
<simpleError in .find_bundles(available): subscript out of bounds>
Installing external packages...done
Installing braju.com packages...
Packages: R.methodsS3, R.oo, R.utils, R.filesets
Detected R option pkgType="mac.binary", which is not available. Enforcing
installation from source instead for packages: R.methodsS3, R.oo, R.utils,
R.filesets
Updating packages: R.methodsS3, R.oo, R.utils, R.filesets
01/04. R.methodsS3: v1.0.3, i.e. up to date.
02/04. R.oo: v1.4.8, i.e. up to date.
03/04. R.utils: v1.1.7, i.e. up to date.
04/04. R.filesets: missing. Installing:
Warning: dependency ‘digest’ is not available
trying URL 'http://www.braju.com/R/repos/R.filesets_0.5.3.tar.gz'
Content type 'application/x-tar' length 35408 bytes (34 Kb)
opened URL
==================================================
downloaded 34 Kb
* Installing *source* package ‘R.filesets’ ...
** R
** inst
** preparing package for lazy loading
R.methodsS3 v1.0.3 (2008-07-02) successfully loaded. See ?R.methodsS3 for
help.
R.oo v1.4.8 (2009-05-18) successfully loaded. See ?R.oo for help.
R.utils v1.1.7 (2009-05-30) successfully loaded. See ?R.utils for help.
Error : package 'digest' required by 'R.filesets' could not be found
ERROR: lazy loading failed for package ‘R.filesets’
* Removing ‘/Users/mrobinson/Library/R/2.9/library/R.filesets’
The downloaded packages are in
‘/private/var/folders/8T/8TpdlpGXGzyAaNQm0Wp-zk++mHo/-Tmp-/Rtmp7MMjod/downloaded_packages’
Installing braju.com packages...done
Warning messages:
1: In hbLite("R.filesets") :
Detected R option pkgType="mac.binary", which is not available.
Enforcing installation from source instead for packages: R.methodsS3,
R.oo, R.utils, R.filesets
2: In install.packages(pkg, lib = lib, ..., available = available) :
installation of package 'R.filesets' had non-zero exit status
> sessionInfo()
R version 2.9.1 (2009-06-26)
i386-apple-darwin8.11.1
locale:
en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tcltk_2.9.1 tools_2.9.1
-------------------------------
>
> Hi,
>
> this seems to be an OSX issue and I cannot reproduce it myself. From
> the error message:
>
> <simpleError: invalid version specification 1.1.3NA>
>
> it looks like it there are some parsing errors when parsing version
> numbers in the PACKAGES file on the repository server, but not sure.
>
> See if this is only a problem with the aroma.affymetrix package or
> with all packages. Can you install individual packages from the
> braju.com server by:
>
> source("http://www.braju.com/R/hbLite.R";);
> hbLite("R.filesets");
> library("R.filesets");
>
> Q1) Does this work?
>
> hbLite("aroma.core");
> library("aroma.core");
>
> Q2) Does this work?
>
> hbLite("aroma.affymetrix");
> library("aroma.affymetrix");
>
> Q3) Does this work?
>
> Mark (Robinson), you mentioned this problem a few weeks ago. Can you
> help me troubleshoot this one?
>
> /Henrik
>
> 2009/7/31 mbaudis <mbau...@gmail.com>:
>>
>> Dear Henrik,
>>
>> currently, I have an installation problem after upgrading to R 2.9.1
>> (Mac OS X 10.5.7):
>>
>> ...
>> everything fine up to here
>> ...
>>
>> Installing/updating: CRAN:aroma.core (>= 1.1.0)
>> Repositories: CRAN
>> Package: aroma.core (>= 1.1.0)
>> Tags:
>> Updating packages: aroma.core from repository 'DEFAULT'
>> 01/01. aroma.core: not available.
>> Installing/updating: CRAN:matrixStats (>= 0.1.4)
>> Repositories: CRAN
>> Package: matrixStats (>= 0.1.4)
>> Tags:
>> Updating packages: matrixStats from repository 'DEFAULT'
>> 01/01. matrixStats: v0.1.6, i.e. up to date.
>> Installing/updating: CRAN:RColorBrewer
>> Repositories: CRAN
>> Package: RColorBrewer
>> Tags:
>> Updating packages: RColorBrewer from repository 'DEFAULT'
>> 01/01. RColorBrewer: v1.0-2, i.e. up to date.
>> Installing/updating: BIOC:aroma.light (>= 1.12.2)
>> Repositories: BIOC
>> Package: aroma.light (>= 1.12.2)
>> Tags:
>> Package up to date: aroma.light (>= 1.12.2)
>> Installing/updating: BIOC:affxparser (>= 1.13.8)
>> Repositories: BIOC
>> Package: affxparser (>= 1.13.8)
>> Tags:
>> Package up to date: affxparser (>= 1.13.8)
>> Installing/updating: BRAJU:aroma.affymetrix (>= 1.1.0)
>> Repositories: BRAJU
>> Package: aroma.affymetrix (>= 1.1.0)
>> Tags:
>> If installation/update of package ' aroma.affymetrix (>= 1.1.0) ' is
>> needed, it is enforced to be from source. The most likely reason for
>> this is that the repository does currently not contain a prebuild
>> binary version for Mac.
>> Updating packages: aroma.affymetrix from repository 'http://
>> www.braju.com/R/repos'
>> 01/01. aroma.affymetrix: missing. Installing:
>> <simpleError: invalid version specification 1.1.3NA>
>> ...
>>
>> So, it seems there is, currently, no fitting source package?
>>
>> Best,
>>
>> Michael.
>> >
>>
>
> >
>
--~--~---------~--~----~------------~-------~--~----~
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe from this group, send email to
aroma-affymetrix-unsubscr...@googlegroups.com
For more options, visit this group at
http://groups.google.com/group/aroma-affymetrix?hl=en
-~----------~----~----~----~------~----~------~--~---
