I have been attempting to install the R devtools package at work. The version of R is 3.1.2 (Pumpkin Helmet). However, the installation of devtools fails because devtools depends on rversions which in turn depends upon the XML package (XML_3.98-1.1.tar.gz), and the XML package is not importing correctly for us. One of our system administrators tried scanning through the files in the XML package, and he said that the particular file: /src/contrib/XML_3.98-1.1.tar.gz/XML/inst/exampleData/dtd.zip looks corrupted. The actual error message he received was: "Archive parsing failed! (Data is corrupted)." For the record, I tried downloading an older version of the XML package (XML_3.95-0.1.tar.gz) but that was also without success -- this time there was a separate error message about not being able to locate xml2-config. (Perhaps XML_3.95-0.1.tar.gz is just not compatible with R version 3.1.2?) I tried browsing over to the "CRAN checks" link for the XML package and noticed several red warning messages under the "Status" column -- not sure if that is typical? Has anyone else had trouble with the XML package lately and if so, how did you resolve it? Would it be possible to remove the potentially corrupted file and then re-upload the package source XML_3.98-1.1.tar.gz to the CRAN webpage? Thanks for your help/suggestions!
Problem with particular file in XML package?
5 messages · Brian Ripley, Keith Jewell, Hadley Wickham +1 more
This really should have been sent to the package maintainer. But that the zip file is corrupt has been reported several times, and does not block installation for anyone else, so your (plural) diagnosis is wrong.
On 28/05/2015 03:56, Gen wrote:
I have been attempting to install the R devtools package at work. The version of R is 3.1.2 (Pumpkin Helmet). However, the installation of devtools fails because devtools depends on rversions which in turn depends upon the XML package (XML_3.98-1.1.tar.gz), and the XML package is not importing correctly for us. One of our system administrators tried scanning through the files in the XML package, and he said that the particular file: /src/contrib/XML_3.98-1.1.tar.gz/XML/inst/exampleData/dtd.zip looks corrupted. The actual error message he received was: "Archive parsing failed! (Data is corrupted)." For the record, I tried downloading an older version of the XML package (XML_3.95-0.1.tar.gz) but that was also without success -- this time there was a separate error message about not being able to locate xml2-config. (Perhaps XML_3.95-0.1.tar.gz is just not compatible with R version 3.1.2?) I tried browsing over to the "CRAN checks" link for the XML package and noticed several red warning messages under the "Status" column -- not sure if that is typical? Has anyone else had trouble with the XML package lately and if so, how did you resolve it? Would it be possible to remove the potentially corrupted file and then re-upload the package source XML_3.98-1.1.tar.gz to the CRAN webpage? Thanks for your help/suggestions! [[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
PLEASE do, including what it says about HTML mail, 'at a minimum' information required and upgrading before posting: R 3.1.2 is already 2 versions obsolete.
Brian D. Ripley, ripley at stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford 1 South Parks Road, Oxford OX1 3TG, UK
The OP asked "Has anyone else had trouble with the XML package lately and if so, how did you resolve it?" For what it's worth... I failed to install XML using install() with the defaults; I can't remember the exact error message, something about access denied. Downloading XML_3.98-1.1.zip with Internet Explorer <http://cran.r-project.org/bin/windows/contrib/3.2/XML_3.98-1.1.zip> gave a more informative error: ======================== Threat Source: http://cran.r-project.or...trib/3.2/XML_3.98-1.1.zip The file requested could not be scanned by Sophos Anti-Virus. This means it could be encrypted or may contain errors that prevent full scanning. As a result, the file was blocked from downloading. ===================== ... so my access was blocked by our systems anti-virus. Our IT people bypassed the anti-virus to download the zip from which I successfully installed. I note that in the library as installed there is a file ...\XML\exampleData\dtd.zip Double-clicking in Windows Explorer gives an error: ========= Windows cannot open the folder. The Compressed (zipped) Folder ... is invalid. ========= I speculate that Sophos Anti-Virus could not scan dtd.zip because it tried to open it as a zipped folder and failed. I don't know if it really is a zipped folder or if that's just its name :-O This 2013 thread seems relevant https://stat.ethz.ch/pipermail/r-sig-mac/2013-November/010494.html
On 28/05/2015 07:38, Prof Brian Ripley wrote:
This really should have been sent to the package maintainer. But that the zip file is corrupt has been reported several times, and does not block installation for anyone else, so your (plural) diagnosis is wrong. On 28/05/2015 03:56, Gen wrote:
I have been attempting to install the R devtools package at work. The
version of R is 3.1.2 (Pumpkin Helmet). However, the installation of
devtools fails because devtools depends on rversions which in turn
depends
upon the XML package (XML_3.98-1.1.tar.gz), and the XML package is not
importing correctly for us.
