Great.
To summarize: The reported problem only occurs on OSX, and for those
who haven't tried installed matrixStats v0.1.3, the standard
installation procedure will work, that is:
source("http://www.braju.com/R/hbLite.R";);
hbInstall("aroma.affymetrix");
It is only those who have tried to install matrixStats (also v0.1.3)
that was build for R v2.7.x, that need to do:
source("http://www.braju.com/R/hbLite.R";);
installPackages("http://www.braju.com/R/repos/matrixStats_0.1.3.tgz";);
For people still running R v2.7.x on OSX, I suggest to update R (it's
old!), because the provided matrixStat is now build for R v2.8.x.
/Henrik
On Mon, Dec 29, 2008 at 9:23 PM, Lynn Amon <la...@fhcrc.org> wrote:
>
> Hey, that does work!!
> Thanks!
> Lynn
>
>
> Henrik Bengtsson wrote:
>> Hi,
>>
>> for matrixStats, try to force the following installation in a fresh R
>> session:
>>
>> source("http://www.braju.com/R/hbLite.R";);
>> installPackages("http://www.braju.com/R/repos/matrixStats_0.1.3.tgz";);
>>
>> Then restart R, and try:
>>
>> library("matrixStats");
>>
>> If this does not work, I'd suggest to update R to R v2.8.1 (because
>> there's been quite a few updates/bug fixes since October) and retry
>> the above.
>>
>> If it still does not work, what does the following give:
>>
>> packageDescription("matrixStats");
>>
>> Cheers
>>
>> Henrik
>>
>>
>> On Mon, Dec 29, 2008 at 8:56 PM, Lynn Amon <la...@fhcrc.org> wrote:
>>
>>> Hello Henrik,
>>> Thanks for following up on this.
>>>
>>>
>>> I guess I'm having a similar problem as Michael had with EBImage.
>>> If I install this way:
>>>
>>> bash-3.2$ R CMD INSTALL
>>> ~/Desktop/matrixStats_0.1.3_R_i386-apple-darwin8.10.1.tar.gz
>>> * Installing to library '/Users/lamon/Library/R/2.8/library'
>>> * Installing *binary* package 'matrixStats' ...
>>> * DONE (matrixStats)
>>>
>>> and then run R from the command line I have no problems.
>>> But if I use the R console, I get:
>>>
>>> > library(matrixStats)
>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>> unable to load shared library
>>> '/Users/lamon/Library/R/2.8/library/matrixStats/libs/i386/matrixStats.so':
>>>
>>> dlopen(/Users/lamon/Library/R/2.8/library/matrixStats/libs/i386/matrixStats.so,
>>> 6): Library not loaded:
>>> /Library/Frameworks/R.framework/Versions/2.7/Resources/lib/libR.dylib
>>> Referenced from:
>>> /Users/lamon/Library/R/2.8/library/matrixStats/libs/i386/matrixStats.so
>>> Reason: image not found
>>> Error: package/namespace load failed for 'matrixStats'
>>> > sessionInfo()
>>> R version 2.8.0 (2008-10-20)
>>> i386-apple-darwin8.11.1
>>>
>>> locale:
>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>>
>>> attached base packages:
>>> [1] stats graphics grDevices utils datasets methods base
>>>
>>>
>>> This is what happens when I try installing from R console using
>>> install.packages
>>>
>>> >
>>> install.packages("~/Desktop/matrixStats_0.1.3_R_i386-apple-darwin8.10.1.tar.gz",repos=NULL)
>>> Warning in
>>> install.packages("~/Desktop/matrixStats_0.1.3_R_i386-apple-darwin8.10.1.tar.gz",
>>> :
>>> argument 'lib' is missing: using '/Users/lamon/Library/R/2.8/library'
>>> Error in gzfile(file, "r") : cannot open the connection
>>> In addition: Warning message:
>>> In gzfile(file, "r") :
>>> cannot open compressed file
>>> 'matrixStats_0.1.3_R_i386-apple-darwin8.10.1.tar.gz/DESCRIPTION',
>>> probable reason 'No such file or directory'
>>>
>>> And this what happens when I try to install from R console using hbInstall
>>>
>>> > source("http://www.braju.com/R/hbLite.R";);
>>> > hbInstall("aroma.affymetrix");
>>> Installing/updating: CRAN:digest (>= 0.3.1)
>>> Repositories: CRAN
>>> Package: digest (>= 0.3.1)
>>> Tags:
>>> Updating packages: digest from repository 'DEFAULT'
>>> 01/01. digest: v0.3.1, i.e. up to date.
>>> Installing/updating: BRAJU:R.utils (>= 1.1.1)
>>> Repositories: BRAJU
>>> Package: R.utils (>= 1.1.1)
>>> Tags:
>>> If installation/update of package ' R.utils (>= 1.1.1) ' 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.
