[Rsiena-help] Error message selecting actors
Maarten Van Zalk
maartenvanzalk at gmail.com
Tue Mar 9 19:49:30 CET 2010
Dear ruth,
this worked perfectly: I got lost between R the program and RSiena the
package: I also found very helpful MAC FAQ's.
Thank you!
Kind regards,
Maarten
On Mar 9, 2010, at 19:30 , Ruth M. Ripley wrote:
> Dear Maarten,
>
> R needs to be updated outside R. You can just download and install
> the new
> version (just double click on the installer, or remove the old one
> first,
> by removing to Trash the application R-app in Appplications and the R
> framework in /Library/Frameworks.
>
> There are some more details about it in the R for MaC FAQ, but I am
> not
> sure what they mean(I know rather little about Macs!), so just let
> me know
> if you have problems and I'll try to help. I don't have an old
> version of
> R on my Mac to practise on, but could probably install one if I need
> to!
>
> Regards,
>
> Ruth
> --
> Ruth M. Ripley, Email:ruth at stats.ox.ac.uk
> Dept. of Statistics, http://www.stats.ox.ac.uk/~ruth/
> University of Oxford, Tel: 01865 282851
> 1 South Parks Road, Oxford OX1 3TG, UK Fax: 01865 272595
>
>
> On Tue, 9 Mar 2010, Maarten Van Zalk wrote:
>
>> Dear Ruth,
>>
>> I keep getting errors when I try to install on my mac.
>>
>> My current version is 1.0.5. I have all administration rights as this
>> is my own bought computer, so this is not the problem.
>>
>>
>> This what I get when I try to update within R:
>>
>> trying URL 'http://ftp.sunet.se/pub/lang/CRAN/bin/macosx/universal/contrib/2.9/VR_7.2-49.tgz'
>> Content type 'application/x-gzip' length 985090 bytes (962 Kb)
>> opened URL
>> ==================================================
>> downloaded 962 Kb
>>
>> trying URL 'http://ftp.sunet.se/pub/lang/CRAN/bin/macosx/universal/contrib/2.9/Matrix_0.999375-31.tgz'
>> Content type 'application/x-gzip' length 2826531 bytes (2.7 Mb)
>> opened URL
>> ==================================================
>> downloaded 2.7 Mb
>>
>> trying URL 'http://ftp.sunet.se/pub/lang/CRAN/bin/macosx/universal/contrib/2.9/boot_1.2-41.tgz'
>> Content type 'application/x-gzip' length 448262 bytes (437 Kb)
>> opened URL
>> ==================================================
>> downloaded 437 Kb
>>
>> trying URL 'http://ftp.sunet.se/pub/lang/CRAN/bin/macosx/universal/contrib/2.9/class_7.3-1.tgz'
>> Content type 'application/x-gzip' length 51893 bytes (50 Kb)
>> opened URL
>> ==================================================
>> downloaded 50 Kb
>>
>> trying URL 'http://ftp.sunet.se/pub/lang/CRAN/bin/macosx/universal/contrib/2.9/cluster_1.12.1.tgz'
>> Content type 'application/x-gzip' length 333414 bytes (325 Kb)
>> opened URL
>> ==================================================
>> downloaded 325 Kb
>>
>> trying URL 'http://ftp.sunet.se/pub/lang/CRAN/bin/macosx/universal/contrib/2.9/foreign_0.8-38.tgz'
>> Content type 'application/x-gzip' length 204134 bytes (199 Kb)
>> opened URL
>> ==================================================
>> downloaded 199 Kb
>>
>> trying URL 'http://ftp.sunet.se/pub/lang/CRAN/bin/macosx/universal/contrib/2.9/lattice_0.17-26.tgz'
>> Content type 'application/x-gzip' length 610668 bytes (596 Kb)
>> opened URL
>> ==================================================
>> downloaded 596 Kb
>>
>> trying URL 'http://ftp.sunet.se/pub/lang/CRAN/bin/macosx/universal/contrib/2.9/mgcv_1.5-6.tgz'
>> Content type 'application/x-gzip' length 817083 bytes (797 Kb)
>> opened URL
>> ==================================================
