[BioC] Installing BioC + R 2.6: warnings

[Paolo Innocenti]

Hi all,

I'm trying to install BioConductor on Ubuntu 7.04, straight after the 
installation of the OS. BioC was working fine with R 2.5 on my previous 
Ubuntu installation.
I installed R 2.6 from scratches using apt-get from a CTAN mirror, and 
then BioC using the following code:

$sudo R
 >source("http://bioconductor.org/biocLite.R")
 >biocLite()

After installing the packages "zlib1g-dev" and the blas library, i still 
get some warnings:

Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In safeSource() : Redefining ‘biocinstallRepos’

Looking through the log, I found this:

* Installing *source* package 'Biostrings' ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic 
  -g -O2 -c align_needwunsQS.c -o align_needwunsQS.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic 
  -g -O2 -c char_frequency.c -o char_frequency.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic 
  -g -O2 -c match_boyermoore.c -o match_boyermoore.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic 
  -g -O2 -c match_naive.c -o match_naive.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic 
  -g -O2 -c match_shiftor.c -o match_shiftor.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic 
  -g -O2 -c normalize_views.c -o normalize_views.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic 
  -g -O2 -c pmatchPattern.c -o pmatchPattern.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic 
  -g -O2 -c reverseComplement.c -o reverseComplement.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic 
  -g -O2 -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic 
  -g -O2 -c utils.c -o utils.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic 
  -g -O2 -c XInteger.c -o XInteger.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic 
  -g -O2 -c XRaw.c -o XRaw.o
gcc -std=gnu99 -shared  -o Biostrings.so align_needwunsQS.o 
char_frequency.o match_boyermoore.o match_naive.o match_shiftor.o 
normalize_views.o pmatchPattern.o reverseComplement.o 
R_init_Biostrings.o utils.o XInteger.o XRaw.o   -L/usr/lib/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for "toString" in "Biostrings"
Creating a new generic function for "nchar" in "Biostrings"
Creating a new generic function for "as.matrix" in "Biostrings"
Creating a new generic function for "as.list" in "Biostrings"
Warning in matchSignature(signature, fdef, where) :
   in the method signature for function "BStringViews" no definition for 
class: "file"
New generic for "substr" does not agree with implicit generic from 
package "base"; a new generic will be assigned with package "Biostrings"
New generic for "substring" does not agree with implicit generic from 
package "base"; a new generic will be assigned with package "Biostrings"
Warning in matchSignature(signature, fdef, where) :
   in the method signature for function "eq" no definition for class: 
"BioString"
** help


And several messages like:

Creating a new generic function for "weights" in "affyPLM"
Creating a new generic function for "summary" in "affyPLM"
Creating a new generic function for "resid" in "affyPLM"
Creating a new generic function for "residuals" in "affyPLM"


I have no clue about the problem here...
Can anyone help me?

Thanks,
Paolo

 > sessionInfo()
R version 2.6.0 (2007-10-03)
i486-pc-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

loaded via a namespace (and not attached):
[1] rcompgen_0.1-15 tools_2.6.0