[R-sig-ME] Unable to install the package glmmADMB
Ben Bolker
bbolker at gmail.com
Wed Dec 11 19:13:18 CET 2013
My best guess is that this is a bug in R. However, it's going to be
hard to replicate on someone else's system, which is the prerequisite
for getting it fixed.
You should actually be able to use
install.packages("glmmADMB",repos="http://glmmadmb.r-forge.r-project.org/repos")
(i.e. you shouldn't need 'type="source"', which is what's causing the
trouble).
For future reference, can you send the results of sessionInfo()? This
will include your R version, platform (Windows), and locale information,
which will all be relevant to the problem?
Ben Bolker
On 13-12-11 12:39 PM, Maria Helena Mourino Silva Nunes wrote:
> Dear Ben,
>
> thanks for your help! The results of your suggestions are the following:
>
> 1) The command "install.packages("R2admb")" is OK!
>
> install.packages("R2admb")
> Installing package into ‘C:/Users/Helena Mouriño/Documents/R/win-library/3.0’
> (as ‘lib’ is unspecified)
> trying URL 'http://cran.ma.imperial.ac.uk/bin/windows/contrib/3.0/R2admb_0.7.10.zip'
> Content type 'application/zip' length 419933 bytes (410 Kb)
> opened URL
> downloaded 410 Kb
>
> package ‘R2admb’ successfully unpacked and MD5 sums checked
>
>
> 2) But.... the computer doesn't like the command "install.packages("R2admb",type="source")"....... and the same happens with "install.packages("plotrix",type="source")?"
>
> In both cases, the computer changes the "n tilde" to "q"... and I don't understand why...
>
> Installing package into ‘C:/Users/Helena Mouriño/Documents/R/win-library/3.0’
> (as ‘lib’ is unspecified)
> trying URL 'http://cran.ma.imperial.ac.uk/src/contrib/R2admb_0.7.10.tar.gz'
> Content type 'application/x-gzip' length 624522 bytes (609 Kb)
> opened URL
> downloaded 609 Kb
>
> * installing *source* package 'R2admb' ...
> ** package 'R2admb' successfully unpacked and MD5 sums checked
> Warning in file(file, ifelse(append, "a", "w")) :
> cannot open file 'C:/Users/Helena Mouriqo/Documents/R/win-library/3.0/R2admb/DESCRIPTION': No such file or directory
> Error in file(file, ifelse(append, "a", "w")) :
> cannot open the connection
> ERROR: installing package DESCRIPTION failed for package 'R2admb'
> * removing 'C:/Users/Helena Mouriño/Documents/R/win-library/3.0/R2admb'
> * restoring previous 'C:/Users/Helena Mouriño/Documents/R/win-library/3.0/R2admb'
>
> The downloaded source packages are in
> ‘C:\Users\Helena Mouriño\AppData\Local\Temp\RtmpQlj4G7\downloaded_packages’
> Warning messages:
> 1: running command '"C:/PROGRA~1/R/R-30~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\Helena Mouriño\Documents\R\win-library\3.0" C:\Users\HELENA~1\AppData\Local\Temp\RtmpQlj4G7/downloaded_packages/R2admb_0.7.10.tar.gz' had status 1
> 2: In install.packages("R2admb", type = "source") :
> installation of package ‘R2admb’ had non-zero exit status
>
>
> install.packages("plotrix",type="source")
> Installing package into ‘C:/Users/Helena Mouriño/Documents/R/win-library/3.0’
> (as ‘lib’ is unspecified)
> trying URL 'http://cran.ma.imperial.ac.uk/src/contrib/plotrix_3.5-2.tar.gz'
> Content type 'application/x-gzip' length 217258 bytes (212 Kb)
> opened URL
> downloaded 212 Kb
>
> * installing *source* package 'plotrix' ...
> ** package 'plotrix' successfully unpacked and MD5 sums checked
> Warning in file(file, ifelse(append, "a", "w")) :
> cannot open file 'C:/Users/Helena Mouriqo/Documents/R/win-library/3.0/plotrix/DESCRIPTION': No such file or directory
> Error in file(file, ifelse(append, "a", "w")) :
> cannot open the connection
> ERROR: installing package DESCRIPTION failed for package 'plotrix'
> * removing 'C:/Users/Helena Mouriño/Documents/R/win-library/3.0/plotrix'
>
> The downloaded source packages are in
> ‘C:\Users\Helena Mouriño\AppData\Local\Temp\RtmpQlj4G7\downloaded_packages’
> Warning messages:
> 1: running command '"C:/PROGRA~1/R/R-30~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\Helena Mouriño\Documents\R\win-library\3.0" C:\Users\HELENA~1\AppData\Local\Temp\RtmpQlj4G7/downloaded_packages/plotrix_3.5-2.tar.gz' had status 1
> 2: In install.packages("plotrix", type = "source") :
> installation of package ‘plotrix’ had non-zero exit status
>
>
> Helena.
