[GenABEL-dev] [Genabel-commits] r713 - in pkg/GenABEL: . R inst/unitTests src/GAlib

[Yurii Aulchenko]

Fixed bug [1388] reported by Marcin. The key was

> -#define MAXIDS 2000000
> +#define MAXIDS 200000

i.e. the constat was way too big, extra zero ... The use of constant
can (and should) be actually avoided in this case.

bw,
Yurii

On Fri, May 13, 2011 at 12:17 PM,  <noreply at r-forge.wu-wien.ac.at> wrote:
> Author: yurii
> Date: 2011-05-13 12:17:57 +0200 (Fri, 13 May 2011)
> New Revision: 713
>
> Added:
>   pkg/GenABEL/inst/unitTests/runit.convert.snp.ped.R
> Modified:
>   pkg/GenABEL/CHANGES.LOG
>   pkg/GenABEL/DESCRIPTION
>   pkg/GenABEL/R/zzz.R
>   pkg/GenABEL/src/GAlib/convert_snp_merlin.cpp
>   pkg/GenABEL/src/GAlib/convert_snp_merlin_wslash.cpp
> Log:
> Fixing bug [1388], added regression test
>
> Modified: pkg/GenABEL/CHANGES.LOG
> ===================================================================
> --- pkg/GenABEL/CHANGES.LOG     2011-05-05 13:06:37 UTC (rev 712)
> +++ pkg/GenABEL/CHANGES.LOG     2011-05-13 10:17:57 UTC (rev 713)
> @@ -1,5 +1,7 @@
> -*** v. 1.6-7 (2011.05.05)
> +*** v. 1.6-7 (2011.05.13)
>
> +Fixing bug [1388], added regression test
> +
>  upgrade version number
>
>  fix in example of polygenic_hglm
>
> Modified: pkg/GenABEL/DESCRIPTION
> ===================================================================
> --- pkg/GenABEL/DESCRIPTION     2011-05-05 13:06:37 UTC (rev 712)
> +++ pkg/GenABEL/DESCRIPTION     2011-05-13 10:17:57 UTC (rev 713)
> @@ -2,7 +2,7 @@
>  Type: Package
>  Title: genome-wide SNP association analysis
>  Version: 1.6-7
> -Date: 2011-05-05
> +Date: 2011-05-13
>  Author: Yurii Aulchenko et al.
>  Maintainer: Yurii Aulchenko <i.aoultchenko at erasmusmc.nl>
>  Depends: R (>= 2.10.0), methods, MASS
>
> Modified: pkg/GenABEL/R/zzz.R
> ===================================================================
> --- pkg/GenABEL/R/zzz.R 2011-05-05 13:06:37 UTC (rev 712)
> +++ pkg/GenABEL/R/zzz.R 2011-05-13 10:17:57 UTC (rev 713)
> @@ -1,6 +1,6 @@
>  .onLoad <- function(lib, pkg) {
>        GenABEL.version <- "1.6-7"
> -       cat("GenABEL v.",GenABEL.version,"(May 05, 2011) loaded\n")
> +       cat("GenABEL v.",GenABEL.version,"(May 13, 2011) loaded\n")
>
>        # check for updates and news
>        address <- c(
>
> Added: pkg/GenABEL/inst/unitTests/runit.convert.snp.ped.R
> ===================================================================
> --- pkg/GenABEL/inst/unitTests/runit.convert.snp.ped.R                          (rev 0)
> +++ pkg/GenABEL/inst/unitTests/runit.convert.snp.ped.R  2011-05-13 10:17:57 UTC (rev 713)
> @@ -0,0 +1,30 @@
> +### --- Test setup ---
> +#
> +# regression test
> +#
> +
> +if(FALSE) {
> +       ## Not really needed, but can be handy when writing tests
> +       library(RUnit)
> +       library(GenABEL)
> +}
> +
> +### do not run
> +#stop("SKIP THIS TEST")
> +###
> +
> +### ---- common functions and data -----
> +
> +#source(paste("../inst/unitTests/shared_functions.R"))
> +#source(paste(path,"/shared_functions.R",sep=""))
> +
> +### --- Test functions ---
> +
> +test.convert.snp.ped <- function()
> +{
> +       pref <- "../inst/exdata/"
> +       pedf <- paste(pref,"pedin.18",sep="")
> +       mapf <- paste(pref,"map.18",sep="")
> +       convert.snp.ped(pedfile=pedf,mapfile=mapf,out="tmp.raw")
> +       unlink("tmp.raw")
> +}
> \ No newline at end of file
>
>
> Property changes on: pkg/GenABEL/inst/unitTests/runit.convert.snp.ped.R
> ___________________________________________________________________
> Added: svn:mime-type
>   + text/plain
>
> Modified: pkg/GenABEL/src/GAlib/convert_snp_merlin.cpp
> ===================================================================
> --- pkg/GenABEL/src/GAlib/convert_snp_merlin.cpp        2011-05-05 13:06:37 UTC (rev 712)
> +++ pkg/GenABEL/src/GAlib/convert_snp_merlin.cpp        2011-05-13 10:17:57 UTC (rev 713)
> @@ -26,7 +26,7 @@
>
>  #include <R.h>
>
> -#define MAXIDS 2000000
> +#define MAXIDS 200000
>
>  string replace_mrl(string in);
>  string replace_mach(string in);
>
> Modified: pkg/GenABEL/src/GAlib/convert_snp_merlin_wslash.cpp
> ===================================================================
> --- pkg/GenABEL/src/GAlib/convert_snp_merlin_wslash.cpp 2011-05-05 13:06:37 UTC (rev 712)
> +++ pkg/GenABEL/src/GAlib/convert_snp_merlin_wslash.cpp 2011-05-13 10:17:57 UTC (rev 713)
> @@ -26,7 +26,7 @@
>
>  #include <R.h>
>
> -#define MAXIDS 100000
> +#define MAXIDS 200000
>
>  string replace_mach(string in);
>
>
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