>>> Updating packages: R.utils from repository 'http://www.braju.com/R/repos'
>>> 01/01. R.utils: v1.1.2, i.e. up to date.
>>> Installing/updating: BRAJU:R.cache (>= 1.0.7)
>>> Repositories: BRAJU
>>> Package: R.cache (>= 1.0.7)
>>> Tags:
>>> If installation/update of package ' R.cache (>= 1.0.7) ' 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: R.cache from repository 'http://www.braju.com/R/repos'
>>> 01/01. R.cache: v0.1.7, i.e. up to date.
>>> Installing/updating: CRAN:R.rsp (>= 0.3.4)
>>> Repositories: CRAN
>>> Package: R.rsp (>= 0.3.4)
>>> Tags:
>>> Updating packages: R.rsp from repository 'DEFAULT'
>>> 01/01. R.rsp: v0.3.4, i.e. up to date.
>>> Installing/updating: BRAJU:R.huge (>= 0.1.6)
>>> Repositories: BRAJU
>>> Package: R.huge (>= 0.1.6)
>>> Tags:
>>> If installation/update of package ' R.huge (>= 0.1.6) ' 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: R.huge from repository 'http://www.braju.com/R/repos'
>>> 01/01. R.huge: v0.1.6, i.e. up to date.
>>> Installing/updating: BRAJU:aroma.apd (>= 0.1.3)
>>> Repositories: BRAJU
>>> Package: aroma.apd (>= 0.1.3)
>>> Tags:
>>> If installation/update of package ' aroma.apd (>= 0.1.3) ' 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.apd from repository 'http://www.braju.com/R/repos'
>>> 01/01. aroma.apd: v0.1.3, i.e. up to date.
>>> Installing/updating: BRAJU:matrixStats (>= 0.1.3),mac=hasBinary
>>> Repositories: BRAJU
>>> Package: matrixStats (>= 0.1.3)
>>> Tags: mac=hasBinary
>>> Installation/update of package ' matrixStats (>= 0.1.3) ', if needed, is
>>> enforced to be from universal binary version on Macs.
>>> Updating packages: matrixStats from repository
>>> 'http://www.braju.com/R/repos'
>>> 01/01. matrixStats: v0.1.3, i.e. up to date.
>>> Installing/updating: BRAJU:aroma.light (>= 1.9.2)
>>> Repositories: BRAJU
>>> Package: aroma.light (>= 1.9.2)
>>> Tags:
>>> If installation/update of package ' aroma.light (>= 1.9.2) ' 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.light from repository
>>> 'http://www.braju.com/R/repos'
>>> 01/01. aroma.light: v1.9.2, i.e. up to date.
>>> 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: BIOC:preprocessCore (>= 1.0.0)
>>> Repositories: BIOC
>>> Package: preprocessCore (>= 1.0.0)
>>> Tags:
>>> Package up to date: preprocessCore (>= 1.0.0)
>>> 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:Biobase (>= 1.16.1)
>>> Repositories: BIOC
>>> Package: Biobase (>= 1.16.1)
>>> Tags:
>>> Package up to date: Biobase (>= 1.16.1)
>>> Installing/updating: BIOC:affy (>= 1.16.0)
>>> Repositories: BIOC
>>> Package: affy (>= 1.16.0)
>>> Tags:
>>> Package up to date: affy (>= 1.16.0)
>>> Installing/updating: BIOC:matchprobes (>= 1.10.0)
>>> Repositories: BIOC
>>> Package: matchprobes (>= 1.10.0)
>>> Tags:
>>> Package up to date: matchprobes (>= 1.10.0)
>>> Installing/updating: CRAN:aws
>>> Repositories: CRAN
>>> Package: aws
>>> Tags:
>>> Updating packages: aws from repository 'DEFAULT'
>>> 01/01. aws: v1.3-3.1, i.e. up to date.
>>> Installing/updating: BIOC:GLAD (>= 1.12.0)
>>> Repositories: BIOC
>>> Package: GLAD (>= 1.12.0)
>>> Tags:
>>> Package up to date: GLAD (>= 1.12.0)
>>> Installing/updating: BIOC:DNAcopy (>= 1.12.0)
>>> Repositories: BIOC
>>> Package: DNAcopy (>= 1.12.0)
>>> Tags:
>>> Package up to date: DNAcopy (>= 1.12.0)
>>> Installing/updating: BRAJU:aroma.core (>= 0.9.6)
>>> Repositories: BRAJU
>>> Package: aroma.core (>= 0.9.6)
>>> Tags:
>>> If installation/update of package ' aroma.core (>= 0.9.6) ' 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.core from repository 'http://www.braju.com/R/repos'
>>> 01/01. aroma.core: v0.9.6, i.e. up to date.
