Hi,
sorry for the delay.
To me it looks like you cannot install any of the packages that are on
CRAN (= 'DEFAULT' in the output). First, try to install 'digest' as
follows:
install.packages("digest")
Verify that it works by loading it, i.e. library("digest"). If it
still doesn't work, please email the r-help mailing list for advice,
because it has nothing to do with aroma.
As soon as you get 'digest' installed, you should be able to install
the rest of the aroma framework, i.e.
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
/Henrik
On Fri, Mar 16, 2012 at 5:44 PM, kritsada katawutpoonphan
<kritkata...@gmail.com> wrote:
> Hi,
> I've got the error. I try to install several time with also restart the R,
> both R and R studio. It seem like previous problem but I try to follow and
> nothing work. I use mac osx 10.7.3 (it seem like most of problem came from
> max! :) ) with updated R. Please anybody help me.
>
> I also try to install some package individually, but it also said something
> like ' package ‘aroma’ is not available (for R version 2.14.2) '.
>
>> source("http://aroma-project.org/hbLite.R";);
>> hbInstall("aroma.affymetrix");
> Installing/updating: CRAN:digest (>= 0.5.1)
> Repositories: CRAN
> Package: digest (>= 0.5.1)
> Tags:
> Updating packages: digest from repository 'DEFAULT'
> 01/01. digest: not available.
> Installing/updating: CRAN:R.methodsS3 (>= 1.2.1)
> Repositories: CRAN
> Package: R.methodsS3 (>= 1.2.1)
> Tags:
> Updating packages: R.methodsS3 from repository 'DEFAULT'
> 01/01. R.methodsS3: not available.
> Installing/updating: CRAN:R.oo (>= 1.8.3)
> Repositories: CRAN
> Package: R.oo (>= 1.8.3)
> Tags:
> Updating packages: R.oo from repository 'DEFAULT'
> 01/01. R.oo: not available.
> Installing/updating: CRAN:R.utils (>= 1.9.9)
> Repositories: CRAN
> Package: R.utils (>= 1.9.9)
> Tags:
> Updating packages: R.utils from repository 'DEFAULT'
> 01/01. R.utils: not available.
> Installing/updating: BRAJU:R.utils (>= 1.9.9)
> Repositories: BRAJU
> Package: R.utils (>= 1.9.9)
> Tags:
> If installation/update of package 'R.utils (>= 1.9.9)' 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 (or
> for the type 'mac.binary.leopard' requested).
> Updating packages: R.utils from repository 'http://www.braju.com/R/repos'
> 01/01. R.utils: v1.11.1, i.e. up to date.
> Installing/updating: CRAN:R.cache (>= 0.5.2)
> Repositories: CRAN
> Package: R.cache (>= 0.5.2)
> Tags:
> Updating packages: R.cache from repository 'DEFAULT'
> 01/01. R.cache: not available.
> Installing/updating: CRAN:R.rsp (>= 0.7.1)
> Repositories: CRAN
> Package: R.rsp (>= 0.7.1)
> Tags:
> Updating packages: R.rsp from repository 'DEFAULT'
> 01/01. R.rsp: not available.
> Installing/updating: BRAJU:R.rsp (>= 0.7.1)
> Repositories: BRAJU
> Package: R.rsp (>= 0.7.1)
> Tags:
> If installation/update of package 'R.rsp (>= 0.7.1)' 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 (or
> for the type 'mac.binary.leopard' requested).
> Updating packages: R.rsp from repository 'http://www.braju.com/R/repos'
> 01/01. R.rsp: v0.7.3, i.e. up to date.
> Installing/updating: CRAN:R.huge (>= 0.3.0)
> Repositories: CRAN
> Package: R.huge (>= 0.3.0)
> Tags:
> Updating packages: R.huge from repository 'DEFAULT'
> 01/01. R.huge: not available.
