[BioC] Installing BioC + R 2.6: warnings

[hpages at fhcrc.org]

Hi Paolo,

Quoting Paolo Innocenti <paolo.innocenti at ebc.uu.se>:

> 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’
> 

Normally you get this when you source the biocLite.R script twice.
On my system I get:

  > source("http://bioconductor.org/biocLite.R")
  > source("http://bioconductor.org/biocLite.R")
  Warning messages:
  1: In safeSource() : Redefining ‘biocinstall’
  2: In safeSource() : Redefining ‘biocinstallPkgGroups’
  3: In safeSource() : Redefining ‘biocinstallRepos’

This is with any version of R, not only R-2.6. Those warnings are
OK and you can safely ignore them.

> 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

These are known issues. But again, you can safely ignore these warnings.

> 
> 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"
> 

Those are not warning messages, just normal notifications when a package
implicitly defines a generic function based on a regular function (you
probably got them with R 2.5.0 + BioC 2.1 too).

Cheers,
H.