One of our system administrators tried scanning through the files in the
XML package, and he said that the particular file:
/src/contrib/XML_3.98-1.1.tar.gz/XML/inst/exampleData/dtd.zip looks
corrupted. The actual error message he received was: "Archive parsing
failed! (Data is corrupted)." For the record, I tried downloading an
older version of the XML package (XML_3.95-0.1.tar.gz) but that was also
without success -- this time there was a separate error message about not
being able to locate xml2-config. (Perhaps XML_3.95-0.1.tar.gz is
just not
compatible with R version 3.1.2?)
I tried browsing over to the "CRAN checks" link for the XML package and
noticed several red warning messages under the "Status" column -- not
sure
if that is typical? Has anyone else had trouble with the XML package
lately and if so, how did you resolve it? Would it be possible to remove
the potentially corrupted file and then re-upload the package source
XML_3.98-1.1.tar.gz to the CRAN webpage? Thanks for your
help/suggestions!
[[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
PLEASE do, including what it says about HTML mail, 'at a minimum' information required and upgrading before posting: R 3.1.2 is already 2 versions obsolete.
I have also seen this problem on a student's windows machine (with R 3.2.0 and on multiple mirrors). It appeared that the package zip itself was being corrupted (with an error to the tune of downloaded file size does not agree with actual file size). The most likely explanation that I could come up with was that a virus checker was hitting a false positive and mangling the zip file. Hadley On Thu, May 28, 2015 at 1:38 AM, Prof Brian Ripley
<ripley at stats.ox.ac.uk> wrote:
This really should have been sent to the package maintainer. But that the zip file is corrupt has been reported several times, and does not block installation for anyone else, so your (plural) diagnosis is wrong. On 28/05/2015 03:56, Gen wrote:
I have been attempting to install the R devtools package at work. The
version of R is 3.1.2 (Pumpkin Helmet). However, the installation of
devtools fails because devtools depends on rversions which in turn depends
upon the XML package (XML_3.98-1.1.tar.gz), and the XML package is not
importing correctly for us.
One of our system administrators tried scanning through the files in the
XML package, and he said that the particular file:
/src/contrib/XML_3.98-1.1.tar.gz/XML/inst/exampleData/dtd.zip looks
corrupted. The actual error message he received was: "Archive parsing
failed! (Data is corrupted)." For the record, I tried downloading an
older version of the XML package (XML_3.95-0.1.tar.gz) but that was also
without success -- this time there was a separate error message about not
being able to locate xml2-config. (Perhaps XML_3.95-0.1.tar.gz is just
not
compatible with R version 3.1.2?)
I tried browsing over to the "CRAN checks" link for the XML package and
noticed several red warning messages under the "Status" column -- not sure
if that is typical? Has anyone else had trouble with the XML package
lately and if so, how did you resolve it? Would it be possible to remove
the potentially corrupted file and then re-upload the package source
XML_3.98-1.1.tar.gz to the CRAN webpage? Thanks for your
help/suggestions!
