I've gotten this error a few times. Each time I rerun getBioC("exprs")
,
it get past it and then it happens again.
* DONE (multtest)
[1] "Installation complete"
Error in if ((is.null(deps)) || (length(deps) == 0) || (deps == ""))
return(NULL) :
missing value where TRUE/FALSE needed
I'm running R 1.9.1 on linux compiled from source.
-Robert
> I've gotten this error a few times. Each time I rerun
getBioC("exprs") ,
> it get past it and then it happens again.
Yes ... I've gotten a rash of these reports, have not been able to
personally reproduce it. Originally the first couple of people were
using
Mac OS X, so thought it was a problem specific to that OS, but now
have a
few people using Win32 and Unix machines. I'm a bit baffled as
everyone
is using release side stuff, and nothing should have changed there,
but
clearly something is not right. Will let folks know ASAP when I
figure
something out.
Thanks
-J
Hello ...
For those of you experiencing errors with getBioC() using R-1.9.1 and
release options, I believe that this problem has been solved. If
you're
still encountering any difficulties, just let me know.
Thanks
-Jeff
While you are at it, can you please allow people to install R without
being root? Our sysadmin will install only RPMs and since
bioconductor
has no RPMS, all of the R users need to compile the source for R.
It is a real pain and many long time R users are frustrated by it.
What
do you guys have to do something special? Every other unix app in the
world has an RPM.
RPM good.
installation scripts bad.
Get the picture.
Jeff Gentry wrote:
>>I've gotten this error a few times. Each time I rerun
getBioC("exprs") ,
>>it get past it and then it happens again.
>>
>>
>
>Yes ... I've gotten a rash of these reports, have not been able to
>personally reproduce it. Originally the first couple of people were
using
>Mac OS X, so thought it was a problem specific to that OS, but now
have a
>few people using Win32 and Unix machines. I'm a bit baffled as
everyone
>is using release side stuff, and nothing should have changed there,
but
>clearly something is not right. Will let folks know ASAP when I
figure
>something out.
>
>Thanks
>-J
>
>
> While you are at it, can you please allow people to install R
without
> being root? Our sysadmin will install only RPMs and since
bioconductor
Considering that I'm not a member of R-core, there's not a whole lot I
can
do to R "while I'm at it". You don't have to be root to install R.
> has no RPMS, all of the R users need to compile the source for R.
That's what I do.
> It is a real pain and many long time R users are frustrated by it.
What
> do you guys have to do something special? Every other unix app in
the
> world has an RPM.
Are you confusing R and Bioconductor? R is the application. You can
install R without being root, obviously you can't install it as a RPM
without being root. Bioconductor is just a set of packages for R. We
happen to provide a script which is a wrapper around one of those
packages
(to provide bootstrapping), aka reposTools, which manages downloads
and
installations.
Here's a hint: You can use a Root-installed R and still install these
packages to any directory that you have permission to. The method of
how
to do this has been discussed on this list and the R-help list many
times. Look at the .libPaths() function.
> RPM good.
> installation scripts bad.
> Get the picture.
We're an open development project. If you would like to provide and
maintain an RPM of R with all of the Bioconductor packages built into
it,
and then keep it up to date - we'd welcome the contribution.
Otherwise,
there is absolutely *no* need to have R installed on your own just to
install packages for R, Bioconductor or otherwise.
-J
Robert Baertsch wrote:
> While you are at it, can you please allow people to install R
without
> being root? Our sysadmin will install only RPMs and since
> bioconductor has no RPMS, all of the R users need to compile the
> source for R.
>
> It is a real pain and many long time R users are frustrated by it.
> What do you guys have to do something special? Every other unix app
in
> the world has an RPM.
There are RPMs for R. Please see
http://cran.us.r-project.org/bin/linux
In addition, this is the Bioconductor listserv. If you have requests
for
R-core, you might try the R-devel listserv: r-devel@stat.math.ethz.ch
Jim
>
> RPM good.
> installation scripts bad.
>
> Get the picture.
>
> Jeff Gentry wrote:
>
>>> I've gotten this error a few times. Each time I rerun
>>> getBioC("exprs") , it get past it and then it happens again.
>>>
>>
>>
>> Yes ... I've gotten a rash of these reports, have not been able to
>> personally reproduce it. Originally the first couple of people
were
>> using
>> Mac OS X, so thought it was a problem specific to that OS, but now
>> have a
>> few people using Win32 and Unix machines. I'm a bit baffled as
everyone
>> is using release side stuff, and nothing should have changed there,
but
>> clearly something is not right. Will let folks know ASAP when I
figure
>> something out.
>>
>> Thanks
>> -J
>>
>>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
Hello Group,
How can I get RefSeq accession IDs instead of LocusLink IDs.
>get("1000_at", env=hguav2LOCUSID)
[1] 5595
Instead of one single probe, how can I get all 12,625 in RefSeq
accession ID for hguav952.
env=hguav2REFSEQ isnt working.
Please help.
Thank you.