>
> ________________________________________
> De: Ben Bolker [bbolker at gmail.com]
> Enviado: quarta-feira, 11 de Dezembro de 2013 16:35
> Para: Maria Helena Mourino Silva Nunes; r-sig-mixed-models
> Assunto: Re: [R-sig-ME] Unable to install the package glmmADMB
>
> On 13-12-11 08:08 AM, Maria Helena Mourino Silva Nunes wrote:
>> Dear all,
>>
>
>
>> I've tried to install the package glmmADMB, but it didn't work. I
>> followed the installation steps of the web page
>> http://glmmadmb.r-forge.r-project.org/, but I've got the messages
>> reported below. I might stress that I entered into R ( R version
>> 3.0.2) as administrator because I clicked in the option "Run as
>> administrator". What can I do to handle this problem?
>>
>
>
>> Thanks in advanced.
>>
>> Regards, Helena.
>>
>> 1)
>>>
>>> install.packages("glmmADMB",
>>> repos="http://r-forge.r-project.org",type="source") Installing
>>> package into ‘C:/Users/Helena Mouriño/Documents/R/win-library/3.0’
>>> (as ‘lib’ is unspecified) Warning message: package ‘glmmADMB’ is
>>> not available (for R version 3.0.2)
>
> This is more or less as expected, for now -- I have to do some work to
> get glmmADMB building on r-forge ...
>
>>>
>>> 2) install.packages("glmmADMB", +
>>> repos=c("http://glmmadmb.r-forge.r-project.org/repos",
>>> getOption("repos")),type="source") Installing package into
>>> ‘C:/Users/Helena Mouriño/Documents/R/win-library/3.0’ (as ‘lib’ is
>>> unspecified) also installing the dependency ‘R2admb’
>>>
>>> trying URL
>>> 'http://cran.ma.imperial.ac.uk/src/contrib/R2admb_0.7.10.tar.gz'
>>> Content type 'application/x-gzip' length 624522 bytes (609 Kb)
>>> opened URL downloaded 609 Kb
>>>
>>> trying URL
>>> 'http://glmmadmb.r-forge.r-project.org/repos/src/contrib/glmmADMB_0.7.7.tar.gz'
>>>
>>>
>>> Content type 'application/x-gzip' length 10358095 bytes (9.9 Mb)
>>> opened URL downloaded 9.9 Mb
>
> So far so good.
>
>>>
>>> * installing *source* package 'R2admb' ...
>>> ** package 'R2admb'
>>> successfully unpacked and MD5 sums checked
>
> So far so good.
>
>>> Warning in file(file,
>>> ifelse(append, "a", "w")) : cannot open file 'C:/Users/Helena
>>> Mouriqo/Documents/R/win-library/3.0/R2admb/DESCRIPTION': No such
>>> file or directory Error in file(file, ifelse(append, "a", "w")) :
>>> cannot open the connection
>>> ERROR: installing package DESCRIPTION
>>> failed for package 'R2admb'
>
> This is where things go wrong. It's a bit bizarre that the
> error message lists the path as
>
> 'C:/Users/Helena Mouriqo/Documents/...'
>
> while elsewhere in the output it's listed as
>
> ‘C:/Users/Helena Mouriño/Documents/...'
>
> Based on the error message I'm *guessing* that this is happening in
> the read.dcf() function, as called from install.packages(), and that
> there's something funny going on with the special character in your file
> path getting mangled.
>
> What happens if you just
>
> install.packages("R2admb")
>
> ?
>
> Does
>
> install.packages("R2admb",type="source")
>
> give you the same error? What about
>
> install.packages("plotrix",type="source")?
> (this is just picking an arbitrary, harmless package to try)
>
> What do you get if you type traceback() after you receive the
> error above?
>
> Ben Bolker
>
>
>>> * removing 'C:/Users/Helena
>>> Mouriño/Documents/R/win-library/3.0/R2admb' ERROR: dependency
>>> 'R2admb' is not available for package 'glmmADMB' * removing
>>> 'C:/Users/Helena Mouriño/Documents/R/win-library/3.0/glmmADMB'
>>>
>>> The downloaded source packages are in ‘C:\Users\Helena
>>> Mouriño\AppData\Local\Temp\RtmpMzOIeU\downloaded_packages’ Warning
>>> messages: 1: running command '"C:/PROGRA~1/R/R-30~1.2/bin/x64/R"
>>> CMD INSTALL -l "C:\Users\Helena
>>> Mouriño\Documents\R\win-library\3.0"
>>> C:\Users\HELENA~1\AppData\Local\Temp\RtmpMzOIeU/downloaded_packages/R2admb_0.7.10.tar.gz'
>>> had status 1 2: In install.packages("glmmADMB", repos =
>>> c("http://glmmadmb.r-forge.r-project.org/repos", : installation of
>>> package ‘R2admb’ had non-zero exit status 3: running command
>>> '"C:/PROGRA~1/R/R-30~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\Helena
>>> Mouriño\Documents\R\win-library\3.0"
>>> C:\Users\HELENA~1\AppData\Local\Temp\RtmpMzOIeU/downloaded_packages/glmmADMB_0.7.7.tar.gz'
>>> had status 1 4: In install.packages("glmmADMB", repos =
>>> c("http://glmmadmb.r-forge.r-project.org/repos", : installation of
>>> package ‘glmmADMB’ had non-zero exit status
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