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[Bioc-devel] update packages not working

10 messages · Mark Kimpel, Seth Falcon, Martin Maechler

Original
Seth Falcon
# 
Hi Mark,

"Kimpel, Mark William" <mkimpel at iupui.edu> writes:
CRAN packages update because:

   a) the CRAN URL is essentially hard-coded into R

   b) CRAN packages, in general, have very few dependencies and those
      that they have are all in the CRAN.
Here's one way to upgrade all of your installed CRAN _and_
Bioconductor packages:

    library("Biobase")
    update.packages(repos=biocReposList())
I can recall some recent cases where folks have had out of date
packages, but version number syncing is not going to help with that.
My impression is that there have been very few, if any, recent cases
of release/devel mixups.

Syncing R and BioC version numbers would not, IMO, solve package
install/upgrade issues and it would lead to confusion that the R and
Bioconductor projects were the same (they are not).
If the above doesn't work, send along the error messages and we'll go
from there.  But perhaps the bioconductor list is a better forum at
that point.

+ seth
Mark Kimpel
# 
Seth,

Regarding synching version numbers of R and BioC, I see your point about
giving the impression that they are the same project, whereas in reality
they are separate. It seems to me, however, that there are many cases on
the list that result from a newer BioC version being used with an older
R version. I think that the bioinformatics folks focus in on getting the
latest and greatest packages for BioC and forget that R is also
evolving. On start-up, could R run a quick check of version numbers of
all packages to see if they are supported by the base R version and, if
not, give a list of those that are not? It might be a more visible
warning that putting a warning up when packages are loaded as these can
get lost in the jumble of scrolling screen output. For myself, I simply
have the commands you gave me in .Rprofile and I update every time R
starts up. It makes the process a little slower, but it was the only way
I could make myself remember to do it on a regular basis and it
certainly beats spending time debugging something only to find that I am
working with an outdated package.

Well, now onto a real-world problem that I am having. I could not get
your code to work for updating my BioC devel packages. It does work for
CRAN. At the end of this post is a screen dump with code, error message
and sessionInfo(). Any thoughts?

Mark



Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
Loading required package: tools

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.
Warning: unable to access index for repository
http://bioconductor.org/packages/2.0/monograph/bin/windows/contrib/2.5
R version 2.5.0 Under development (unstable) (2007-01-19 r40528) 
i386-pc-mingw32 

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

attached base packages:
[1] "tools"     "stats"     "graphics"  "grDevices" "utils"
"datasets"  "methods"   "base"     

other attached packages:
  Biobase 
"1.13.34"
--- Please select a CRAN mirror for use in this session ---

Mark W. Kimpel MD 

 

(317) 490-5129 Work, & Mobile

 

(317) 663-0513 Home (no voice mail please)

1-(317)-536-2730 FAX


-----Original Message-----
From: Seth Falcon [mailto:sfalcon at fhcrc.org] 
Sent: Monday, January 22, 2007 12:18 AM
To: Kimpel, Mark William
Cc: bioc-devel at stat.math.ethz.ch
Subject: Re: [Bioc-devel] update packages not working

Hi Mark,

"Kimpel, Mark William" <mkimpel at iupui.edu> writes:
CRAN packages update because:

   a) the CRAN URL is essentially hard-coded into R

   b) CRAN packages, in general, have very few dependencies and those
      that they have are all in the CRAN.
Here's one way to upgrade all of your installed CRAN _and_
Bioconductor packages:

    library("Biobase")
    update.packages(repos=biocReposList())
I can recall some recent cases where folks have had out of date
packages, but version number syncing is not going to help with that.
My impression is that there have been very few, if any, recent cases
of release/devel mixups.

Syncing R and BioC version numbers would not, IMO, solve package
install/upgrade issues and it would lead to confusion that the R and
Bioconductor projects were the same (they are not).
If the above doesn't work, send along the error messages and we'll go
from there.  But perhaps the bioconductor list is a better forum at
that point.

+ seth
Seth Falcon
# 
"Kimpel, Mark William" <mkimpel at iupui.edu> writes:
Please post links to posts where you think this is happening.  When
users follow the directions for installing Bioconductor packages using
biocLite it is virtually impossible to get a mismatch.

Have there been cases of such mixups?  Yes.  But the ones that I can
recall were the result of users being confused about how to install
BioC packages in the first place -- I just fail to see how version
numbers would help these users.
If the packages were installed using any of the recommended methods,
then I don't think it is possible to have a package that isn't
supported by your version of R.  Adding such a feature to R is
something for the R email lists and not something we can do much about
here at BioC HQ ;-)
I'm glad you've found a solution that works for you.  The code in your
.Rprofile file keeps packages updated with respect to bug fixes,
etc. -- that's fine, but it leaves me a bit confused about how this
relates to arguments about R <-> BioC version number syncing or
mismatches between R version and package version.
Aside from the warning message (which will be fixed, but hey, you are
using devel), what didn't work?
Mark Kimpel
# 
Seth,

My thoughts on version numbers were really just an aside. You are
certainly correct that if new users do everything correctly they will
have no problems. Here, however, is one scenario where I can see someone
screwing something up. User only used R/BioC intermittently and has
version R 2.1 on his machine. He reads about a new package in
Bioinformatics, goes to the BioC website, downloads this new package
(created to run in R 2.4.1) and installs from zip file. Couldn't this
cause problems for the user? Perhaps this is just theoretical and never
happens in practice. The next time I see what I think is a real world
example, I'll forward it to you. Unless someone else has something to
add, let's just drop this for now.

