[BioC] problem updating packages importing the package "MASS"

[Sean Davis]

On Fri, May 29, 2009 at 10:43 PM, Mark Kimpel <mwkimpel at gmail.com> wrote:
> I went to update packages and discovered multiple packages that import or
> depend on MASS to have non-zero exit status. An example is the BioC package
> "multtest". I must confess that I don't remember what MASS does/did but I
> believe it was a CRAN package. When I went there, it wasn't there, nor is it
> listed as a BioC package. What could be the problem? My output and
> sessionInfo() follows.  Mark
>
>> biocLite("multtest")
> Running biocinstall version 2.4.10 with R version 2.9.0
> Your version of R requires version 2.4 of Bioconductor.
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>  argument 'lib' is missing: using '/home/mkimpel/R_HOME/site-library-2.9.0'
> Warning: dependency ‘MASS’ is not available

MASS is a recommended package, so it is usually installed when you
install R.  It appears that it was not for some reason, so you can get
it as part of the VR bundle, I believe.  Doing biocLite('VR') should
get you what you need.  I'm not sure how biocLite() is supposed to
behave with "bundles", but it appears to not pick up the fact that
MASS is in the VR bundle.

Sean

> trying URL '
> http://bioconductor.org/packages/2.4/bioc/src/contrib/multtest_2.0.0.tar.gz'
> Content type 'application/x-gzip' length 1446401 bytes (1.4 Mb)
> opened URL
> ==================================================
> downloaded 1.4 Mb
>
> * Installing *source* package ‘multtest’ ...
> ** libs
> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-2.9.0/R-build/lib64/R/include
> -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2 -c Rpack.c -o Rpack.o
> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-2.9.0/R-build/lib64/R/include
> -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2 -c VScount.c -o VScount.o
> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-2.9.0/R-build/lib64/R/include
> -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2 -c block_sampling_fixed.c
> -o block_sampling_fixed.o
> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-2.9.0/R-build/lib64/R/include
> -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2 -c bootloop.c -o bootloop.o
> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-2.9.0/R-build/lib64/R/include
> -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2 -c mt.c -o mt.o
> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-2.9.0/R-build/lib64/R/include
> -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2 -c pairt_sampling.c -o
> pairt_sampling.o
> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-2.9.0/R-build/lib64/R/include
> -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2 -c pairt_sampling_fixed.c
> -o pairt_sampling_fixed.o
> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-2.9.0/R-build/lib64/R/include
> -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2 -c random.c -o random.o
> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-2.9.0/R-build/lib64/R/include
> -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2 -c sampling.c -o sampling.o
> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-2.9.0/R-build/lib64/R/include
> -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2 -c sampling_fixed.c -o
> sampling_fixed.o
> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-2.9.0/R-build/lib64/R/include
> -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2 -c stat_func.c -o
> stat_func.o
> gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-2.9.0/R-build/lib64/R/include
> -I/usr/local/include   -DUSEDOUBLE -fpic  -g -O2 -c stat_order.c -o
> stat_order.o
> gcc -std=gnu99 -shared -L/usr/local/lib64 -o multtest.so Rpack.o VScount.o
> block_sampling_fixed.o bootloop.o mt.o pairt_sampling.o
> pairt_sampling_fixed.o random.o sampling.o sampling_fixed.o stat_func.o
> stat_order.o -lm
> ** R
> ** data
> ** inst
> ** preparing package for lazy loading
>
> Welcome to Bioconductor
>
>  Vignettes contain introductory material. To view, type
>  'openVignette()'. To cite Bioconductor, see
>  'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) :
>  there is no package called 'MASS'
> ERROR: lazy loading failed for package ‘multtest’
> * Removing ‘/home/mkimpel/R_HOME/site-library-2.9.0/multtest’
>
> The downloaded packages are in
>    ‘/tmp/RtmphnsZE8/downloaded_packages’
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>  installation of package 'multtest' had non-zero exit status
>> sessionInfo()
> R version 2.9.0 (2009-04-17)
> x86_64-unknown-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=C;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] tcltk_2.9.0 tools_2.9.0
> ------------------------------------------------------------
> 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) 399-1219  Home
> Skype:  mkimpel
>
> "The real problem is not whether machines think but whether men do." -- B.
> F. Skinner
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