No subject

** building package indices ...
** testing if installed package can be loaded
Error in namespaceExport(ns, exports) : undefined exports: var.test.gwaa
ERROR: loading failed
* removing =91/Library/Frameworks/R.framework/Resources/library/VariABEL=92
* restoring previous
=91/Library/Frameworks/R.framework/Resources/library/VariABEL=92

It looks like in NAMESPACE you export var.test.gwaa, while the
function name is var_test_gwaa


Yurii

On Mon, Mar 7, 2011 at 6:10 PM,  <noreply at r-forge.wu-wien.ac.at> wrote:
> Author: maksim
> Date: 2011-03-07 18:10:10 +0100 (Mon, 07 Mar 2011)
> New Revision: 684
>
> Added:
> =A0 pkg/VariABEL/man/var_test_gwaa.Rd
> Removed:
> =A0 pkg/VariABEL/man/var.test.homogeneity.Rd
> Modified:
> =A0 pkg/VariABEL/NAMESPACE
> =A0 pkg/VariABEL/R/var.meta.gwaa.R
> =A0 pkg/VariABEL/R/var.test.gwaa.R
> Log:
> fix errors from R CMD check
>
> Modified: pkg/VariABEL/NAMESPACE
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> --- pkg/VariABEL/NAMESPACE =A0 =A0 =A02011-03-07 15:18:02 UTC (rev 683)
> +++ pkg/VariABEL/NAMESPACE =A0 =A0 =A02011-03-07 17:10:10 UTC (rev 684)
> @@ -2,7 +2,7 @@
>
>
> =A0export(
> - =A0 =A0 =A0 var.meta.gwaa,
> +# =A0 =A0 =A0var.meta.gwaa,
> =A0 =A0 =A0 =A0var.test.gwaa#,
> =A0 =A0 =A0 =A0#test_databel
> =A0 =A0 =A0 =A0)
>
> Modified: pkg/VariABEL/R/var.meta.gwaa.R
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> --- pkg/VariABEL/R/var.meta.gwaa.R =A0 =A0 =A02011-03-07 15:18:02 UTC (re=
v 683)
> +++ pkg/VariABEL/R/var.meta.gwaa.R =A0 =A0 =A02011-03-07 17:10:10 UTC (re=
v 684)
> @@ -16,36 +16,36 @@
> =A0#=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
>
>
> -
> -
> -"var.meta.gwaa" <-
> -function(input_filenames,
> - =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0testname=
,
> - =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0output_f=
ilename=3D"output.variance.metaanalysis",
> - =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0exclude_=
snp_below_threshold=3DF,
> - =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0threshol=
d=3D30,
> - =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0all_warn=
ings=3DF,
> - =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0skip_fir=
st_lines_amount=3D0,
> - =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0delim=3D=
' ') {
> -
> -
> -file_amount <- length(filenames_array)
> -
> -
> -return_val <- =A0.C("var_meta_gwaa_C", input_filenames, as.integer(file_=
amount), output_filename, as.integer(skip_first_lines_amount), delim,
> - =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=
 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 lambda=
s =3D double(file_amount+1),
> - =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=
 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 lambda=
s_NA =3D integer(file_amount+1),
> - =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=
 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 as.log=
ical(exclude_snp_below_threshold),
> - =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=
 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 as.int=
eger(threshold),
> - =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=
 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 as.log=
ical(all_warnings),
> - =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=
 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 as.cha=
racter(testname))
> -
> -
> -return_val$lambdas[return_val$lambdas_NA=3D=3D1] <- NA
> -
> -lambda_df <- data.frame(filename=3Dfilenames_array, lambda=3Dreturn_val$=
lambdas[1:file_amount])
> -
> -lambda_df <- rbind(lambda_df, data.frame(filename=3Doutput_filename, lam=
bda=3Dreturn_val$lambdas[file_amount+1]))
> -
> -lambda_df
> -}
> +#
> +#
> +#"var.meta.gwaa" <-
> +#function(input_filenames,
> +# =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 testname,
> +# =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 output_fil=
ename=3D"output.variance.metaanalysis",
