Hi,
I decided to upgrade to 1.8 today... :-)
Anyway, we are writing our own package that is dependent on a
bioconductor library - 'affy'.
I've checked and when I fire up R, library(affy) behaves as expected...
so it all seems to be installed and OK...
In the DESCRIPTION file in my package source I have the line:
Depends: affy
When I run R CMD check simpleaffy
I get to:
...
* checking package dependencies ... ERROR
Packages required but not available:
WARNING: ignoring environment value of R_HOME
Prompt >
Any ideas what is going on - as far as I can see the only dependency is
to affy which is there and OK... I get no list of packages that are
missing :-(
I'm assuming the warning comes because I have R_ENVIRON pointing to a
.Renviron file in my home directory...
Any help would be much appreciated!
Cheers,
Crispin
--------------------------------------------------------
This email is confidential and intended solely for the use o...{{dropped}}
Hi, Firstly, sorry to reply to my own posting... Also for not having done more trawling before I sent the original message... The problems we are having were down to R being installed in a different directory to the default one (for various sysadmin reasons)... We've successfully got R runnning on a single machine in the default directories where it likes to be - it is happy, and 'R CMD check' works fine... :-) Alas, this is not a good long-term solution for us can anyone help us work out the easiest way to get R installed in another directory structure instead of the default ones? I appreciate that very similar questions have been asked before, but I suspect that 1.8 is slightly different (since R CMD check ... worked fine for us in 1.7.1). Crispin> -----Original Message----- > From: Crispin Miller > Sent: 31 October 2003 14:51 > To: R-help at stat.math.ethz.ch > Subject: [R] Creating packages in 1.8 > > > Hi, > I decided to upgrade to 1.8 today... :-) > Anyway, we are writing our own package that is dependent on a > bioconductor library - 'affy'. I've checked and when I fire > up R, library(affy) behaves as expected... so it all seems to > be installed and OK... > > In the DESCRIPTION file in my package source I have the line: > > Depends: affy > > When I run R CMD check simpleaffy > > I get to: > > ... > * checking package dependencies ... ERROR > Packages required but not available: > WARNING: ignoring environment value of R_HOME > Prompt > > > Any ideas what is going on - as far as I can see the only > dependency is to affy which is there and OK... I get no list > of packages that are missing :-( > > I'm assuming the warning comes because I have R_ENVIRON > pointing to a .Renviron file in my home directory... > > Any help would be much appreciated! > Cheers, > Crispin > > -------------------------------------------------------- > > > This email is confidential and intended solely for the use > o...{{dropped}} > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://www.stat.math.ethz.ch/mailman/listinfo> /r-help >-------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}
Does R CMD check succeed if you unset R_HOME (or unset R_ENVIRON?). The R shell wrapper script writes the warning message to STDOUT if R_HOME is set to something other the setting hard-coded into the wrapper. This can be a problem if other scripts are depending upon the output of R CMD <BLAH> stuff. For example, I could not build RPy until I unset R_HOME b/c RPy's build script relies upon the output of R CMD HOME and it didn't like "WARNING: ..." as an include path ;-) + seth On Fri, Oct 31, 2003 at 02:50:39PM -0000, Crispin Miller wrote:> Hi, > I decided to upgrade to 1.8 today... :-) > Anyway, we are writing our own package that is dependent on a > bioconductor library - 'affy'. > I've checked and when I fire up R, library(affy) behaves as expected... > so it all seems to be installed and OK... > > In the DESCRIPTION file in my package source I have the line: > > Depends: affy > > When I run R CMD check simpleaffy > > I get to: > > ... > * checking package dependencies ... ERROR > Packages required but not available: > WARNING: ignoring environment value of R_HOME > Prompt > > > Any ideas what is going on - as far as I can see the only dependency is > to affy which is there and OK... I get no list of packages that are > missing :-( > > I'm assuming the warning comes because I have R_ENVIRON pointing to a > .Renviron file in my home directory... > > Any help would be much appreciated! > Cheers, > Crispin > > -------------------------------------------------------- > > > This email is confidential and intended solely for the use o...{{dropped}} > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-help