[BioC] pdInfoBuilder - problem installing the annotation package

[James W. MacDonald]

And on Windows, you also need to include the argument

type = "source"

Best,

Jim



On Thursday, March 27, 2014 9:34:02 AM, Benilton Carvalho wrote:
> Hi Tommaso,
>
> could you please try:
>
> install.packages('C:/HY-data/TORAFFAE/R_projects/Pine
> Microarray/pd.110224.pinus.fa.exp.modified', repo=NULL)
>
> and let us know what you get?
>
> thank you,
>
> benilton
>
>
> 2014-03-27 10:26 GMT-03:00 Tommaso Raffaello <tommaso.raffaello at helsinki.fi>
> :
>
>> Hi,
>>
>> in the pdInfoBuilder manual itæ„€ written "After the package is created,
>> the user must install it and
>> not just copy it to the library tree."
>>
>> I have created the annotation file with the pdInfoBuilder package,
>> however I canæ„’ install it.
>>
>> The error message is:
>>
>> Warning in install.packages :
>>     package 'C:/HY-data/TORAFFAE/R_projects/Pine
>> Microarray/pd.110224.pinus.fa.exp.modified.zip' is not available (for R
>> version 3.0.2)
>> Installing package into 'C:/Rlibs/3.0.2'
>> (as 'lib' is unspecified)
>>
>>> sessionInfo()
>> R version 3.0.2 (2013-09-25)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>>
>> locale:
>> [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
>> Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
>> [4] LC_NUMERIC=C                            LC_TIME=English_United
>> Kingdom.1252
>>
>> attached base packages:
>> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>> base
>>
>> other attached packages:
>>    [1] pdInfoBuilder_1.26.0 affxparser_1.34.2    RSQLite_0.11.4
>> DBI_0.2-7            oligo_1.26.2
>>    [6] Biostrings_2.30.1    XVector_0.2.0        IRanges_1.20.6
>> Biobase_2.22.0       oligoClasses_1.24.0
>> [11] BiocGenerics_0.8.0   BiocInstaller_1.12.0
>>
>> loaded via a namespace (and not attached):
>>    [1] affyio_1.30.0         bit_1.1-11            codetools_0.2-8
>> ff_2.2-12             foreach_1.4.1
>>    [6] GenomicRanges_1.14.4  iterators_1.0.6       preprocessCore_1.24.0
>> splines_3.0.2         stats4_3.0.2
>> [11] tools_3.0.2           zlibbioc_1.8.0
>>
>>
>> I惴 quite new in R and Bioconductor, hopefully this is not a stupid problem.
>>
>> Thanks!
>>
>> --
>> Tommaso Raffaello, PhD
>>
>> University of Helsinki
>> Department of Forest Sciences
>> Latokartanonkaari 7 PO Box 27
>> 00014 Helsinki (Finland)
>>
>> Phone number: +358 9 191 58136
>> email: tommaso.raffaello at helsinki.fi
>> email: tommaso.raffaello at gmail.com
>>
>>
>>          [[alternative HTML version deleted]]
>>
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
> 	[[alternative HTML version deleted]]
>
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099