>> downloaded 797 Kb
>>
>> trying URL 'http://ftp.sunet.se/pub/lang/CRAN/bin/macosx/universal/contrib/2.9/nlme_3.1-96.tgz'
>> Content type 'application/x-gzip' length 1249422 bytes (1.2 Mb)
>> opened URL
>> ==================================================
>> downloaded 1.2 Mb
>>
>> trying URL 'http://ftp.sunet.se/pub/lang/CRAN/bin/macosx/universal/contrib/2.9/nnet_7.3-1.tgz'
>> Content type 'application/x-gzip' length 61916 bytes (60 Kb)
>> opened URL
>> ==================================================
>> downloaded 60 Kb
>>
>> trying URL 'http://ftp.sunet.se/pub/lang/CRAN/bin/macosx/universal/contrib/2.9/spatial_7.3-1.tgz'
>> Content type 'application/x-gzip' length 84723 bytes (82 Kb)
>> opened URL
>> ==================================================
>> downloaded 82 Kb
>>
>>
>> The downloaded packages are in
>> /var/folders/fp/fp69YKRoHIqhZmwhT4VqxE+++TI/-Tmp-//RtmpBsgWSv/
>> downloaded_packages
>> trying URL 'http://ftp.sunet.se/pub/lang/CRAN/src/contrib/RSiena_1.0.9.tar.gz'
>> Content type 'application/x-gzip' length 848088 bytes (828 Kb)
>> opened URL
>> ==================================================
>> downloaded 828 Kb
>>
>> During startup - Warning messages:
>> 1: Setting LC_CTYPE failed, using "C"
>> 2: Setting LC_TIME failed, using "C"
>> 3: Setting LC_MESSAGES failed, using "C"
>> * Installing *source* package 'RSiena' ...
>> ** libs
>> ** arch - i386
>> sh: make: command not found
>> ERROR: compilation failed for package 'RSiena'
>> * Removing '/Library/Frameworks/R.framework/Versions/2.9/Resources/
>> library/RSiena'
>> * Restoring previous '/Library/Frameworks/R.framework/Versions/2.9/
>> Resources/library/RSiena'
>>
>> The downloaded packages are in
>> '/private/var/folders/fp/fp69YKRoHIqhZmwhT4VqxE+++TI/-Tmp-/
>> RtmpBsgWSv/
>> downloaded_packages'
>> also installing the dependency 'xtable'
>>
>> trying URL 'http://ftp.sunet.se/pub/lang/CRAN/src/contrib/xtable_1.5-6.tar.gz'
>> Content type 'application/x-gzip' length 142697 bytes (139 Kb)
>> opened URL
>> ==================================================
>> downloaded 139 Kb
>>
>> trying URL 'http://ftp.sunet.se/pub/lang/CRAN/src/contrib/Matrix_0.999375-37.tar.gz'
>> Content type 'application/x-gzip' length 2587244 bytes (2.5 Mb)
>> opened URL
>> ==================================================
>> downloaded 2.5 Mb
>>
>> trying URL 'http://ftp.sunet.se/pub/lang/CRAN/src/contrib/RSiena_1.0.9.tar.gz'
>> Content type 'application/x-gzip' length 848088 bytes (828 Kb)
>> opened URL
>> ==================================================
>> downloaded 828 Kb
>>
>> trying URL 'http://ftp.sunet.se/pub/lang/CRAN/src/contrib/foreign_0.8-39.tar.gz'
>> Content type 'application/x-gzip' length 330828 bytes (323 Kb)
>> opened URL
>> ==================================================
>> downloaded 323 Kb
>>
>> trying URL 'http://ftp.sunet.se/pub/lang/CRAN/src/contrib/mgcv_1.6-1.tar.gz'
>> Content type 'application/x-gzip' length 395943 bytes (386 Kb)
>> opened URL
>> ==================================================
>> downloaded 386 Kb
>>
>> trying URL 'http://ftp.sunet.se/pub/lang/CRAN/src/contrib/survival_2.35-8.tar.gz'
>> Content type 'application/x-gzip' length 672616 bytes (656 Kb)
>> opened URL
>> ==================================================
>> downloaded 656 Kb
>>
>> During startup - Warning messages:
>> 1: Setting LC_CTYPE failed, using "C"
>> 2: Setting LC_TIME failed, using "C"
>> 3: Setting LC_MESSAGES failed, using "C"
>> * Installing *source* package 'xtable' ...