My real problem is that I am not sure if the update packages code is
working in R 2.5.0. Is the warning message itself a bug or is the update
not working? So far I haven't been prompted to enter "y" to update a
BioC package, whereas I have for CRAN packages.

Thanks,
Mark

Mark W. Kimpel MD 

 

(317) 490-5129 Work, & Mobile

 

(317) 663-0513 Home (no voice mail please)

1-(317)-536-2730 FAX

-----Original Message-----
From: Seth Falcon [mailto:sfalcon at fhcrc.org] 
Sent: Monday, January 22, 2007 11:52 AM
To: Kimpel, Mark William
Cc: Seth Falcon; bioc-devel at stat.math.ethz.ch
Subject: Re: [Bioc-devel] update packages not working

"Kimpel, Mark William" <mkimpel at iupui.edu> writes:
about
reality
on
older
Please post links to posts where you think this is happening.  When
users follow the directions for installing Bioconductor packages using
biocLite it is virtually impossible to get a mismatch.

Have there been cases of such mixups?  Yes.  But the ones that I can
recall were the result of users being confused about how to install
BioC packages in the first place -- I just fail to see how version
numbers would help these users.
If the packages were installed using any of the recommended methods,
then I don't think it is possible to have a package that isn't
supported by your version of R.  Adding such a feature to R is
something for the R email lists and not something we can do much about
here at BioC HQ ;-)
I'm glad you've found a solution that works for you.  The code in your
.Rprofile file keeps packages updated with respect to bug fixes,
etc. -- that's fine, but it leaves me a bit confused about how this
relates to arguments about R <-> BioC version number syncing or
mismatches between R version and package version.
for
message
Aside from the warning message (which will be fixed, but hey, you are
using devel), what didn't work?
Seth Falcon
# 
"Kimpel, Mark William" <mkimpel at iupui.edu> writes:
Sure.
The warning message you posted should not prevent updates, but it is
difficult for me to tell if something else is going on.

+ seth
Mark Kimpel
# 
Seth,

Do you have an older, outdated WinBinary version of one of your packages
for BioC 2.0? If you send it to me, I could manually install it, then
restart R with my update script in place, and see if it is updated,
warning or not. Would tell us IF there is a real problem, but wouldn't
pinpoint the source. Still, a small step in the right direction?

Mark

Mark W. Kimpel MD 

 

(317) 490-5129 Work, & Mobile

 

(317) 663-0513 Home (no voice mail please)

1-(317)-536-2730 FAX


-----Original Message-----
From: Seth Falcon [mailto:sfalcon at fhcrc.org] 
Sent: Tuesday, January 23, 2007 9:59 AM
To: Kimpel, Mark William
Cc: Seth Falcon; bioc-devel at stat.math.ethz.ch
Subject: Re: [Bioc-devel] update packages not working

"Kimpel, Mark William" <mkimpel at iupui.edu> writes:
Sure.
update
The warning message you posted should not prevent updates, but it is
difficult for me to tell if something else is going on.

+ seth
2 days later
Mark Kimpel
# 
Seth,

Today the warning message again appeared, but shortly thereafter I was
prompted to update a host of BioC packages. So, I think the warning is a
bug, but not one that prevents the updates from taking place.

Mark

Mark W. Kimpel MD 

 

(317) 490-5129 Work, & Mobile

 

(317) 663-0513 Home (no voice mail please)

1-(317)-536-2730 FAX


-----Original Message-----
From: Seth Falcon [mailto:sfalcon at fhcrc.org] 
Sent: Tuesday, January 23, 2007 9:59 AM
To: Kimpel, Mark William
Cc: Seth Falcon; bioc-devel at stat.math.ethz.ch
Subject: Re: [Bioc-devel] update packages not working

"Kimpel, Mark William" <mkimpel at iupui.edu> writes:
Sure.
update
The warning message you posted should not prevent updates, but it is
difficult for me to tell if something else is going on.

+ seth
Seth Falcon
# 
"Kimpel, Mark William" <mkimpel at iupui.edu> writes:
Thanks for the update.  I will see about fixing the bug to eliminate
the warning.

+ seth
Martin Maechler
# 
Seth> Hi Mark,
    Seth> "Kimpel, Mark William" <mkimpel at iupui.edu> writes:
    >> I'm having difficulty auto-updating packages in R 2.5/BioC 2.0. R
    >> packages update without problem, BioC packages result in following
    >> error. 

    Seth> CRAN packages update because:

    Seth> a) the CRAN URL is essentially hard-coded into R

    Seth> b) CRAN packages, in general, have very few dependencies and those
    Seth> that they have are all in the CRAN.

not quite (but almost, I agree),
e.g., there is at least one CRAN package that depends on BioC 'graph'.

   [................]

Martin