[[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
PLEASE do, including what it says about HTML mail, 'at a minimum' information required and upgrading before posting: R 3.1.2 is already 2 versions obsolete. -- Brian D. Ripley, ripley at stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford 1 South Parks Road, Oxford OX1 3TG, UK
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
Keith Jewell-2 wrote
The OP asked "Has anyone else had trouble with the XML package lately and if so, how did you resolve it?" For what it's worth... I failed to install XML using install() with the defaults; I can't remember the exact error message, something about access denied. Downloading XML_3.98-1.1.zip with Internet Explorer <http://cran.r-project.org/bin/windows/contrib/3.2/XML_3.98-1.1.zip> gave a more informative error: ======================== Threat Source: http://cran.r-project.or...trib/3.2/XML_3.98-1.1.zip The file requested could not be scanned by Sophos Anti-Virus. This means it could be encrypted or may contain errors that prevent full scanning. As a result, the file was blocked from downloading. ===================== ... so my access was blocked by our systems anti-virus. Our IT people bypassed the anti-virus to download the zip from which I successfully installed. I note that in the library as installed there is a file ...\XML\exampleData\dtd.zip Double-clicking in Windows Explorer gives an error: ========= Windows cannot open the folder. The Compressed (zipped) Folder ... is invalid. ========= I speculate that Sophos Anti-Virus could not scan dtd.zip because it tried to open it as a zipped folder and failed. I don't know if it really is a zipped folder or if that's just its name :-O
Thanks a bunch; I suspect something similar to the Sophos Anti-Virus detection is happening at my workplace that results in the XML package being blocked. I am one step removed from the installation process there (also the reason why I am working with R version 3.1.2) -- the frustrating thing is that I am able to download and get everything working correctly at home. Knowing that your IT folks had to bypass the anti-virus software to get it installed gives me some additional info. to try to resolve this issue. I am wondering if the package maintainer or others might be able to modify dtd.zip?
On 28/05/2015 07:38, Prof Brian Ripley wrote:
This really should have been sent to the package maintainer.
Yes, I actually sent an email to the package maintainer on May 21 but figured I would try the R help forum as well.
On Thu, May 28, 2015 at 8:12 AM, Hadley Wickham <h.wickham at gmail.com> wrote:
I have also seen this problem on a student's windows machine (with R 3.2.0 and on multiple mirrors). It appeared that the package zip itself was being corrupted (with an error to the tune of downloaded file size does not agree with actual file size). The most likely explanation that I could come up with was that a virus checker was hitting a false positive and mangling the zip file. Hadley On Thu, May 28, 2015 at 1:38 AM, Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:
This really should have been sent to the package maintainer. But that
the
zip file is corrupt has been reported several times, and does not block installation for anyone else, so your (plural) diagnosis is wrong. On 28/05/2015 03:56, Gen wrote:
I have been attempting to install the R devtools package at work. The version of R is 3.1.2 (Pumpkin Helmet). However, the installation of devtools fails because devtools depends on rversions which in turn
depends
upon the XML package (XML_3.98-1.1.tar.gz), and the XML package is not importing correctly for us. One of our system administrators tried scanning through the files in the XML package, and he said that the particular file: /src/contrib/XML_3.98-1.1.tar.gz/XML/inst/exampleData/dtd.zip looks corrupted. The actual error message he received was: "Archive parsing failed! (Data is corrupted)." For the record, I tried downloading an older version of the XML package (XML_3.95-0.1.tar.gz) but that was also without success -- this time there was a separate error message about
not
being able to locate xml2-config. (Perhaps XML_3.95-0.1.tar.gz is just not compatible with R version 3.1.2?) I tried browsing over to the "CRAN checks" link for the XML package and noticed several red warning messages under the "Status" column -- not
sure
if that is typical? Has anyone else had trouble with the XML package lately and if so, how did you resolve it? Would it be possible to
remove
the potentially corrupted file and then re-upload the package source
XML_3.98-1.1.tar.gz to the CRAN webpage? Thanks for your
help/suggestions!
[[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
PLEASE do, including what it says about HTML mail, 'at a minimum' information required and upgrading before posting: R 3.1.2 is already 2 versions obsolete. -- Brian D. Ripley, ripley at stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford 1 South Parks Road, Oxford OX1 3TG, UK
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see 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. -- http://had.co.nz/