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

Robert Gentleman rgentlem at fhcrc.org
Sat May 30 06:27:55 CEST 2009 


Sean Davis wrote:
> 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.

 This is the important part.  Very recently a decision was made to abandon the
notion of package bundles, and MASS was in one.  With that gone, the whole
install process changed and updating requires not just the code, but also
getting all required packages.

  Robert

> 
> 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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>>>>
>>
> 
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org

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