[Rsiena-help] Error message selecting actors
Ruth M. Ripley
ruth at stats.ox.ac.uk
Tue Mar 9 19:30:58 CET 2010
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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