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
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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