> Installing/updating: BIOC:affxparser (>= 1.22.0)
> Repositories: BIOC
> Package: affxparser (>= 1.22.0)
> Tags:
> Package up to date: affxparser (>= 1.22.0)
> Installing/updating: CRAN:aroma.apd (>= 0.2.0)
> Repositories: CRAN
> Package: aroma.apd (>= 0.2.0)
> Tags:
> Updating packages: aroma.apd from repository 'DEFAULT'
> 01/01. aroma.apd: not available.
> Installing/updating: CRAN:R.filesets (>= 1.1.4)
> Repositories: CRAN
> Package: R.filesets (>= 1.1.4)
> Tags:
> Updating packages: R.filesets from repository 'DEFAULT'
> 01/01. R.filesets: not available.
> Installing/updating: BRAJU:R.filesets (>= 1.1.4)
> Repositories: BRAJU
> Package: R.filesets (>= 1.1.4)
> Tags:
> If installation/update of package 'R.filesets (>= 1.1.4)' 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 (or
> for the type 'mac.binary.leopard' requested).
> Updating packages: R.filesets from repository 'http://www.braju.com/R/repos'
> 01/01. R.filesets: missing. Installing:
> Warning in install.packages :
> dependency ‘digest’ is not available
> trying URL 'http://www.braju.com/R/repos/R.filesets_1.1.4.tar.gz'
> Content type 'application/x-tar' length 77759 bytes (75 Kb)
> opened URL
> ==================================================
> downloaded 75 Kb
>
> ERROR: dependency ‘digest’ is not available for package ‘R.filesets’
> * removing
> ‘/Library/Frameworks/R.framework/Versions/2.14/Resources/library/R.filesets’
> Warning in install.packages :
> installation of package ‘R.filesets’ had non-zero exit status
>
> The downloaded packages are in
> ‘/private/var/folders/f0/6c0wdh7n68b2cwlw103q3htw0000gn/T/RtmpOpAnGV/downloaded_packages’
> Installing/updating: CRAN:matrixStats (>= 0.4.3)
> Repositories: CRAN
> Package: matrixStats (>= 0.4.3)
> Tags:
> Updating packages: matrixStats from repository 'DEFAULT'
> 01/01. matrixStats: not available.
> Installing/updating: CRAN:RColorBrewer (>= 1.0-5)
> Repositories: CRAN
> Package: RColorBrewer (>= 1.0-5)
> Tags:
> Updating packages: RColorBrewer from repository 'DEFAULT'
> 01/01. RColorBrewer: not available.
> Installing/updating: BIOC:aroma.light (>= 1.22.0)
> Repositories: BIOC
> Package: aroma.light (>= 1.22.0)
> Tags:
> Package up to date: aroma.light (>= 1.22.0)
> Installing/updating: CRAN:aroma.core (>= 2.4.1)
> Repositories: CRAN
> Package: aroma.core (>= 2.4.1)
> Tags:
> Updating packages: aroma.core from repository 'DEFAULT'
> 01/01. aroma.core: not available.
> Installing/updating: BRAJU:aroma.core (>= 2.4.1)
> Repositories: BRAJU
> Package: aroma.core (>= 2.4.1)
> Tags:
> If installation/update of package 'aroma.core (>= 2.4.1)' 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 (or
> for the type 'mac.binary.leopard' requested).
> Updating packages: aroma.core from repository 'http://www.braju.com/R/repos'
> 01/01. aroma.core: missing. Installing:
> Error in install.packages : invalid version specification ‘NA’
> Installing/updating: CRAN:aroma.affymetrix (>= 2.4.0)
> Repositories: CRAN
> Package: aroma.affymetrix (>= 2.4.0)
> Tags:
> Updating packages: aroma.affymetrix from repository 'DEFAULT'
> 01/01. aroma.affymetrix: not available.
> Installing/updating: BRAJU:aroma.affymetrix (>= 2.4.0)
> Repositories: BRAJU
> Package: aroma.affymetrix (>= 2.4.0)
> Tags:
> If installation/update of package 'aroma.affymetrix (>= 2.4.0)' 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
> (or for the type 'mac.binary.leopard' requested).