>> ** R
>> ** data
>> ** inst
>> ** preparing package for lazy loading
>> ** help
>> *** installing help indices
>> perl: warning: Setting locale failed.
>> perl: warning: Please check that your locale settings:
>> LC_ALL = (unset),
>> LC_COLLATE = "C",
>> LANG = "en_SE.UTF-8"
>> are supported and installed on your system.
>> perl: warning: Falling back to the standard locale ("C").
>>>>> Building/Updating help pages for package 'xtable'
>> Formats: text html latex example
>> print.xtable text html latex
>> string text html latex
>> table.attributes text html latex
>> tli text html latex
>> xtable text html latex example
>> ** building package indices ...
>> * DONE (xtable)
>> During startup - Warning messages:
>> 1: Setting LC_CTYPE failed, using "C"
>> 2: Setting LC_TIME failed, using "C"
>> 3: Setting LC_MESSAGES failed, using "C"
>> * Installing *source* package 'Matrix' ...
>> ** libs
>> ** arch - i386
>> sh: make: command not found
>> ERROR: compilation failed for package 'Matrix'
>> * Removing '/Library/Frameworks/R.framework/Versions/2.9/Resources/
>> library/Matrix'
>> * Restoring previous '/Library/Frameworks/R.framework/Versions/2.9/
>> Resources/library/Matrix'
>> During startup - Warning messages:
>> 1: Setting LC_CTYPE failed, using "C"
>> 2: Setting LC_TIME failed, using "C"
>> 3: Setting LC_MESSAGES failed, using "C"
>> * Installing *source* package 'foreign' ...
>> /Library/Frameworks/R.framework/Resources/bin/config: line 143: make:
>> command not found
>> /Library/Frameworks/R.framework/Resources/bin/config: line 144: make:
>> command not found
>> /Library/Frameworks/R.framework/Resources/bin/config: line 220: make:
>> command not found
>> /Library/Frameworks/R.framework/Resources/bin/config: line 143: make:
>> command not found
>> checking for gcc... no
>> checking for cc... no
>> checking for cc... no
>> checking for cl... no
>> /Library/Frameworks/R.framework/Resources/bin/config: line 144: make:
>> command not found
>> /Library/Frameworks/R.framework/Resources/bin/config: line 220: make:
>> command not found
>> configure: error: no acceptable C compiler found in $PATH
>> See `config.log' for more details.
>> ERROR: configuration failed for package 'foreign'
>> * Removing '/Library/Frameworks/R.framework/Versions/2.9/Resources/
>> library/foreign'
>> * Restoring previous '/Library/Frameworks/R.framework/Versions/2.9/
>> Resources/library/foreign'
>> During startup - Warning messages:
>> 1: Setting LC_CTYPE failed, using "C"
>> 2: Setting LC_TIME failed, using "C"
>> 3: Setting LC_MESSAGES failed, using "C"
>> * Installing *source* package 'survival' ...
>> ** libs
>> ** arch - i386
>> sh: make: command not found
>> ERROR: compilation failed for package 'survival'
>> * Removing '/Library/Frameworks/R.framework/Versions/2.9/Resources/
>> library/survival'
>> * Restoring previous '/Library/Frameworks/R.framework/Versions/2.9/
>> Resources/library/survival'
>> During startup - Warning messages:
>> 1: Setting LC_CTYPE failed, using "C"
>> 2: Setting LC_TIME failed, using "C"
>> 3: Setting LC_MESSAGES failed, using "C"
>> * Installing *source* package 'RSiena' ...
>> ** libs
>> ** arch - i386
>> sh: make: command not found
>> ERROR: compilation failed for package 'RSiena'
>> * Removing '/Library/Frameworks/R.framework/Versions/2.9/Resources/
>> library/RSiena'
>> * Restoring previous '/Library/Frameworks/R.framework/Versions/2.9/
>> Resources/library/RSiena'
>> During startup - Warning messages:
>> 1: Setting LC_CTYPE failed, using "C"
>> 2: Setting LC_TIME failed, using "C"
>> 3: Setting LC_MESSAGES failed, using "C"
>> * Installing *source* package 'mgcv' ...
