Create the package using a local disk. I've seen this issue raising when
one creates the package on, for example, a slow NFS share.


2014-03-28 18:13 GMT-03:00 dhivya arasappan <darasappan@gmail.com>:

> Thanks. Im seeing the following error when I try that. Do I need to
> install an sql R module?
> R CMD INSTALL pd.at35b.mr.v04
> * installing to library
> '/home1/01184/daras/R/x86_64-unknown-linux-gnu-library/2.15'
> * installing *source* package 'pd.at35b.mr.v04' ...
> ** R
> ** data
> ** inst
> ** preparing package for lazy loading
> Error in sqliteExecStatement(con, statement, bind.data) :
>   RS-DBI driver: (error in statement: database disk image is malformed)
> Error : unable to load R code in package 'pd.at35b.mr.v04'
> ERROR: lazy loading failed for package 'pd.at35b.mr.v04'
> * removing
> '/home1/01184/daras/R/x86_64-unknown-linux-gnu-library/2.15/pd.at35b.mr.v04'
>
> Thanks
> dhivya
>
>
> On Mar 28, 2014, at 2:48 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
>
> >
> >
> > ----- Original Message -----
> >> From: "dhivya [guest]" <guest@bioconductor.org>
> >> To: bioconductor@r-project.org, darasappan@gmail.com
> >> Sent: Friday, March 28, 2014 12:45:22 PM
> >> Subject: [BioC] Cannot find the package created by pdInfoBuilder package
> >>
> >>
> >> Hello,
> >>
> >> Iā EURO (tm) m a bioinformatician at UT Austin and Iā EURO (tm)m trying to do time
> >> series analysis of an arabidopsis tiling array.  I used the
> >> makePdInfoPackage function to create a pdinfpackage using my bpmap
> >> files.  It worked successfully and I can see a directory called
> >> pd.at35b.mr.v04:
> >>
> >> ls pd.at35b.mr.v04/
> >> data  DESCRIPTION  inst  man  NAMESPACE  R
> >>
> >> For further analysis, I need to provide the name of the "package
> >> containing the array probe and annotation information, as produces
> >> by the pdInfoBuilder-package".  Just providing the name of this
> >> directory does not seem to work (no such package error). Do I need
> >> to do some installation or additional step after creating this
> >> package, to use it?  Iā EURO (tm)m having difficulty finding this from the
> >> documentation and any help would be really appreciated.
> >>
> >
> > I think you just need to do this from the command line:
> >
> > R CMD INSTALL pd.at35b.mr.v04
> >
> > Dan
> >
> >
> >> thanks for any help
> >> dhivya arasappan
> >> Bioinformatician
> >> UT Austin
> >>
> >> -- output of sessionInfo():
> >>
> >> R version 2.15.3 (2013-03-01)
> >> Platform: x86_64-unknown-linux-gnu (64-bit)
> >>
> >> locale:
> >> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> >> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> >> [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> >> [7] LC_PAPER=C                 LC_NAME=C
> >> [9] LC_ADDRESS=C               LC_TELEPHONE=C
> >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >>
> >> attached base packages:
> >> [1] grid      stats     graphics  grDevices utils     datasets
> >> methods
> >> [8] base
> >>
> >> other attached packages:
> >> [1] pdInfoBuilder_1.22.0                 affxparser_1.30.2
> >> [3] BSgenome.Athaliana.TAIR.TAIR9_1.3.18 BSgenome_1.26.1
> >> [5] GenomicRanges_1.10.7                 pd.atdschip.tiling_0.0.4
> >> [7] RSQLite_0.11.4                       DBI_0.2-7
> >> [9] waveTilingData_0.99.1                waveTiling_1.0.0
> >> [11] GenomeGraphs_1.18.0                  biomaRt_2.14.0
> >> [13] Biostrings_2.26.3                    IRanges_1.16.6
> >> [15] oligo_1.22.0                         Biobase_2.18.0
> >> [17] oligoClasses_1.20.0                  BiocGenerics_0.4.0
> >> [19] R.utils_1.29.8                       R.oo_1.18.0
> >> [21] R.methodsS3_1.6.1
> >>
> >> loaded via a namespace (and not attached):
> >> [1] affy_1.36.1           affyio_1.26.0         BiocInstaller_1.8.3
> >> [4] bit_1.1-11            codetools_0.2-8       ff_2.2-12
> >> [7] foreach_1.4.1         iterators_1.0.6       parallel_2.15.3
> >> [10] preprocessCore_1.20.0 RCurl_1.95-4.1        splines_2.15.3
> >> [13] stats4_2.15.3         waveslim_1.7.3        XML_3.98-1.1
> >> [16] zlibbioc_1.4.0
> >>
> >>
> >> --
> >> Sent via the guest posting facility at bioconductor.org.
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@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@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]]