Robert Baertsch <baertsch@soe.ucsc.edu> wrote:
While you are at it, can you please allow people to install R without
being root? Our sysadmin will install only RPMs and since bioconductor
has no RPMS, all of the R users need to compile the source for R.
It is a real pain and many long time R users are frustrated by it.
What
do you guys have to do something special? Every other unix app in the
world has an RPM.
RPM good.
installation scripts bad.
Get the picture.
Jeff Gentry wrote:
>>I've gotten this error a few times. Each time I rerun
getBioC("exprs") ,
>>it get past it and then it happens again.
>>
>>
>
>Yes ... I've gotten a rash of these reports, have not been able to
>personally reproduce it. Originally the first couple of people were
using
>Mac OS X, so thought it was a problem specific to that OS, but now
have a
>few people using Win32 and Unix machines. I'm a bit baffled as
everyone
>is using release side stuff, and nothing should have changed there,
but
>clearly something is not right. Will let folks know ASAP when I
figure
>something out.
>
>Thanks
>-J
>
>
_______________________________________________
Bioconductor mailing list
Bioconductor@stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/bioconductor
---------------------------------
[[alternative HTML version deleted]]
You can download pre-compiled .rpm for R from CRAN eg.
http://www.cran.mirrors.pair.com/bin/linux/
You should also note that not everybody in the world uses an RPM based
Linux distribution.
As for installing BioC as a non root user. Try setting the R_LIBS
environment variable eg for bash
export R_LIBS=/home/myaccount/MyRpacks
thanks,
Ben
On Tue, 2004-08-24 at 11:10, Robert Baertsch wrote:
> While you are at it, can you please allow people to install R
without
> being root? Our sysadmin will install only RPMs and since
bioconductor
> has no RPMS, all of the R users need to compile the source for R.
>
> It is a real pain and many long time R users are frustrated by it.
What
> do you guys have to do something special? Every other unix app in
the
> world has an RPM.
>
> RPM good.
> installation scripts bad.
>
> Get the picture.
>
> Jeff Gentry wrote:
>
> >>I've gotten this error a few times. Each time I rerun
getBioC("exprs") ,
> >>it get past it and then it happens again.
> >>
> >>
> >
> >Yes ... I've gotten a rash of these reports, have not been able to
> >personally reproduce it. Originally the first couple of people
were using
> >Mac OS X, so thought it was a problem specific to that OS, but now
have a
> >few people using Win32 and Unix machines. I'm a bit baffled as
everyone
> >is using release side stuff, and nothing should have changed there,
but
> >clearly something is not right. Will let folks know ASAP when I
figure
> >something out.
> >
> >Thanks
> >-J
> >
> >
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
--
Ben Bolstad <bolstad@stat.berkeley.edu>
http://www.stat.berkeley.edu/~bolstad
thanks Ben,
export R_LIBS sounds like a good solution. I will try it.
Ben Bolstad wrote:
>You can download pre-compiled .rpm for R from CRAN eg.
>
>http://www.cran.mirrors.pair.com/bin/linux/
>
>You should also note that not everybody in the world uses an RPM
based
>Linux distribution.
>
>As for installing BioC as a non root user. Try setting the R_LIBS
>environment variable eg for bash
>
>export R_LIBS=/home/myaccount/MyRpacks
>
>thanks,
>
>Ben
>
>
>
>On Tue, 2004-08-24 at 11:10, Robert Baertsch wrote:
>
>
>>While you are at it, can you please allow people to install R
without
>>being root? Our sysadmin will install only RPMs and since
bioconductor
>>has no RPMS, all of the R users need to compile the source for R.
>>
>>It is a real pain and many long time R users are frustrated by it.
What
>>do you guys have to do something special? Every other unix app in
the
>>world has an RPM.
>>
>>RPM good.
>>installation scripts bad.
>>
>>Get the picture.
>>
>>Jeff Gentry wrote:
>>
>>
>>
>>>>I've gotten this error a few times. Each time I rerun
getBioC("exprs") ,
>>>>it get past it and then it happens again.
>>>>
>>>>
>>>>
>>>>
>>>Yes ... I've gotten a rash of these reports, have not been able to
>>>personally reproduce it. Originally the first couple of people
were using
>>>Mac OS X, so thought it was a problem specific to that OS, but now
have a
>>>few people using Win32 and Unix machines. I'm a bit baffled as
everyone
>>>is using release side stuff, and nothing should have changed there,
but
>>>clearly something is not right. Will let folks know ASAP when I
figure
>>>something out.
>>>
>>>Thanks
>>>-J
>>>
>>>
>>>
>>>
>>_______________________________________________
>>Bioconductor mailing list
>>Bioconductor@stat.math.ethz.ch
>>https://stat.ethz.ch/mailman/listinfo/bioconductor
>>
>>
You can compile R without being root. Why not just do that?
i.e.
unpack, then ./configure --prefix=/home/your/placement/directory
for example...
best,
-tony
Robert Baertsch <baertsch@soe.ucsc.edu> writes:
> While you are at it, can you please allow people to install R
without
> being root? Our sysadmin will install only RPMs and since
> bioconductor has no RPMS, all of the R users need to compile the
> source for R.