>> ** libs
>> ** arch - i386
>> sh: make: command not found
>> ERROR: compilation failed for package 'mgcv'
>> * Removing '/Library/Frameworks/R.framework/Versions/2.9/Resources/
>> library/mgcv'
>> * Restoring previous '/Library/Frameworks/R.framework/Versions/2.9/
>> Resources/library/mgcv'
>>
>> The downloaded packages are in
>> '/private/var/folders/fp/fp69YKRoHIqhZmwhT4VqxE+++TI/-Tmp-/
>> RtmpBsgWSv/
>> downloaded_packages'
>>>
>>
>>
>> As you can see, I get some errors referring to the C drive (which
>> does
>> not exist on the MAC). Does anytone else have a mac and has this
>> problem?
>>
>> Kind regards,
>>
>> Maarten
>>
>>
>>
>>
>>
>>
>>
>> On Mar 8, 2010, at 17:15 , Ruth M. Ripley wrote:
>>
>>> Dear Maarten,
>>>
>>> Are you only wanting to include 14 actors?
>>>
>>> I am not sure what the problem is. If you want to save the workspace
>>> and send me a copy, I will look at it. (There is an option on the
>>> menu to save workspaces.) And confirm which version of R and RSiena
>>> you are using.
>>>
>>> Regards,
>>>
>>> Ruth
>>> --
>>> Ruth M. Ripley, Email:ruth at stats.ox.ac.uk
>>> Dept. of Statistics, http://www.stats.ox.ac.uk/~ruth/
>>> University of Oxford, Tel: 01865 282851
>>> 1 South Parks Road, Oxford OX1 3TG, UK Fax: 01865 272595
>>>
>>> On Mon, 8 Mar 2010, Maarten Van Zalk wrote:
>>>
>>>> Dear Ruth,
>>>>
>>>> I tried the 'sum' command, and now run into the following problem:
>>>>
>>>>
>>>>> sum(use)
>>>> [1] 14
>>>>> friendship <- sienaNet(array(c(net.w1[use, use], net.w2[use,
>>>>> use],net.w3[use, use]),dim=c(sum(use), sum(use), 3)))
>>>>> mydata <- sienaDataCreate(friendship,shy,self,depr)
>>>>> myeff <- getEffects(mydata)
>>>> Error in rep(shortnames, times = (1 + as.numeric(endowment))) :
>>>> invalid 'times' argument
>>>>
>>>> Is there something I am missing?
>>>>
>>>> Kind regards,
>>>>
>>>> Maarten
>>>>
>>>>
>>>> On Mar 8, 2010, at 15:55 , Ruth M. Ripley wrote:
>>>>
>>>>> Dear Maarten,
>>>>> If the 796 is all the actors, you need to reduce it to the number
>>>>> you
>>>>> actually include. This can be found as sum(use):
>>>>> friendship <- sienaNet(array(c(net.w1[use, use], net.w2[use, use],
>>>>>> net.w3[use, use]),dim=c(sum(use), sum(use), 3)))
>>>>> Regards,
>>>>> Ruth
>>>>> --
>>>>> Ruth M. Ripley, Email:ruth at stats.ox.ac.uk
>>>>> Dept. of Statistics, http://www.stats.ox.ac.uk/~ruth/
>>>>> University of Oxford, Tel: 01865 282851
>>>>> 1 South Parks Road, Oxford OX1 3TG, UK Fax: 01865 272595
>>>>> On Mon, 8 Mar 2010, Maarten Van Zalk wrote:
>>>>>> Dear ruth,
>>>>>> An additional question on selecting specific actors:
>>>>>> As I run the following syntax, I get the error:
>>>>>>> library(RSiena)
>>>>>>> library(snow)
>>>>>>> library(rlecuyer)
>>>>>>> setwd('/Users/maartenselfhout/Desktop/CrowdStudy/justin')
>>>>>>> net.w1 <- as.matrix(read.table("W3SIENA.dat"))
>>>>>>> net.w2 <- as.matrix(read.table("W4SIENA.dat"))
>>>>>>> net.w3 <- as.matrix(read.table("W5SIENA.dat"))
>>>>>>> rad <- as.matrix(read.table("radical.dat"))
>>>>>>> depr <- as.matrix(read.table("depress.dat"))
>>>>>>> self <- as.matrix(read.table("selfesteem.dat"))
>>>>>>> shy <- as.matrix(read.table("shy.dat"))
>>>>>>> net.w1[net.w1 %in% c(6,9)] <- NA