> Updating packages: aroma.affymetrix from repository
> 'http://www.braju.com/R/repos'
> 01/01. aroma.affymetrix: missing. Installing:
> Error in install.packages : invalid version specification ‘NA’
> Installing/updating: BIOC:DNAcopy (>= 1.24.0)
> Repositories: BIOC
> Package: DNAcopy (>= 1.24.0)
> Tags:
> Package up to date: DNAcopy (>= 1.24.0)
> Installing/updating: BIOC:Biobase (>= 2.9.0)
> Repositories: BIOC
> Package: Biobase (>= 2.9.0)
> Tags:
> Package up to date: Biobase (>= 2.9.0)
> Installing/updating: BIOC:preprocessCore (>= 1.8.0)
> Repositories: BIOC
> Package: preprocessCore (>= 1.8.0)
> Tags:
> Package up to date: preprocessCore (>= 1.8.0)
> Installing/updating: BIOC:gcrma (>= 2.10.0)
> Repositories: BIOC
> Package: gcrma (>= 2.10.0)
> Tags:
> Package up to date: gcrma (>= 2.10.0)
> Installing/updating: BIOC:affyio (>= 1.6.0)
> Repositories: BIOC
> Package: affyio (>= 1.6.0)
> Tags:
> Package up to date: affyio (>= 1.6.0)
> Installing/updating: BIOC:affy (>= 1.24.0)
> Repositories: BIOC
> Package: affy (>= 1.24.0)
> Tags:
> Package up to date: affy (>= 1.24.0)
> Installing/updating: CRAN:aws
> Repositories: CRAN
> Package: aws
> Tags:
> Updating packages: aws from repository 'DEFAULT'
> 01/01. aws: not available.
> Installing/updating: CRAN:gsmoothr (>= 0.1.5)
> Repositories: CRAN
> Package: gsmoothr (>= 0.1.5)
> Tags:
> Updating packages: gsmoothr from repository 'DEFAULT'
> 01/01. gsmoothr: not available.
> Installing/updating: BRAJU:sfit (>= 0.1.9),mac=hasBinary
> Repositories: BRAJU
> Package: sfit (>= 0.1.9)
> Tags: mac=hasBinary
> Installation/update of package 'sfit (>= 0.1.9)', if needed, is enforced to
> be from universal binary version on Macs.
> Updating packages: sfit from repository 'http://www.braju.com/R/repos'
> 01/01. sfit: v0.2.0, i.e. up to date.
> ------------------------------------------------------------
> - Trying to install patches
> ------------------------------------------------------------
> Loading required package: R.cache
> Loading required package: R.methodsS3
> R.methodsS3 v1.2.2 (2010-11-17) successfully loaded. See ?R.methodsS3 for
> help.
> Loading required package: R.oo
> R.oo v1.8.3 (2011-11-01) successfully loaded. See ?R.oo for help.
>
> Attaching package: ‘R.oo’
>
> The following object(s) are masked from ‘package:R.methodsS3’:
>
> throw.default
>
> The following object(s) are masked from ‘package:methods’:
>
> getClass, getClasses, getMethods
>
> The following object(s) are masked from ‘package:base’:
>
> attach, detach, environment, gc, load, save
>
> Loading required package: R.utils
> R.utils v1.11.1 (2012-02-28) successfully loaded. See ?R.utils for help.
>
> Attaching package: ‘R.utils’
>
> The following object(s) are masked _by_ ‘.GlobalEnv’:
>
> installPackages
>
> The following object(s) are masked from ‘package:utils’:
>
> timestamp
>
> The following object(s) are masked from ‘package:base’:
>
> cat, commandArgs, getOption, inherits, isOpen, lapply, parse, remove,
> warnings
>
> R.cache v0.6.1 (2012-01-22) successfully loaded. See ?R.cache for help.
>
> ############################################################
> # #
> # Packages installed/updated. Please restart R. #
> # #
> ############################################################
>
> --
> 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 with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
--
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 with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