>>> Installing/updating: BRAJU:aroma.affymetrix (>= 0.9.6)
>>> Repositories: BRAJU
>>> Package: aroma.affymetrix (>= 0.9.6)
>>> Tags:
>>> If installation/update of package ' aroma.affymetrix (>= 0.9.6) ' 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: v0.9.6, i.e. up to date.
>>> Installing/updating: BRAJU:sfit (>= 0.1.5),mac=hasBinary
>>> Repositories: BRAJU
>>> Package: sfit (>= 0.1.5)
>>> Tags: mac=hasBinary
>>> Installation/update of package ' sfit (>= 0.1.5) ', 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: v0.1.5, i.e. up to date.
>>> ############################################################
>>> # #
>>> # Packages installed/updated. Please restart R. #
>>> # #
>>> ############################################################
>>>
>>> But after I restart R console, I get this:
>>>
>>> > library(aroma.affymetrix)
>>> Loading required package: R.utils
>>> Loading required package: R.oo
>>> Loading required package: R.methodsS3
>>> R.methodsS3 v1.0.3 (2008-07-02) successfully loaded. See ?R.methodsS3
>>> for help.
>>> R.oo v1.4.6 (2008-08-11) successfully loaded. See ?R.oo for help.
>>> R.utils v1.1.2 (2008-12-27) successfully loaded. See ?R.utils for help.
>>> Loading required package: aroma.core
>>> Loading required package: R.cache
>>> R.cache v0.1.7 (2008-02-27) successfully loaded. See ?R.cache for help.
>>> Loading required package: R.rsp
>>> R.rsp v0.3.4 (2008-03-06) successfully loaded. See ?R.rsp for help.
>>> Type browseRsp() to open the RSP main menu in your browser.
>>> Loading required package: matrixStats
>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>> unable to load shared library
>>> '/Users/lamon/Library/R/2.8/library/matrixStats/libs/i386/matrixStats.so':
>>>
>>> dlopen(/Users/lamon/Library/R/2.8/library/matrixStats/libs/i386/matrixStats.so,
>>> 6): Library not loaded:
>>> /Library/Frameworks/R.framework/Versions/2.7/Resources/lib/libR.dylib
>>> Referenced from:
>>> /Users/lamon/Library/R/2.8/library/matrixStats/libs/i386/matrixStats.so
>>> Reason: image not found
>>> Error: package 'matrixStats' could not be loaded
>>>
>>> Lynn
>>>
>>>
>>> Henrik Bengtsson wrote:
>>>
>>>> FYI, I'm now using rforge.net to build OSX universal binaries for
>>>> matrixStats. Please try again and see if matrixStats now install
>>>> using:
>>>>
>>>> source("http://www.braju.com/R/hbLite.R";);
>>>> hbInstall("aroma.affymetrix");
>>>>
>>>> Please let us know if this works.
>>>>
>>>> FYI, the matrixStats binaries are now build for R v2.8.x; backward
>>>> compatibility to R v2.7.x is not guaranteed/supported, but for now,
>>>> such binaries can be downloaded from:
>>>>
>>>> http://www.braju.com/R/repos/2.7/
>>>>
>>>> /Henrik
>>>>
>>>> On Mon, Dec 15, 2008 at 10:31 PM, Mark Robinson <mrobin...@wehi.edu.au>
>>>> wrote:
>>>>
>>>>
>>>>> Lynn.
>>>>>
>>>>> How did you INSTALL it? It seems to work ok for me ...
>>>>>
>>>>> --------------------------
>>>>> mac1618:~ mrobinson$ R CMD INSTALL matrixStats_0.1.3_R_i386-apple-
>>>>> darwin8.11.1.tar.gz
>>>>> * Installing to library '/Users/mrobinson/Library/R/2.8/library/'
>>>>> * Installing *binary* package 'matrixStats' ...
>>>>> * DONE (matrixStats)
>>>>> mac1618:~ mrobinson$ R
>>>>>
>>>>> R version 2.8.0 (2008-10-20)
>>>>> Copyright (C) 2008 The R Foundation for Statistical Computing
>>>>> ISBN 3-900051-07-0
>>>>>
>>>>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>>>>> You are welcome to redistribute it under certain conditions.
>>>>> Type 'license()' or 'licence()' for distribution details.
>>>>>
>>>>> Natural language support but running in an English locale
>>>>>
>>>>> R is a collaborative project with many contributors.
>>>>> Type 'contributors()' for more information and
>>>>> 'citation()' on how to cite R or R packages in publications.
>>>>>
>>>>> Type 'demo()' for some demos, 'help()' for on-line help, or
>>>>> 'help.start()' for an HTML browser interface to help.
