On 11-08-25 9:52 PM, Seth Schommer wrote:
Dear R-Users,
I think I have encountered a potential bug (or at least unwanted behavior),
but I'm not sure so I wanted to post here first. Lately I've been
I'd say it's a bug with your network setup: when a URL is not found, an
error should be generated. "Helpful" servers that give you ads or a
search page instead are not following the rules.
Unfortunately, this is a pretty common misconfiguration, so perhaps R
should try to work around it. If you want to put together a suggested
patch, I'll take a look. The source is in
https://svn.r-project.org/R/trunk/src/library/utils/R/packages.R.
Duncan Murdoch
encountering an error when running a package I put together. I have my
package set up to check for updates when it loads but this error occurs and
stops the package from loading:
Error : .onLoad failed in loadNamespace() for 'rNMR', details:
call: read.dcf(file = tmpf)
error: Line starting '<SCRIPT language=Jav ...' is malformed!
Error: package/namespace load failed for 'rNMR'
I tracked to the following line of code from my package:
available.packages(contrib.url(repos = "http://rnmr.nmrfam.wisc.edu/R/";,
type = "win.binary"))
I dug a little deeper and found the following line of code from
available.packages() to be causing the problem:
z<- tryCatch(download.file(url = paste(repos, "PACKAGES.gz", sep = "/"),
destfile = tmpf, method = method, cacheOK = FALSE, quiet = TRUE, mode =
"wb"), error = identity)
The problem occurs because "PACKAGES.gz" does not exist in the repository,
so my router redirects the invalid URL to a search page and some JavaScript
is downloaded instead. The error is generated when R tries to read the
downloaded file:
res0<- read.dcf(file = tmpf)
Error in read.dcf(file = tmpf) :
Line starting '<SCRIPT language=Jav ...' is malformed!
The repository does have a "PACKAGES" file, but it never gets read because
download.file() does not generate an error. I've fixed the issue by
uploading a "PACKAGES.gz" file to the repository, but I wanted to point out
the issue in case anybody else has encountered this problem. This problem
may be unique to my particular system configuration, in which case a fix may
not be justified. Otherwise, it may be a good idea to check for
a "PACKAGES" file in the repository if an error is encountered when trying
to read the downloaded "PACKAGES.gz" file.
Thanks,
Seth
R Version:
platform = i386-pc-mingw32
arch = i386
os = mingw32
system = i386, mingw32
status = Patched
major = 2
minor = 13.1
year = 2011
month = 08
day = 19
svn rev = 56771
language = R
version.string = R version 2.13.1 Patched (2011-08-19 r56771)
Windows 7 (build 7601) Service Pack 1
Locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
Search Path:
.GlobalEnv, package:tcltk, package:stats, package:graphics,
package:grDevices, package:utils,
package:datasets, package:methods, Autoloads, package:base
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
