Where has reposTools web page moved to? I just attempted to review reposTools while browsing the BioC FAQ http://www.bioconductor.org/docs/faq/ reposTools Tools for dealing with file repositories and allow users to easily install, update, and distribute packages, vignettes, and other files. Clicking on the reposTools link (linked to the following URL) http://www.bioconductor.org/packages/bioc/stable/src/contrib/html/reposTools.html yields Object not found! The requested URL was not found on this server. The link on the referring page seems to be wrong or outdated. Please inform the author of that page about the error. If you think this is a server error, please contact the webmaster. Error 404 www.bioconductor.org Wed Nov 8 12:32:25 2006 Apache/2.0.49 (Linux/SuSE) Any info appreciated. Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: smckinney at bccrc.ca tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada
[Bioc-devel] stale link to reposTools in BioC FAQ?
9 messages · Steven McKinney, James W. MacDonald, Hervé Pagès +1 more
Hi Steven, reposTools is now defunct (see #5): Packages in 1.8 that didn't make it to 1.9 ========================================== 1. exprExternal (depends on externalVector) 2. externalVector (unable to pass check) 3. goCluster (removed at maintainer request) 4. MiPP (unable to pass check) 5. reposTools (defunct) 6. rfcdmin (moved to experiment data repository) 7. RLMM (version < 0.99.0) 8. SNAData (moved to experiment data repository) 9. y2hStat (defunct, replaced by more general ppiStats) The functionality that allowed for downloading depencies was moved to install.packages(), so this package was no longer needed. For instance, biocLite() is really just a wrapper that figures out which version of R you are using, so it can feed the correct repository information to install.packages(). Best, Jim
Steven McKinney wrote:
Where has reposTools web page moved to? I just attempted to review reposTools while browsing the BioC FAQ http://www.bioconductor.org/docs/faq/ reposTools Tools for dealing with file repositories and allow users to easily install, update, and distribute packages, vignettes, and other files. Clicking on the reposTools link (linked to the following URL) http://www.bioconductor.org/packages/bioc/stable/src/contrib/html/reposTools.html yields Object not found! The requested URL was not found on this server. The link on the referring page seems to be wrong or outdated. Please inform the author of that page about the error. If you think this is a server error, please contact the webmaster. Error 404 www.bioconductor.org Wed Nov 8 12:32:25 2006 Apache/2.0.49 (Linux/SuSE) Any info appreciated. Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: smckinney at bccrc.ca tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
James W. MacDonald wrote:
Hi Steven, reposTools is now defunct (see #5):
Right, and the FAQ needs an update. Thanks for pointing this out! Regards, H.
Hi Herve,
[First things first - I want to thank all the
maintainers of update methods - installing and
updating packages is noticeably easier than
even 4 or 5 months ago. Dependencies are more
reliably identified and installed in order,
etc.]
Thanks to you and James for the update
info.
It seems quite a few things in the documented
method for updating packages have changed, so
there are several stale/outdated links and
info items in the FAQ and elsewhere in the
BioC web site.
I just ran an update using
update.packages(ask = FALSE) ## CRAN updates
update.packages(repos = getOption("BioC.Repos"), ask = FALSE) ## BioC updates
Am I missing anything doing it this way?
Any update suggestions/recommendations/pointers
to documentation I've missed would be appreciated.
Steven McKinney
Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre
email: smckinney at bccrc.ca
tel: 604-675-8000 x7561
BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C.
V5Z 1L3
Canada
-----Original Message-----
From: Herve Pages [mailto:hpages at fhcrc.org]
Sent: Wed 11/8/2006 2:05 PM
To: Steven McKinney
Cc: Bioc-devel at stat.math.ethz.ch
Subject: Re: [Bioc-devel] stale link to reposTools in BioC FAQ?
James W. MacDonald wrote:
Hi Steven, reposTools is now defunct (see #5):
Right, and the FAQ needs an update. Thanks for pointing this out! Regards, H.
Hi Steven,
Steven McKinney wrote:
Hi Herve,
[...]
It seems quite a few things in the documented method for updating packages have changed, so there are several stale/outdated links and info items in the FAQ and elsewhere in the BioC web site.
Can you please provide the URLs?
I just ran an update using
update.packages(ask = FALSE) ## CRAN updates
update.packages(repos = getOption("BioC.Repos"), ask = FALSE) ## BioC updates
Where did you get this code from? Did it work for you? On my system it doesn't:
getOption("BioC.Repos")
NULL If you are using R >= 2.3.0, you can try this instead:
library(Biobase) update.packages(rep=biocReposList(), ask = FALSE)
Cheers, H.
Hi Herve,
-----Original Message----- From: Herve Pages [mailto:hpages at fhcrc.org] Sent: Wed 11/8/2006 4:02 PM To: Steven McKinney Cc: Bioc-devel at stat.math.ethz.ch Subject: Re: [Bioc-devel] stale link to reposTools in BioC FAQ? Hi Steven, Steven McKinney wrote:
Hi Herve,
[...]
It seems quite a few things in the documented method for updating packages have changed, so there are several stale/outdated links and info items in the FAQ and elsewhere in the BioC web site.
Can you please provide the URLs?
------------------------------------------------------------- reposTools link is on this page: http://www.bioconductor.org/docs/faq/ reposTools Tools for dealing with file repositories and allow users to easily install, update, and distribute packages, vignettes, and other files. ------------------------------------------------------------- Another link is on this page: http://www.bioconductor.org/whatisit The vignettes are generated using the Sweave function from the R package tools. They are documents that intermix text, code, and output (textual and graphical) and can be regenerated automatically whenever the data or analyses change. Additional supporting software for vignettes will aid users in obtaining data and sample code, step through specific analyses, and apply these analyses to their own data (reposTools package). ------------------------------------------------------------- This page still refers to reposTools: http://www.bioconductor.org/docs/install-howto.html In an R command window, type the following: source("http://www.bioconductor.org/biocLite.R") biocLite() This will install the following subset of packages by default: affy affydata affyPLM annaffy annotate Biobase Biostrings DynDoc gcrma genefilter geneplotter hgu95av2 limma marray matchprobes multtest reposTools ROC vsn xtable ------------------------------------------------------------- Although this page/node states that packages can be updated with bioClite and getBioC, the sections describing bioClite and getBioC only discuss installing new packages, not updating packages periodically to keep up with changes. http://www.bioconductor.org/docs/faq/index.html#For%20Unix/Linux Users are encouraged to use biocLite.R or getBioC to obtain, install and update their packages. Information on how to use these functions can be found in the biocLite and getBioC sections of this document. -------------------------------------------------------------
I just ran an update using
update.packages(ask = FALSE) ## CRAN updates
update.packages(repos = getOption("BioC.Repos"), ask = FALSE) ## BioC updates
Where did you get this code from? Did it work for you?
I tried various combinations of calls to update.packages, looked in the internals of getBioC, getOption, install.packages, etc. The above calls seemed to work best. Your suggestion below looks better. I have not yet determined which function set up list item BioC.Repos in my options, information from anyone who knows this would be appreciated.
getOption("BioC.Repos")
[1] "http://www.bioconductor.org/packages/1.9/bioc" "http://www.bioconductor.org/packages/1.9/data/annotation" [3] "http://www.bioconductor.org/packages/1.9/data/experiment" "http://www.bioconductor.org/packages/1.9/omegahat"
options()$BioC.Repos
[1] "http://www.bioconductor.org/packages/1.9/bioc" "http://www.bioconductor.org/packages/1.9/data/annotation" [3] "http://www.bioconductor.org/packages/1.9/data/experiment" "http://www.bioconductor.org/packages/1.9/omegahat"
On my system it doesn't:
getOption("BioC.Repos")
NULL If you are using R >= 2.3.0, you can try this instead:
library(Biobase) update.packages(rep=biocReposList(), ask = FALSE)
Yes, I have close to the latest and greatest.
sessionInfo()
R version 2.4.0 Patched (2006-10-31 r39758) powerpc-apple-darwin8.8.0 locale: en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" "base" other attached packages: polycor mvtnorm ellipse "0.7-2" "0.7-5" "0.3-2"
Cheers, H.
Steven McKinney wrote:
Hi Herve,
-----Original Message----- From: Herve Pages [mailto:hpages at fhcrc.org]
[...]
Can you please provide the URLs?
------------------------------------------------------------- reposTools link is on this page: http://www.bioconductor.org/docs/faq/ reposTools Tools for dealing with file repositories and allow users to easily install, update, and distribute packages, vignettes, and other files. ------------------------------------------------------------- Another link is on this page: http://www.bioconductor.org/whatisit The vignettes are generated using the Sweave function from the R package tools. They are documents that intermix text, code, and output (textual and graphical) and can be regenerated automatically whenever the data or analyses change. Additional supporting software for vignettes will aid users in obtaining data and sample code, step through specific analyses, and apply these analyses to their own data (reposTools package). ------------------------------------------------------------- This page still refers to reposTools: http://www.bioconductor.org/docs/install-howto.html In an R command window, type the following: source("http://www.bioconductor.org/biocLite.R") biocLite() This will install the following subset of packages by default: affy affydata affyPLM annaffy annotate Biobase Biostrings DynDoc gcrma genefilter geneplotter hgu95av2 limma marray matchprobes multtest reposTools ROC vsn xtable ------------------------------------------------------------- Although this page/node states that packages can be updated with bioClite and getBioC, the sections describing bioClite and getBioC only discuss installing new packages, not updating packages periodically to keep up with changes. http://www.bioconductor.org/docs/faq/index.html#For%20Unix/Linux Users are encouraged to use biocLite.R or getBioC to obtain, install and update their packages. Information on how to use these functions can be found in the biocLite and getBioC sections of this document. -------------------------------------------------------------
Thanks Steven for the useful feedback! I will try to update those pages ASAP.
I just ran an update using
update.packages(ask = FALSE) ## CRAN updates
update.packages(repos = getOption("BioC.Repos"), ask = FALSE) ## BioC updates
Where did you get this code from? Did it work for you?
I tried various combinations of calls to update.packages, looked in the internals of getBioC, getOption, install.packages, etc. The above calls seemed to work best. Your suggestion below looks better. I have not yet determined which function set up list item BioC.Repos in my options, information from anyone who knows this would be appreciated.
getOption("BioC.Repos")
This should be OK too. The CRAN and monograph repos are missing
compared to biocReposList() but, if you don't have any package
from the monograph repo, then doing (in this order):
> update.packages()
followed by
> update.packages(getOption("BioC.Repos"))
should be equivalent to
> update.packages(rep=biocReposList())
Cheers,
H.
Hi Herve
I have been following the thread regarding reposTools and was interestred in the
update.packages comments near the end of this interchange. In particular:
> > update.packages()
>
> followed by
>
> > update.packages(getOption("BioC.Repos"))
>
> should be equivalent to
>
> > update.packages(rep=biocReposList())
>
I have R2.4.0 on Windows. They are not equivalent for me.
I run
> library(Biobase)
> update.packages()
and I'm prompted to select a CRAN mirror, which I do (Australia VIC has been a
good mirror for me).
I am not prompted to update any packages.
I run
> update.packages(getOption("BioC.Repos"))
and I'm not prompted to update any packages.
I run
> update.packages(rep=biocReposList())
and I'm prompted to update 7 packages; Biostrings, GO, humanCHRLOC,
humanLLMappings, KEGG, mouseCHRLOC and mouseLLMappings. I responded N for now so
I can test further.
biocReposList() responds with 6 repositories(5 bioc + 1 cran) as shown below.
getOption("BioC.Repos") responds with NULL.
getOption("repos") responds with the CRAN and CRANextra repositories.
Hence, for me the procedures are not equivalent. Should they be?
NB. I automatically load up biocLite from my .Rprofile in "My Documents" each
time I start R. It contains:
tryCatch({
source("http://bioconductor.org/biocLite.R")
}, error=function(e) invisible(NULL),
warning=function(w) cat("Not connected to the net\n"))
Below is a copy and paste from my Rgui window.
============================
> library(Biobase)
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.
> sessionInfo()
R version 2.4.0 (2006-10-03)
i386-pc-mingw32
locale:
LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252
attached base packages:
[1] "tools" "methods" "stats" "graphics" "grDevices" "utils"
"datasets" "base"
other attached packages:
Biobase
"1.12.2"
> ls()
[1] "biocLite" "getBioC"
> ge<-getOption("BioC.Repos")
> ge
NULL
> update.packages()
--- Please select a CRAN mirror for use in this session ---
> update.packages()
> update.packages(getOption("BioC.Repos"))
> update.packages(rep=biocReposList())
Biostrings :
Version 2.2.0 installed in C:/R/R-2.4.0/library
Version 2.2.1 available at http://bioconductor.org/packages/1.9/bioc
Update (y/N/c)? n
GO :
Version 1.14.0 installed in C:/R/R-2.4.0/library
Version 1.14.1 available at http://bioconductor.org/packages/1.9/data/annotation
Update (y/N/c)? n
humanCHRLOC :
Version 1.14.0 installed in C:/R/R-2.4.0/library
Version 1.14.1 available at http://bioconductor.org/packages/1.9/data/annotation
Update (y/N/c)? n
humanLLMappings :
Version 1.14.0 installed in C:/R/R-2.4.0/library
Version 1.14.2 available at http://bioconductor.org/packages/1.9/data/annotation
Update (y/N/c)? n
KEGG :
Version 1.14.0 installed in C:/R/R-2.4.0/library
Version 1.14.1 available at http://bioconductor.org/packages/1.9/data/annotation
Update (y/N/c)? n
mouseCHRLOC :
Version 1.14.0 installed in C:/R/R-2.4.0/library
Version 1.14.1 available at http://bioconductor.org/packages/1.9/data/annotation
Update (y/N/c)? n
mouseLLMappings :
Version 1.14.0 installed in C:/R/R-2.4.0/library
Version 1.14.2 available at http://bioconductor.org/packages/1.9/data/annotation
Update (y/N/c)? n
> biocReposList()
bioc
"http://bioconductor.org/packages/1.9/bioc"
aData
"http://bioconductor.org/packages/1.9/data/annotation"
eData
"http://bioconductor.org/packages/1.9/data/experiment"
oh
"http://bioconductor.org/packages/1.9/omegahat"
mo
"http://bioconductor.org/packages/1.9/monograph"
cran
"http://cran.fhcrc.org"
> getOption("BioC.Repos")
NULL
>
> getOption("repos")
CRAN CRANextra
"http://cran.ms.unimelb.edu.au" "http://www.stats.ox.ac.uk/pub/RWin"
>
==============================
cheers,
Keith
========================
Keith Satterley
Bioinformatics Division
The Walter and Eliza Hall Institute of Medical Research
Parkville, Melbourne,
Victoria, Australia
=======================
Herve Pages wrote:
Steven McKinney wrote:
cut ---
I just ran an update using
update.packages(ask = FALSE) ## CRAN updates
update.packages(repos = getOption("BioC.Repos"), ask = FALSE) ## BioC updates
Where did you get this code from? Did it work for you?
I tried various combinations of calls to update.packages, looked in the internals of getBioC, getOption, install.packages, etc. The above calls seemed to work best. Your suggestion below looks better. I have not yet determined which function set up list item BioC.Repos in my options, information from anyone who knows this would be appreciated.
getOption("BioC.Repos")
[1] "http://www.bioconductor.org/packages/1.9/bioc" "http://www.bioconductor.org/packages/1.9/data/annotation" [3] "http://www.bioconductor.org/packages/1.9/data/experiment" "http://www.bioconductor.org/packages/1.9/omegahat"
This should be OK too. The CRAN and monograph repos are missing compared to biocReposList() but, if you don't have any package from the monograph repo, then doing (in this order):
> update.packages()
followed by
> update.packages(getOption("BioC.Repos"))
should be equivalent to
> update.packages(rep=biocReposList())
Cheers, H.
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Hi Keith,
Of course they are not equivalent for you, or for me, or
for anybody who doesn't have the "BioC.Repos" option set like
Steven.
Steven has:
> getOption("BioC.Repos")
[1] "http://www.bioconductor.org/packages/1.9/bioc"
[2] "http://www.bioconductor.org/packages/1.9/data/annotation"
[3] "http://www.bioconductor.org/packages/1.9/data/experiment"
[4] "http://www.bioconductor.org/packages/1.9/omegahat"
So in _his_ case (and only if he doesn't have any package from
the monograph repo), this
> update.packages()
> update.packages(getOption("BioC.Repos"))
should be equivalent to
> update.packages(rep=biocReposList())
Anyway, the recommended way to update all BioC + CRAN packages is
to use the latter command.
Cheers,
H.
Keith Satterley wrote:
Hi Herve I have been following the thread regarding reposTools and was interestred in the update.packages comments near the end of this interchange. In particular:
> update.packages()
followed by
> update.packages(getOption("BioC.Repos"))
should be equivalent to
> update.packages(rep=biocReposList())
I have R2.4.0 on Windows. They are not equivalent for me. I run
library(Biobase) update.packages()
and I'm prompted to select a CRAN mirror, which I do (Australia VIC has been a good mirror for me). I am not prompted to update any packages. I run
update.packages(getOption("BioC.Repos"))
and I'm not prompted to update any packages. I run
update.packages(rep=biocReposList())
and I'm prompted to update 7 packages; Biostrings, GO, humanCHRLOC,
humanLLMappings, KEGG, mouseCHRLOC and mouseLLMappings. I responded N
for now so I can test further.
biocReposList() responds with 6 repositories(5 bioc + 1 cran) as shown
below.
getOption("BioC.Repos") responds with NULL.
getOption("repos") responds with the CRAN and CRANextra repositories.
Hence, for me the procedures are not equivalent. Should they be?
NB. I automatically load up biocLite from my .Rprofile in "My Documents"
each time I start R. It contains:
tryCatch({
source("http://bioconductor.org/biocLite.R")
}, error=function(e) invisible(NULL),
warning=function(w) cat("Not connected to the net\n"))
Below is a copy and paste from my Rgui window.
============================
library(Biobase)
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.
sessionInfo()
R version 2.4.0 (2006-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" "datasets" "base" other attached packages: Biobase "1.12.2"
ls()
[1] "biocLite" "getBioC"
ge<-getOption("BioC.Repos")
ge
NULL
update.packages()
--- Please select a CRAN mirror for use in this session ---
update.packages()
update.packages(getOption("BioC.Repos"))
update.packages(rep=biocReposList())
Biostrings : Version 2.2.0 installed in C:/R/R-2.4.0/library Version 2.2.1 available at http://bioconductor.org/packages/1.9/bioc Update (y/N/c)? n GO : Version 1.14.0 installed in C:/R/R-2.4.0/library Version 1.14.1 available at http://bioconductor.org/packages/1.9/data/annotation Update (y/N/c)? n humanCHRLOC : Version 1.14.0 installed in C:/R/R-2.4.0/library Version 1.14.1 available at http://bioconductor.org/packages/1.9/data/annotation Update (y/N/c)? n humanLLMappings : Version 1.14.0 installed in C:/R/R-2.4.0/library Version 1.14.2 available at http://bioconductor.org/packages/1.9/data/annotation Update (y/N/c)? n KEGG : Version 1.14.0 installed in C:/R/R-2.4.0/library Version 1.14.1 available at http://bioconductor.org/packages/1.9/data/annotation Update (y/N/c)? n mouseCHRLOC : Version 1.14.0 installed in C:/R/R-2.4.0/library Version 1.14.1 available at http://bioconductor.org/packages/1.9/data/annotation Update (y/N/c)? n mouseLLMappings : Version 1.14.0 installed in C:/R/R-2.4.0/library Version 1.14.2 available at http://bioconductor.org/packages/1.9/data/annotation Update (y/N/c)? n
biocReposList()
bioc
"http://bioconductor.org/packages/1.9/bioc"
aData
"http://bioconductor.org/packages/1.9/data/annotation"
eData
"http://bioconductor.org/packages/1.9/data/experiment"
oh
"http://bioconductor.org/packages/1.9/omegahat"
mo
"http://bioconductor.org/packages/1.9/monograph"
cran
"http://cran.fhcrc.org"
getOption("BioC.Repos")
NULL
getOption("repos")
CRAN CRANextra
"http://cran.ms.unimelb.edu.au" "http://www.stats.ox.ac.uk/pub/RWin"
============================== cheers, Keith ======================== Keith Satterley Bioinformatics Division The Walter and Eliza Hall Institute of Medical Research Parkville, Melbourne, Victoria, Australia ======================= Herve Pages wrote:
Steven McKinney wrote:
cut ---
I just ran an update using
update.packages(ask = FALSE) ## CRAN updates
update.packages(repos = getOption("BioC.Repos"), ask = FALSE) ##
BioC updates
Where did you get this code from? Did it work for you?
I tried various combinations of calls to update.packages, looked in the internals of getBioC, getOption, install.packages, etc. The above calls seemed to work best. Your suggestion below looks better. I have not yet determined which function set up list item BioC.Repos in my options, information from anyone who knows this would be appreciated.
getOption("BioC.Repos")
[1] "http://www.bioconductor.org/packages/1.9/bioc" "http://www.bioconductor.org/packages/1.9/data/annotation" [3] "http://www.bioconductor.org/packages/1.9/data/experiment" "http://www.bioconductor.org/packages/1.9/omegahat"
This should be OK too. The CRAN and monograph repos are missing compared to biocReposList() but, if you don't have any package from the monograph repo, then doing (in this order):
> update.packages()
followed by
> update.packages(getOption("BioC.Repos"))
should be equivalent to
> update.packages(rep=biocReposList())
Cheers, H.
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel