[Bioc-devel] tab completion for library()

Thu Nov 14 12:49:26 CET 2013

On Wed, Nov 13, 2013 at 10:55 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> On 11/13/2013 09:17 AM, Tim Triche, Jr. wrote:
>>
>> This seems like what I'm looking for, but it doesn't do what I'd expect:
>>
>> R> rc.options(ipck=TRUE)
>> R> rc.options()$ipck
>> [1] TRUE
>> R> require(Biostr\t
>> # nothing happens
>>
>> Should I be using one of the intermediate/undocumented functions to grab a
>> list of possible completions?
>
>
> should be rc.settings(ipck=TRUE)

Yes, sorry, my bad :-)

-Deepayan

> Tab completion can be pretty useful to customize for class developers, for
> instance library(GenomicRanges); .DollarNames.GenomicRanges is what enables
> tab completion on the metadata column names
>
>> gr = GRanges("chr1", IRanges(1, 10), foo=1, bar=2)
>> gr$f<tab>
>
> Martin
>
>>
>> Thanks,
>>
>> --t
>>
>>
>> R> sessionInfo()
>> R Under development (unstable) (2013-11-11 r64202)
>> 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=en_US.UTF-8       LC_NAME=C
>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] parallel  stats     graphics  grDevices datasets  utils     methods
>> [8] base
>>
>> other attached packages:
>>   [1] Matrix_1.1-0
>>   [2] frma_1.15.1
>>   [3] BSgenome.Hsapiens.UCSC.hg19_1.3.19
>>   [4] BSgenome_1.31.6
>>   [5] Biostrings_2.31.1
>>   [6] Homo.sapiens_1.1.1
>>   [7] TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1
>>   [8] org.Hs.eg.db_2.10.1
>>   [9] GO.db_2.10.1
>> [10] RSQLite_0.11.4
>> [11] DBI_0.2-7
>> [12] OrganismDbi_1.5.0
>> [13] GenomicFeatures_1.15.2
>> [14] AnnotationDbi_1.25.3
>> [15] Biobase_2.23.2
>> [16] chromophobe_0.79
>> [17] fastcluster_1.1.11
>> [18] pheatmap_0.7.7
>> [19] ggplot2_0.9.3.1
>> [20] reshape2_1.2.2
>> [21] GenomicRanges_1.15.9
>> [22] XVector_0.3.1
>> [23] IRanges_1.21.8
>> [24] BiocGenerics_0.9.0
>> [25] BiocInstaller_1.13.2
>> [26] gtools_3.1.1
>> [27] devtools_1.3
>>
>> loaded via a namespace (and not attached):
>>   [1] affxparser_1.35.0        affy_1.41.1              affyio_1.31.0
>>
>>   [4] biomaRt_2.19.1           bit_1.1-10               bitops_1.0-6
>>
>>   [7] codetools_0.2-8          colorspace_1.2-4         dichromat_2.0-0
>>
>> [10] digest_0.6.3             evaluate_0.5.1           ff_2.2-12
>>
>> [13] foreach_1.4.1            GenomicAlignments_0.99.2 graph_1.41.1
>>
>> [16] grid_3.1.0               gtable_0.1.2             httr_0.2
>>
>> [19] iterators_1.0.6          labeling_0.2             lattice_0.20-24
>>
>> [22] MASS_7.3-29              matrixStats_0.8.12       memoise_0.1
>>
>> [25] munsell_0.4.2            oligo_1.27.0             oligoClasses_1.25.1
>>
>> [28] plyr_1.8                 preprocessCore_1.25.0    proto_0.3-10
>>
>> [31] R.methodsS3_1.5.2        RBGL_1.39.1              RColorBrewer_1.0-5
>>
>> [34] RCurl_1.95-4.1           Rsamtools_1.15.7         rtracklayer_1.23.3
>>
>> [37] scales_0.2.3             splines_3.1.0            stats4_3.1.0
>>
>> [40] stringr_0.6.2            tools_3.1.0              whisker_0.3-2
>>
>> [43] XML_3.98-1.1             zlibbioc_1.9.0
>>
>>
>> *He that would live in peace and at ease, *
>> *Must not speak all he knows, nor judge all he sees.*
>>
>> Benjamin Franklin, Poor Richard's
>> Almanack<http://archive.org/details/poorrichardsalma00franrich>
>>
>>
>> On Wed, Nov 13, 2013 at 8:43 AM, Deepayan Sarkar
>> <deepayan.sarkar at gmail.com>wrote:
>>
>>> On Wed, Nov 13, 2013 at 10:06 PM, Tim Triche, Jr. <tim.triche at gmail.com>
>>> wrote:
>>>>
>>>> How hard would this be to set up (e.g. using a mechanism like
>>>> AnnotationHub's)?
>>>>
>>>> I'm really lazy and wondering if the time spent writing a little package
>>>> might be recovered when I want to load a BSgenome or SNPlocs (or...)
>>>> package this way.
>>>>
>>>> Plus if the mechanism could involve caching, maybe that could work for
>>>> biocLite too.
>>>>
>>>> Just a thought.  How much trouble am I looking at and what should I
>>>> watch
>>>> out for?
>>>
>>>
>>> Set
>>>
>>> rc.options(ipck = TRUE)
>>>
>>> and try again. Is this what you are looking for?
>>>
>>> -Deepayan
>>>
>>>> thanks,
>>>>
>>>> --t
>>>>
>>>>
>>>> *He that would live in peace and at ease, *
>>>> *Must not speak all he knows, nor judge all he sees.*
>>>>
>>>> Benjamin Franklin, Poor Richard's
>>>> Almanack<http://archive.org/details/poorrichardsalma00franrich>
>>>>
>>>>          [[alternative HTML version deleted]]
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>
>>         [[alternative HTML version deleted]]
>>
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>>
>
>
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