[Bioc-devel] droplevels method for DataFrame?

Tue Oct 7 19:37:47 CEST 2014

Cool. We should consider moving some of the infrastructure pieces to the
github bridge.

I added a droplevels method for List that should take care of things.

On Mon, Oct 6, 2014 at 6:11 PM, Ryan C. Thompson <rct at thompsonclan.org>
wrote:

> Hi,
>
> Yes, if something is on Github (or just any git/hg repo that I can clone)
> then I'm much more likely to try to fix simple bugs that I discover and
> submit patches or pull requests rather than report them as bugs. It doesn't
> hurt that Github provides tools to submit pull requests from the terminal.
> I've never learned cvs or svn because I mostly haven't had the need in the
> past (haven't been working on projects that use cvs/svn).
>
> So in my case, yes, if S4Vectors was on Github I probably would have
> cloned it and tried to fix it before reporting the issue here, and I would
> have either reported it with a patch or explained what I tried and where I
> got stuck.
>
> -Ryan
>
> On Mon 06 Oct 2014 05:55:02 PM PDT, Michael Lawrence wrote:
>
>> Makes sense to me. Just wondering: if S4Vectors were say on github,
>> would this be something that you would be comfortable resolving via a
>> pull request? Would social coding increase external contributions to
>> the infrastructure?
>>
>> On Mon, Oct 6, 2014 at 5:13 PM, Ryan C. Thompson <rct at thompsonclan.org
>> <mailto:rct at thompsonclan.org>> wrote:
>>
>>     Hi,
>>
>>     I've just noticed that DataFrame doesn't have a "droplevels"
>>     method, but "data.frame" does. In fact, "droplevels.data.frame"
>>     seems to work just fine on DataFrame objects. Could this be added?
>>
>>     -Ryan
>>
>>
>>     > sessionInfo()
>>     R version 3.1.0 (2014-04-10)
>>     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] splines   grDevices datasets  parallel  graphics  stats utils
>>     [8] methods   base
>>
>>     other attached packages:
>>      [1] DESeq2_1.4.5               RcppArmadillo_0.4.450.1.0
>>      [3] Rcpp_0.11.2                cqn_1.10.0
>>      [5] quantreg_5.05              SparseM_1.05
>>      [7] preprocessCore_1.26.1      nor1mix_1.2-0
>>      [9] mclust_4.4                 baySeq_1.18.0
>>     [11] DESeq_1.16.0               lattice_0.20-29
>>     [13] locfit_1.5-9.1             edgeR_3.6.8
>>     [15] limma_3.20.9               arrayQualityMetrics_3.20.0
>>     [17] partitions_1.9-15          biomaRt_2.20.0
>>     [19] functional_0.6             sqldf_0.4-7.1
>>     [21] RSQLite.extfuns_0.0.1      RSQLite_0.11.4
>>     [23] DBI_0.3.1                  gsubfn_0.6-6
>>     [25] proto_0.3-10               GenomicFeatures_1.16.2
>>     [27] AnnotationDbi_1.26.0       chipseq_1.14.0
>>     [29] inline_0.3.13              affy_1.42.3
>>     [31] Biobase_2.24.0             ShortRead_1.22.0
>>     [33] GenomicAlignments_1.0.6    BSgenome_1.32.0
>>     [35] BiocParallel_0.6.1         Rsamtools_1.16.1
>>     [37] Biostrings_2.32.1          XVector_0.4.0
>>     [39] doParallel_1.0.8           iterators_1.0.7
>>     [41] rtracklayer_1.24.2         GenomicRanges_1.16.4
>>     [43] GenomeInfoDb_1.0.2         Matrix_1.1-4
>>     [45] RColorBrewer_1.0-5         foreach_1.4.2
>>     [47] plyr_1.8.1                 stringr_0.6.2
>>     [49] ggplot2_1.0.0              IRanges_1.22.10
>>     [51] BiocGenerics_0.10.0        BiocInstaller_1.14.2
>>
>>     loaded via a namespace (and not attached):
>>      [1] acepack_1.3-3.3      affyio_1.32.0        affyPLM_1.40.1
>>      [4] annotate_1.42.1      base64_1.2           base64enc_0.1-2
>>      [7] BatchJobs_1.4        BBmisc_1.7           beadarray_2.14.1
>>     [10] BeadDataPackR_1.16.0 bitops_1.0-6         brew_1.0-6
>>     [13] Cairo_1.5-6          checkmate_1.4        chron_2.3-45
>>     [16] cluster_1.15.3       codetools_0.2-9      colorspace_1.2-4
>>     [19] compiler_3.1.0       digest_0.6.4         fail_1.2
>>     [22] foreign_0.8-61       Formula_1.1-2        gcrma_2.36.0
>>     [25] genefilter_1.46.1    geneplotter_1.42.0   gmp_0.5-12
>>     [28] grid_3.1.0           gridSVG_1.4-0        gtable_0.1.2
>>     [31] Hmisc_3.14-5         hwriter_1.3.2        illuminaio_0.6.1
>>     [34] latticeExtra_0.6-26  MASS_7.3-34          munsell_0.4.2
>>     [37] nnet_7.3-8           polynom_1.3-8        RCurl_1.96-0
>>     [40] reshape2_1.4         RJSONIO_1.2-0.2      rpart_4.1-8
>>     [43] scales_0.2.4         sendmailR_1.2-1      setRNG_2013.9-1
>>     [46] stats4_3.1.0         survival_2.37-7      SVGAnnotation_0.93-1
>>     [49] tools_3.1.0          vsn_3.32.0           XML_3.98-1.1
>>     [52] xtable_1.7-4         zlibbioc_1.10.0
>>
>>     _________________________________________________
>>     Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org> mailing
>>     list
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>>
>>
>>

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