[Rsiena-help] Error message selecting actors
Maarten Van Zalk
maartenvanzalk at gmail.com
Tue Mar 9 16:08:24 CET 2010
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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