R help - Mar 2008 - Problems installing packages using the inbuilt facility: "Error i n gzfile(file, "r") : unable to open connection"

Hi 

I have been trawling the web, FAQs, and R manuals for help on the following
issue, but have failed and was wondering if anyone has a solution to the
following problem:

After having installed R 2.6.2 for Windows (binary), I tried to install various
packages. Every time I try loading a package (any package) via the built-in
menu, I run into the following error message.
> utils:::menuInstallPkgs()
trying URL
'http://cran.uk.r-project.org/bin/windows/contrib/2.6/ada_2.0-1.zip
<http://cran.uk.r-project.org/bin/windows/contrib/2.6/ada_2.0-1.zip> '
Content type 'application/zip' length 971893 bytes (949 Kb)
opened URL
downloaded 949 Kb

Warning in gzfile(file, "r") :
  cannot open compressed file 'ada/DESCRIPTION', probable reason 'No
such file or directory'
Error in gzfile(file, "r") : unable to open
connection
> traceback()
6: gzfile(file, "r")
5: read.dcf(file.path(curPkg, "DESCRIPTION"), c("Package",
"Version",
       "Type"))
4: unpackPkg(foundpkgs[okp, 2], foundpkgs[okp, 1], lib, installWithVers)
3: .install.winbinary(pkgs = pkgs, lib = lib, contriburl = contriburl, 
       method = method, available = available, destdir = destdir, 
       installWithVers = installWithVers, dependencies = dependencies)
2: install.packages(NULL, .libPaths()[1], dependencies = NA, type = type)
1: utils:::menuInstallPkgs()

I tried saving the ZIP  of the package to my C drive, and then installing from
that, but I get the same error message. I then tried calling gzfile with the
filename of the ZIP directly, and I seem to get a file handle without any error
message:

gzfile("C:/Program
Files/R/R-2.6.2/library/ada_2.0-1.zip","r")
                                       description                              
class
"C:/Program Files/R/R-2.6.2/library/ada_2.0-1.zip"                    
"gzfile"
                                              mode                              
text
                                             "rb6"                    
"binary"
                                            opened                              
can read
                                          "opened"                    
"yes"
                                         can write 
                                              "no" 



It might be worth noting, that I initially I also had problems with the internet
download facility, which I fixed starting R with the flag --internet2, as
indicated in the FAQs.

Can you please help?

Many thanks - Philipp

PS: I did the same on my PC at home, and there everything works without
problems.


=============================================================================Please
access the attached hyperlink for an important el...{{dropped:8}}

Works fine for me on the same setup.  Try this and compare (especially
the size of the downloaded file):
> url <-
"http://cran.uk.r-project.org/bin/windows/contrib/2.6/ada_2.0-1.zip";
> download.file(url, basename(url), mode="wb")  # Note
"wb"!!!
trying URL
'http://cran.uk.r-project.org/bin/windows/contrib/2.6/ada_2.0-1.zip'
Content type 'application/zip' length 971893 bytes (949 Kb)
opened URL
downloaded 949 Kb
> file.info(basename(url))
                size isdir mode               mtime               ctime
ada_2.0-1.zip 971893 FALSE  666 2008-03-07 15:43:52 2008-03-07 15:43:28
                            atime exe
ada_2.0-1.zip 2008-03-07 15:43:52  no
> install.packages(basename(url), repos=NULL)
package 'ada' successfully unpacked and MD5 sums checked
updating HTML package descriptions
> library(ada)
Loading required package: rpart
>
/Henrik