>>>>> Type 'q()' to quit R.
>>>>>
>>>>> > library(matrixStats)
>>>>> > sessionInfo()
>>>>> R version 2.8.0 (2008-10-20)
>>>>> i386-apple-darwin8.11.1
>>>>>
>>>>> locale:
>>>>> en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8
>>>>>
>>>>> attached base packages:
>>>>> [1] stats graphics grDevices utils datasets methods base
>>>>>
>>>>> other attached packages:
>>>>> [1] matrixStats_0.1.3
>>>>> --------------------------
>>>>>
>>>>>
>>>>>
>>>>> On 16/12/2008, at 5:16 AM, Lynn Amon wrote:
>>>>>
>>>>>
>>>>>
>>>>>> These packages won't install because there is no DESCRIPTION file.
>>>>>> Thanks,
>>>>>> Lynn
>>>>>>
>>>>>> Mark Robinson wrote:
>>>>>>
>>>>>>
>>>>>>> Attached.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Cheers,
>>>>>>> Mark
>>>>>>>
>>>>>>> On 15/12/2008, at 9:48 AM, Henrik Bengtsson wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> thanks for reporting this. Could someone out there, please build
>>>>>>>> OSX
>>>>>>>> universal binaries of matrixStats on *R v2.8.x*? You can get the
>>>>>>>> source of latest version by:
>>>>>>>>
>>>>>>>> source("http://www.braju.com/R/hbLite.R";);
>>>>>>>> hbGet("matrixStats", "0.1.3", "tar.gz");
>>>>>>>>
>>>>>>>> For more details, see on how to build a universal binary, see thread
>>>>>>>> 'Could some please build matrixStats_0.1.2.tgz for OSX?' on on July
>>>>>>>> 30, 2008:
>>>>>>>>
>>>>>>>> http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/ae4323a94ce8b494
>>>>>>>>
>>>>>>>> Forward it to the list or me, and I'll make it available on the
>>>>>>>> servers.
>>>>>>>>
>>>>>>>> Cheers
>>>>>>>>
>>>>>>>> Henrik
>>>>>>>>
>>>>>>>> On Thu, Dec 11, 2008 at 2:26 PM, mbaudis <mbau...@gmail.com> wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> while updating to R 2.8, I ran into (up to now) 2 erors:
>>>>>>>>>
>>>>>>>>> 1. matrixstats doesn't load, since it references to R 2.7:
>>>>>>>>>
>>>>>>>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>>>>>>>> unable to load shared library '/Library/Frameworks/R.framework/
>>>>>>>>> Resources/library/matrixStats/libs/i386/matrixStats.so':
>>>>>>>>> dlopen(/Library/Frameworks/R.framework/Resources/library/
>>>>>>>>> matrixStats/
>>>>>>>>> libs/i386/matrixStats.so, 6): Library not loaded: /Library/
>>>>>>>>> Frameworks/
>>>>>>>>> R.framework/Versions/2.7/Resources/lib/libR.dylib
>>>>>>>>> Referenced from: /Library/Frameworks/R.framework/Resources/library/
>>>>>>>>> matrixStats/libs/i386/matrixStats.so
>>>>>>>>> Reason: image not found
>>>>>>>>>
>>>>>>>>> I tried to change the 2.7 to 2.8 (in matrixStats.so). At least
>>>>>>>>> seems
>>>>>>>>> to load ...
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>> [snip]
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> Help & comments appreciated!
>>>>>>>>>
>>>>>>>>> Best,
>>>>>>>>>
>>>>>>>>> Michael.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>> ------------------------------
>>>>>>> Mark Robinson
>>>>>>> Epigenetics Laboratory, Garvan
>>>>>>> Bioinformatics Division, WEHI
>>>>>>> e: m.robin...@garvan.org.au
>>>>>>> e: mrobin...@wehi.edu.au
>>>>>>> p: +61 (0)3 9345 2628
>>>>>>> f: +61 (0)3 9347 0852
>>>>>>> ------------------------------
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>> ------------------------------
>>>>> Mark Robinson
>>>>> Epigenetics Laboratory, Garvan
>>>>> Bioinformatics Division, WEHI
>>>>> e: m.robin...@garvan.org.au
>>>>> e: mrobin...@wehi.edu.au
>>>>> p: +61 (0)3 9345 2628
>>>>> f: +61 (0)3 9347 0852
>>>>> ------------------------------
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>> >>
>>>
>>>
>>
>> >>
>>
>
> --~--~---------~--~----~------------~-------~--~----~
> 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
> -~----------~----~----~----~------~----~------~--~---
>
>
--~--~---------~--~----~------------~-------~--~----~
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
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-~----------~----~----~----~------~----~------~--~---