>>>>>>> net.w2[net.w2 %in% c(6,9)] <- NA
>>>>>>> net.w3[net.w3 %in% c(6,9)] <- NA
>>>>>>> rad[rad %in% c(99)] <- NA
>>>>>>> depr[depr %in% c(99)] <- NA
>>>>>>> self[self %in% c(99)] <- NA
>>>>>>> shy[shy %in% c(99)] <- NA
>>>>>>> use <- rad[, 1] == 1
>>>>>>> friendship <- sienaNet(array(c(net.w1[use, use], net.w2[use,
>>>>>>> use],
>>>>>> net.w3[use, use]),dim=c(796, 796, 3)))
>>>>>>> shy <- sienaNet(shy[use, ], type='behavior')
>>>>>>> depr <- varCovar(val = depr[use, ])
>>>>>>> self <- varCovar(val = self2[use, ])
>>>>>> Error in varCovar(val = self2[use, ]) : object 'self2' not found
>>>>>>> self <- varCovar(val = self[use, ])
>>>>>>> mymodel <- model.create(useStdInits = TRUE, projname = 'crowd')
>>>>>>> mydata <- sienaDataCreate(friendship,depr,self,shy,rad)
>>>>>> Error: invalid object in sienaDataCreate matrix
>>>>>>> mydata <- sienaDataCreate(friendship,depr,self,shy)
>>>>>>> myeff <- getEffects(mydata)
>>>>>> Error in storage.mode(test) <- "logical" : subscript out of
>>>>>> bounds
>>>>>> Do you have any idea why this error arises?
>>>>>> It does NOT arise when I run the syntax without the 'use' command
>>>>>> Thanks!
>>>>>> Kind regards,
>>>>>> Maarten Selfhout-Van Zalk
>>>>>> On Feb 15, 2010, at 12:59 , Ruth M. Ripley wrote:
>>>>>>> Dear Maarten,
>>>>>>> There are no special facilities: you would need to extract the
>>>>>>> subsets of
>>>>>>> the matrices yourself before creating the Siena network object.
>>>>>>> Using the
>>>>>>> command line, after reading in some data:
>>>>>>> friend.data.w1 <- as.matrix(read.table("s50-network1.dat"))
>>>>>>> friend.data.w2 <- as.matrix(read.table("s50-network2.dat"))
>>>>>>> drink <- as.matrix(read.table("s50-alcohol.dat"))
>>>>>>> smoke <- as.matrix(read.table("s50-smoke.dat"))
>>>>>>> To select the actors with the first column of smoke equal to 1,
>>>>>>> say,
>>>>>>> use <- smoke[, 1] == 1
>>>>>>> friendship <- sienaNet(array(c(friend.data.w1[use, use],
>>>>>>> friend.data.w2[use, use]), dim=c(38, 38, 2)))
>>>>>>> alcohol <- sienaNet(drink[use, ], type="behavior")
>>>>>>> To do this via the gui, you would need to do the subsetting
>>>>>>> outside R.
>>>>>>> Regards,
>>>>>>> Ruth
>>>>>>> PS I have copied this message to the rsiena-help mailing list. I
>>>>>>> see
>>>>>>> two
>>>>>>> benefits to using the lists: others might find the information
>>>>>>> useful too,
>>>>>>> and if I am busy someone else might be able to help!
>>>>>>> --
>>>>>>> Ruth M. Ripley,
>>>>>>> Email:ruth at stats.ox.ac.uk
>>>>>>> Dept. of Statistics, http://www.stats.ox.ac.uk/~ruth/
>>>>>>> University of Oxford, Tel: 01865 282851
>>>>>>> 1 South Parks Road, Oxford OX1 3TG, UK Fax: 01865 272595
>>>>>>> On Mon, 15 Feb 2010, Maarten Van Zalk wrote:
>>>>>>>> Dear Ruth,
>>>>>>>> Is it possible in RSiena to select certain actors for the
>>>>>>>> analysis?
>>>>>>>> So
>>>>>>>> if you have a variable X you want to use to select individuals
>>>>>>>> (for
>>>>>>>> example, all individuals with a score of 1), Can you select
>>>>>>>> only
>>>>>>>> these
>>>>>>>> individuals?
>>>>>>>> Thanks for your help!
>>>>>>>> Kind regards,
>>>>>>>> Maarten Van Zalk
>>>>
>>
>>
>
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