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

[Sean Davis]

On Fri, May 29, 2009 at 11:01 PM, Mark Kimpel <mwkimpel at gmail.com> wrote:
> Thanks Sean, that fixed it. I didn't get any errors when I installed R
> (Linux from source) so I don't know what could have happened. Fixed anyway,
> good pick up! Mark

You will want to be sure to do tools/rsync-recommended when installing
from source, I think.  I'm not sure exactly which tarballs are
supposed to include what, but doing the rsync first won't hurt.

Sean


>
> On Fri, May 29, 2009 at 10:53 PM, Sean Davis <seandavi at gmail.com> wrote:
>>
>> 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
>> > ******************************************************************
>> >
>> >        [[alternative HTML version deleted]]
>> >
>> >
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