similar to: Problem on loading annotation for BioC - error: RS-DBI driver: (error in statement: near "s": syntax error)

Hi All, I am having trouble executing SQL statements on a few dataframes, but the funny thing is that I am able to execute the statement on some other dataframes. To test, I have 2 very small dataframes (6 rows and some columns). One is 'lessliq', the dput is given below. > dput(head(lessliq)) structure(list(V1 = c(50464677L, 50464846L, 50432581L, 50426614L, 50504329L, 50504735L), V2

On 03/27/2014 02:13 AM, Ulrich Bodenhofer wrote: > I fully agree, Michael, that this would be a great thing to have! I have > often wondered why R and the standard packages are still sticking so > much to the old-style S3 flavor though S4 is part of standard R. I > acknowledge that backward compatibility is important, but, as far as I > got it, redefining a function or S3 generic as

On 03/27/2014 06:31 PM, Herv? Pag?s wrote: > On 03/27/2014 02:13 AM, Ulrich Bodenhofer wrote: >> [...] >> >> For the time being, it seems I have three options: >> >> 1) not supplying the sort() function yet (it is not yet in the release, >> but only in my internal devel version) >> 2) including a dependency to BiocGenerics >> 3) leaving the

I fully agree, Michael, that this would be a great thing to have! I have often wondered why R and the standard packages are still sticking so much to the old-style S3 flavor though S4 is part of standard R. I acknowledge that backward compatibility is important, but, as far as I got it, redefining a function or S3 generic as an S4 generic should not harm existing functionality (if done

[cross-posted to R-devel and bioc-devel] Hi, I am trying to implement a 'sort' method in one of the CRAN packages I am maintaining ('apcluster'). I started with using setMethod("sort", ...) in my package, which worked fine. Since many users of my package are from the bioinformatics field, I want to ensure that my package works smoothly with Bioconductor. The problem

Hi, this is tangentially related to the recent discussion on vignettes. vignette() currently produces a listing of available vignettes, but these are not clickable. Since R has a browseURL() function, it seems natural to have a version that produces HTML with clickable links. Here's an attempt at that: source("http://dsarkar.fhcrc.org/R/vignette-browser.R") browseVignettes()

> R.version.string [1] "R Under development (unstable) (2012-02-26 r58493)" In the recent addition "It is important if you export S4 methods that the corresponding generics are available: the requirementa on this are stricter as from R 2.15.0. You may for example need to import plot from graphics to make visible a function to be converted into its implicit generic. But it is

In ?Sweave, it refers to Sweave User Manual. In the doc folder of utils package, I see "Sweave.pdf". However, I can't find it from within R > vignette("Sweave User Manual") Warning message: vignette ?Sweave User Manual? not found > browseVignettes("utils") No vignettes found by browseVignettes("utils") > library(help=utils) does not

I am trying to exclude integer values from a small data frame 1, d1 that have matching hits in data frame 2, d2 (Very big) which involves matching those hits first. I am trying to use sqldf on the df's in the following fashion: df1: V1 12675 14753 16222 18765 df2: head(df2) V1 V2 13647 rd1500 14753 rd1580 15987 rd1590 16222 rd2020.....

In pvec(list(1, 2), FUN, mc.cores=2) FUN sees integer() arguments whereas pvec(list(1, 2, 3), FUN, mc.cores=2) FUN sees list() arguments; the latter seems consistent with pvec's description. This came up in a complicated Bioconductor thread about generics and parallel evaluation https://stat.ethz.ch/pipermail/bioc-devel/2012-October/003745.html One relevant point is that a

That might be worth thinking about generally, but it would still be nice to have the base generics pre-defined, so that people are not copy and pasting the definitions everywhere, hoping that they stay consistent. On Wed, Mar 26, 2014 at 6:13 AM, Gabriel Becker <gmbecker@ucdavis.edu>wrote: > Perhaps a patch to R such that generics don't clobber each-other's method > tables

Hi, On a Win7 64 bit, I have installed: *R-15.0 and I am running it in 64bits *Rtools215.exe*MySQL 5.5.23 64bits My PATH start with D:\BenSave\Rtools\bin;D:\BenSave\Rtools\MinGW64\bin;D:\BenSave\R\R-2.15.0\bin;D:\BenSave\Rtools\MinGW\bin;D:\BenSave\Rtools\gcc-4.6.3\bin; Note that I place MinGW64\bin has I want the package in 64 bits, so just in case it helps... To install RMySQL 64 bits, I

Should functions or the user be responsible for coercing an S4 object argument containing the proper object (and thus should below be considered a bug in the packages or not)? The example is with RSQLite but the same thing happens with RMySQL, and other DBI packages. > library("RSQLite") Loading required package: DBI > m <- dbDriver("SQLite") > con <-

You are doing a lot of things that are non-standard, so I doubt if anyone is going to be able to help you without access to a simple reproducible example of a package that does what you do. Try to cut out as much as you can to make it minimal. For example, devtools::document() (indeed, most of your code) is probably irrelevant to your problem with vignettes, but things like your

Dear all, I am struggling with an issue related to static vignettes: they work, but only when present in double in the tarball -- in the folder inst/doc and vignettes; see below for details. Details: I am pre-compiling heavy vignettes thanks to the vignette builder R.rsp. So basically, I have PDF files which I want the package to use as Vignettes. For this, I have the following in my

Hi there, I had an error when using RSQLite. My code and the error message are the following: > dbGetQuery(sql.dispersion, + "create table monthly_data_temp as + select a.*, b.industry + from monthly_data as a left join + siccd_industry_ff49 as b + on a.siccd = b.siccd + order by permno, date") Error

Noted Duncan and TRUE... I cannot do more immediately unfortunately, that is always the issue of asking a last minute panic attack question before teaching a course involving the package... I do have /doc in my .Rbuildignore for reasons I can no longer remember... I will dig and create a MRE/reprex. The students will download heavy packages, but they probably won't notice. *Apologies* In the

I have a (very big - 1.5 rows) dataframe with a (POSIXt" "POSIXlt") column h (hour). Surprisingly, I cannot calculate a simple aggregate over the dataframe. > n.h1 = sqldf("select distinct h, count(*) from x group by h") Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: no such table: x) In addition: Warning message: In

Dear R developers, I observed that the html help page index entry "Read overview or browse directory" for package vignettes is missing in recent R-devel. This happened on two independent computers (WinXP Prof. SP3, German) with R-devel compiled from sources svn rev. 48125 resp. 48128 It's the same for my own and also for more prominent packages as well (e.g. grid). The

Hi, I am new to bioconductor, trying to install KEGGSOAP package, but got warnings() when installing and error message when trying to load the package, can anyone suggest what went wrong? many thanks John > source("http://bioconductor.org/biocLite.R") Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help > biocLite("KEGGSOAP") BioC_mirror: