[BioC] Keeping all BioC and CRAN installed packages up to date the easy way

[Mark W Kimpel]

Jim,

Thanks for your advice.

Your little code snippet might me a good inclusion in the "how to 
install bioconductor" page of the website under "how to update your 
packages". It is perhaps obvious to an experienced user, but may be very 
helpful to many, as it was to me.

I'm posting this as a new thread on the main list just so your response 
is seen by others who may find it useful.

Mark

---

Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN  46074

(317) 490-5129 Work, & Mobile & VoiceMail
(317) 663-0513 Home (no voice mail please)

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James MacDonald wrote:
 > Hi Mark,
 >
 > I think a much easier and safer way to update is as follows:
 >
 > source("http://www.bioconductor.org/biocLite.R")
 >
 > ## I just have the above in my .Rprofile file, so biocLite() is always
 > there for me.
 >
 > biocLite("Biobase")
 > repos <- biocReposList()
 > update.packages(repos=repos, ask=FALSE)
 >
 > this will get all CRAN and BioC packages, and got me correctly updated
 > this morning.
 >
 > Probably the problem with your script is you are hitting the IL mirror,
 > and it might be out of synch with fhcrc. Try the above and see if it 
helps.
 >
 > Best,
 >
 > Jim
 >
-- 

---

Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN  46074

(317) 490-5129 Work, & Mobile & VoiceMail
(317) 663-0513 Home (no voice mail please)