I've discovered that if you have old package data has been cached,
attempting to load the newest reposTools will fail with this message:
Synching your local package management information ...
Error in if (e1[i] != e2[i]) return(TRUE) :
missing value where TRUE/FALSE needed
In addition, the devel affy package depends on affydata, which depends
on
affy, resulting in a situation where install.packages2() can't install
either one or anthing depending on them.
-Greg
LEGAL NOTICE\ Unless expressly stated otherwise, this message is...
{{dropped}}
> I've discovered that if you have old package data has been cached,
> attempting to load the newest reposTools will fail with this
message:
I'm not sure what you mean here by "old package data has been cached".
> In addition, the devel affy package depends on affydata, which
depends on
> affy, resulting in a situation where install.packages2() can't
install
> either one or anthing depending on them.
This is fixed in the latest version of reposTools (1.1.37)
> -----Original Message-----
> From: Jeff Gentry [mailto:jgentry@jimmy.harvard.edu]
> Sent: Tuesday, May 13, 2003 12:44 PM
> To: Warnes, Gregory R
> Cc: 'bioconductor@stat.math.ethz.ch'
> Subject: Re: [BioC] Error loading reposTools
>
>
> > I've discovered that if you have old package data has been cached,
> > attempting to load the newest reposTools will fail with
> this message:
>
> I'm not sure what you mean here by "old package data has been
cached".
Sorry, if a "liblisting.Rda" fike created by an older (broken?)
reposTools
exists in the package directory syncLocalLibList() will fail with the
message:
Error in if (e1[i] != e2[i]) return(TRUE) :
?missing value where TRUE/FALSE needed
Which bails out of library(reposTools), preventing the loading of
libraries
depending on reposTools. Perhaps it would be good to store a version
number in the "liblisting.Rda" file so that an obsolete one can be
ignored &
a new one regenerated?
>
> > In addition, the devel affy package depends on affydata,
> which depends on
> > affy, resulting in a situation where install.packages2()
> can't install
> > either one or anthing depending on them.
>
> This is fixed in the latest version of reposTools (1.1.37)
I got this problem with 1.1.37, using install.packages, and had to
manually
install affy and affydata to fix the problem.
-Greg
>
LEGAL NOTICE\ Unless expressly stated otherwise, this message is...
{{dropped}}
On Tue, 13 May 2003, Warnes, Gregory R wrote:
> Sorry, if a "liblisting.Rda" fike created by an older (broken?)
reposTools
> exists in the package directory syncLocalLibList() will fail with
the
Gotcha.
> Error in if (e1[i] != e2[i]) return(TRUE) :
> missing value where TRUE/FALSE needed
You wouldn't happen ot have the "Spot" package installed, would you?
> Which bails out of library(reposTools), preventing the loading of
libraries
> depending on reposTools. Perhaps it would be good to store a
version
> number in the "liblisting.Rda" file so that an obsolete one can be
ignored &
> a new one regenerated?
The problem here is that the format of the liblisting.Rda file has not
changed, ever. So tagging it with a version isn't going to help in
that respect. The problem is that there have been bugs in reposTools
which *could* lead to corruption in one's liblisting.Rda file - we
could
say that tehre's a certain minimum version of reposTools that a
liblisting.Rda must be associated with if we come across something
that
leads to liblisting corruption -> but an older liblisting is not (and
probably not for most people) going to be corrupted.
(btw, the short term solution here for you in particular right now, is
to
remove the liblisting.Rda file)
> I got this problem with 1.1.37, using install.packages, and had to
manually
> install affy and affydata to fix the problem.
I've run install.packages2 on affy using BIOCDevel from multiple
installs
of R w/ varying degrees of cleanliness and do not get this problem
whatsoever. Does anyone else get still have this problem?
-J