On Fri, Mar 7, 2008 at 10:02 AM, Kauer, Philipp
<philipp.kauer at credit-suisse.com> wrote:
> Hi
>
>  I have been trawling the web, FAQs, and R manuals for help on the
following issue, but have failed and was wondering if anyone has a solution to
the following problem:
>
>  After having installed R 2.6.2 for Windows (binary), I tried to install
various packages. Every time I try loading a package (any package) via the
built-in menu, I run into the following error message.
>
>  > utils:::menuInstallPkgs()
>  trying URL
'http://cran.uk.r-project.org/bin/windows/contrib/2.6/ada_2.0-1.zip
<http://cran.uk.r-project.org/bin/windows/contrib/2.6/ada_2.0-1.zip> '
>  Content type 'application/zip' length 971893 bytes (949 Kb)
>  opened URL
>  downloaded 949 Kb
>
>  Warning in gzfile(file, "r") :
>   cannot open compressed file 'ada/DESCRIPTION', probable reason
'No such file or directory'
>  Error in gzfile(file, "r") : unable to open connection
>  > traceback()
>  6: gzfile(file, "r")
>  5: read.dcf(file.path(curPkg, "DESCRIPTION"),
c("Package", "Version",
>        "Type"))
>  4: unpackPkg(foundpkgs[okp, 2], foundpkgs[okp, 1], lib, installWithVers)
>  3: .install.winbinary(pkgs = pkgs, lib = lib, contriburl = contriburl,
>        method = method, available = available, destdir = destdir,
>        installWithVers = installWithVers, dependencies = dependencies)
>  2: install.packages(NULL, .libPaths()[1], dependencies = NA, type = type)
>  1: utils:::menuInstallPkgs()
>
>  I tried saving the ZIP  of the package to my C drive, and then installing
from that, but I get the same error message. I then tried calling gzfile with
the filename of the ZIP directly, and I seem to get a file handle without any
error message:
>
>  gzfile("C:/Program
Files/R/R-2.6.2/library/ada_2.0-1.zip","r")
>                                        description                         
class
>  "C:/Program Files/R/R-2.6.2/library/ada_2.0-1.zip"              
"gzfile"
>                                               mode                         
text
>                                              "rb6"               
"binary"
>                                             opened                         
can read
>                                           "opened"               
"yes"
>                                          can write
>                                               "no"
>
>
>
>  It might be worth noting, that I initially I also had problems with the
internet download facility, which I fixed starting R with the flag --internet2,
as indicated in the FAQs.
>
>  Can you please help?
>
>  Many thanks - Philipp
>
>  PS: I did the same on my PC at home, and there everything works without
problems.
>
>
> 
=============================================================================>
Please access the attached hyperlink for an important el...{{dropped:8}}
>
>  ______________________________________________
>  R-help at r-project.org mailing list
>  https://stat.ethz.ch/mailman/listinfo/r-help
>  PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
>  and provide commented, minimal, self-contained, reproducible code.
>

Thank you Henrik for your response. 

As I indicated at the end of my e-mail, I only have this problem at work, and
was not be able to replicate it at home (ie packages load fine there). I
followed the steps you suggested, but unfortunately no luck (below is the
output). Essentially, the error messages are the same to the one shown in my
initial e-mail.

I noticed that Bob Green posted a very similar request on Friday, when he had
problems performing 'update packages' on a new install of 2.6.2 on
Windows XP, and it was suggested that some things in the startup directories
were not working. After some further investigation, I noticed that various
packages that I instruct to load in my site Rprofile(I am upgrading from an
older version of R), were not loading properly either, and after removing them,
AND using the --internet2 option, the problem disappeared.

To recap for anyone else who is experiencing a similar problem: Try starting R
with the option --internet2 (to get rid of any problems with
-open.connection(con, "r") : unable to resolve
'cran.r-project.org' etc), and remove any packages in the site and local
Rprofile, which do not load properly (that seemed to fix the problems
experienced with gzfile).

Regards - Philipp



> url =
"http://cran.uk.r-project.org/bin/windows/contrib/2.6/ada_2.0-1.zip"
> download.file(url, basename(url), mode="wb") 
trying URL
'http://cran.uk.r-project.org/bin/windows/contrib/2.6/ada_2.0-1.zip'
Error in download.file(url, basename(url), mode = "wb") : 
  cannot open URL
'http://cran.uk.r-project.org/bin/windows/contrib/2.6/ada_2.0-1.zip'
In addition: Warning message:
In download.file(url, basename(url), mode = "wb") :
  unable to resolve 'cran.uk.r-project.org'
>  file.info(basename(url))
              size isdir mode               mtime               ctime           
atime exe
ada_2.0-1.zip    0 FALSE  666 2008-03-10 08:31:16 2008-03-10 08:20:53 2008-03-10
08:20:53  no
> install.packages(basename(url), repos=NULL)
Error in gzfile(file, "r") : unable to open connection
In addition: Warning messages:
1: In zip.unpack(pkg, tmpDir) : error 1 in extracting from zip file
2: In gzfile(file, "r") :
  cannot open compressed file 'ada/DESCRIPTION', probable reason 'No
such file or directory'