>
> It is a real pain and many long time R users are frustrated by it.
> What do you guys have to do something special? Every other unix app
in
> the world has an RPM.
>
> RPM good.
> installation scripts bad.
>
> Get the picture.
>
> Jeff Gentry wrote:
>
>>> I've gotten this error a few times. Each time I rerun
>>> getBioC("exprs") , it get past it and then it happens again.
>>>
>>>
>>
>>Yes ... I've gotten a rash of these reports, have not been able to
>>personally reproduce it. Originally the first couple of people were
using
>>Mac OS X, so thought it was a problem specific to that OS, but now
have a
>>few people using Win32 and Unix machines. I'm a bit baffled as
everyone
>>is using release side stuff, and nothing should have changed there,
but
>>clearly something is not right. Will let folks know ASAP when I
figure
>>something out.
>>
>>Thanks
>>-J
>>
>>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
--
Anthony Rossini Research Associate Professor
rossini@u.washington.edu
http://www.analytics.washington.edu/
Biomedical and Health Informatics University of Washington
Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research
Center
UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable
FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email
CONFIDENTIALITY NOTICE: This e-mail message and any
attachme...{{dropped}}
We have R installed with RPMs (by root), sorry for the confusion. My
request was for a RPM install of bioconductor. I guess that is not
possible.
When I tried to install bioconductor myself, I got a permission
problem
with /usr/lib since it is root owned.
Can someone tell my how to use the .libPath command to get around
that?
Better yet, it would be nice if these incantations were on the
bioconductor website.
-Robert
A.J. Rossini wrote:
>You can compile R without being root. Why not just do that?
>
>i.e.
>
> unpack, then ./configure --prefix=/home/your/placement/directory
>
>for example...
>
>best,
>-tony
>
>
>Robert Baertsch <baertsch@soe.ucsc.edu> writes:
>
>
>
>>While you are at it, can you please allow people to install R
without
>>being root? Our sysadmin will install only RPMs and since
>>bioconductor has no RPMS, all of the R users need to compile the
>>source for R.
>>
>>It is a real pain and many long time R users are frustrated by it.
>>What do you guys have to do something special? Every other unix app
in
>>the world has an RPM.
>>
>>RPM good.
>>installation scripts bad.
>>
>>Get the picture.
>>
>>Jeff Gentry wrote:
>>
>>
>>
>>>>I've gotten this error a few times. Each time I rerun
>>>>getBioC("exprs") , it get past it and then it happens again.
>>>>
>>>>
>>>>
>>>>
>>>Yes ... I've gotten a rash of these reports, have not been able to
>>>personally reproduce it. Originally the first couple of people
were using
>>>Mac OS X, so thought it was a problem specific to that OS, but now
have a
>>>few people using Win32 and Unix machines. I'm a bit baffled as
everyone
>>>is using release side stuff, and nothing should have changed there,
but
>>>clearly something is not right. Will let folks know ASAP when I
figure
>>>something out.
>>>
>>>Thanks
>>>-J
>>>
>>>
>>>
>>>
>>_______________________________________________
>>Bioconductor mailing list
>>Bioconductor@stat.math.ethz.ch
>>https://stat.ethz.ch/mailman/listinfo/bioconductor
>>
>>
>>
>
>
>
Robert Baertsch wrote:
> We have R installed with RPMs (by root), sorry for the confusion. My
> request was for a RPM install of bioconductor. I guess that is not
> possible.
>
> When I tried to install bioconductor myself, I got a permission
problem
> with /usr/lib since it is root owned.
>
> Can someone tell my how to use the .libPath command to get around
that?
.libPaths("/somewhere/you/have/write/access")
Note that this only affects the current R session. You will have to
either follow Ben Bolstad's suggestion or put the .libPath() command
in
either an .Rprofile or .First file.
Please see ?.libPaths and ?.Rprofile for more information.
Best,
Jim
--
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
Robert Baertsch <baertsch@soe.ucsc.edu> writes:
> Better yet, it would be nice if these incantations were on the
> bioconductor website.
We are waiting for someone to write them!
Alternatively, I thought that a BioC-installer package for Debian
exists (at least on the recent Quantian bootable DVDs, I think).
best,
-tony
--
Anthony Rossini Research Associate Professor
rossini@u.washington.edu
http://www.analytics.washington.edu/
Biomedical and Health Informatics University of Washington
Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research
Center
UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable
FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email
CONFIDENTIALITY NOTICE: This e-mail message and any
attachme...{{dropped}}
>RPM good.
>installation scripts bad.
>Get the picture.
To be honest, I've had nothing but trouble with RPMs and always
install
from source.
The Marlboro man wouldn't use RPMs. John Wayne wouldn't use RPMs. Be
a
real man, install from source ;-)