-----Original Message-----
From: henrik.bengtsson at gmail.com [mailto:henrik.bengtsson at gmail.com] On
Behalf Of Henrik Bengtsson
Sent: 07 March 2008 23:47
To: Kauer, Philipp
Cc: r-help at lists.R-project.org
Subject: Re: [R] Problems installing packages using the inbuilt facility:
"Error i n gzfile(file, "r") : unable to open connection"

Works fine for me on the same setup.  Try this and compare (especially the size
of the downloaded file):
> url <- 
>
"http://cran.uk.r-project.org/bin/windows/contrib/2.6/ada_2.0-1.zip";
> download.file(url, basename(url), mode="wb")  # Note
"wb"!!!
trying URL
'http://cran.uk.r-project.org/bin/windows/contrib/2.6/ada_2.0-1.zip'
Content type 'application/zip' length 971893 bytes (949 Kb) opened URL
downloaded 949 Kb
> file.info(basename(url))
                size isdir mode               mtime               ctime
ada_2.0-1.zip 971893 FALSE  666 2008-03-07 15:43:52 2008-03-07 15:43:28
                            atime exe
ada_2.0-1.zip 2008-03-07 15:43:52  no
> install.packages(basename(url), repos=NULL)
package 'ada' successfully unpacked and MD5 sums checked updating HTML
package descriptions
> library(ada)
Loading required package: rpart
>
/Henrik

On Fri, Mar 7, 2008 at 10:02 AM, Kauer, Philipp <philipp.kauer at
credit-suisse.com> wrote:
> Hi
>
>  I have been trawling the web, FAQs, and R manuals for help on the
following issue, but have failed and was wondering if anyone has a solution to
the following problem:
>
>  After having installed R 2.6.2 for Windows (binary), I tried to install
various packages. Every time I try loading a package (any package) via the
built-in menu, I run into the following error message.
>
>  > utils:::menuInstallPkgs()
>  trying URL
'http://cran.uk.r-project.org/bin/windows/contrib/2.6/ada_2.0-1.zip
<http://cran.uk.r-project.org/bin/windows/contrib/2.6/ada_2.0-1.zip> '
>  Content type 'application/zip' length 971893 bytes (949 Kb) 
opened
> URL  downloaded 949 Kb
>
>  Warning in gzfile(file, "r") :
>   cannot open compressed file 'ada/DESCRIPTION', probable reason
'No such file or directory'
>  Error in gzfile(file, "r") : unable to open connection  >
traceback()
>  6: gzfile(file, "r")
>  5: read.dcf(file.path(curPkg, "DESCRIPTION"),
c("Package", "Version",
>        "Type"))
>  4: unpackPkg(foundpkgs[okp, 2], foundpkgs[okp, 1], lib, 
> installWithVers)
>  3: .install.winbinary(pkgs = pkgs, lib = lib, contriburl = contriburl,
>        method = method, available = available, destdir = destdir,
>        installWithVers = installWithVers, dependencies = dependencies)
>  2: install.packages(NULL, .libPaths()[1], dependencies = NA, type = 
> type)
>  1: utils:::menuInstallPkgs()
>
>  I tried saving the ZIP  of the package to my C drive, and then installing
from that, but I get the same error message. I then tried calling gzfile with
the filename of the ZIP directly, and I seem to get a file handle without any
error message:
>
>  gzfile("C:/Program
Files/R/R-2.6.2/library/ada_2.0-1.zip","r")
>                                        description                         
class
>  "C:/Program Files/R/R-2.6.2/library/ada_2.0-1.zip"              
"gzfile"
>                                               mode                         
text
>                                              "rb6"               
"binary"
>                                             opened                         
can read
>                                           "opened"               
"yes"
>                                          can write
>                                               "no"
>
>
>
>  It might be worth noting, that I initially I also had problems with the
internet download facility, which I fixed starting R with the flag --internet2,
as indicated in the FAQs.
>
>  Can you please help?
>
>  Many thanks - Philipp
>
>  PS: I did the same on my PC at home, and there everything works without
problems.
>
>
>  
> =====================================================================>
========  Please access the attached hyperlink for an important
> el...{{dropped:8}}
>
>  ______________________________________________
>  R-help at r-project.org mailing list
>  https://stat.ethz.ch/mailman/listinfo/r-help
>  PLEASE do read the posting guide 
> http://www.R-project.org/posting-guide.html
>  and provide commented, minimal, self-contained, reproducible code.
>
=============================================================================Please
access the attached hyperlink for an important el...{{dropped:5}}