> +# =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 exclude_sn=
p_below_threshold=3DF,
> +# =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 threshold=
=3D30,
> +# =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 all_warnin=
gs=3DF,
> +# =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 skip_first=
_lines_amount=3D0,
> +# =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 delim=3D' =
') {
> +#
> +#
> +#file_amount <- length(filenames_array)
> +#
> +#
> +#return_val <- =A0.C("var_meta_gwaa_C", input_filenames, as.integer(file=
_amount), output_filename, as.integer(skip_first_lines_amount), delim,
> +# =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0lamb=
das =3D double(file_amount+1),
> +# =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0lamb=
das_NA =3D integer(file_amount+1),
> +# =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0as.l=
ogical(exclude_snp_below_threshold),
> +# =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0as.i=
nteger(threshold),
> +# =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0as.l=
ogical(all_warnings),
> +# =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0as.c=
haracter(testname))
> +#
> +#
> +#return_val$lambdas[return_val$lambdas_NA=3D=3D1] <- NA
> +#
> +#lambda_df <- data.frame(filename=3Dfilenames_array, lambda=3Dreturn_val=
$lambdas[1:file_amount])
> +#
> +#lambda_df <- rbind(lambda_df, data.frame(filename=3Doutput_filename, la=
mbda=3Dreturn_val$lambdas[file_amount+1]))
> +#
> +#lambda_df
> +#}
>
> Modified: pkg/VariABEL/R/var.test.gwaa.R
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> --- pkg/VariABEL/R/var.test.gwaa.R =A0 =A0 =A02011-03-07 15:18:02 UTC (re=
v 683)
> +++ pkg/VariABEL/R/var.test.gwaa.R =A0 =A0 =A02011-03-07 17:10:10 UTC (re=
v 684)
> @@ -24,7 +24,7 @@
> =A0#_____________________________________________________________________=
________________________________________________________
> =A0#Available for user function for genome-wide testing variance homogene=
ity of trait's distribution.
> =A0#
> -"var.test.gwaa" <- function(formula, genodata, phenodata, genodata_info=
=3DNULL, testname=3D"sqlm", analysis_type=3D"AAvsABvsBB")
> +"var_test_gwaa" <- function(formula, genodata, phenodata, genodata_info=
=3DNULL, testname=3D"sqlm", analysis_type=3D"AAvsABvsBB")
> =A0{
>
>
>
> Deleted: pkg/VariABEL/man/var.test.homogeneity.Rd
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> --- pkg/VariABEL/man/var.test.homogeneity.Rd =A0 =A02011-03-07 15:18:02 U=
TC (rev 683)
> +++ pkg/VariABEL/man/var.test.homogeneity.Rd =A0 =A02011-03-07 17:10:10 U=
TC (rev 684)
> @@ -1,54 +0,0 @@
> -\name{var.test.homogeneity}
> -\alias{var.test.homogeneity}
> -\title{Function performs compariosn of genotypic variances.}
> -\description{
> -Presence of significant difference of genotypic variances points to poss=
ible
> - =A0 =A0 =A0 =A0 =A0 =A0 =A0 Significant variance difference points to p=
ossible presence of interaction between a tested SNP and a factor (or set o=
f factors).
> -}
> -\usage{
> -var.test.gwaa(formula, genodata, phenodata, genodata_info=3DNULL, testna=
me=3D"sqlm", analysis_type=3D"AAvsABvsBB")
> -}
> -\arguments{
> -
> - =A0 =A0 =A0 \item{formula} Regression model used for analysis. In the f=
irst stage linear regression is run to exclude main snp effect. In this sta=
ge adjustment for covariates is performed.
> - =A0 =A0 =A0 \item{genodata} The genotypes data in format of genabel or =
databel object
> - =A0\item{phenodata} The phenotypes data in format of data.frame object
> - =A0 =A0 =A0 \item{genodata_info} The file with snp information (name, p=
osition). Used if genodata is databel object.
> - =A0 =A0 =A0 \item{testname} Name of variance heterogeneity test to perf=
orm. sqlm (for imputed genotype data), levene, and bartlett test are suppor=
ted.
> - =A0 =A0 =A0 \item{analysis_type} Type of analsysis to perform. AAvsABvs=
BB - additive model where B allele additivly increase risk, AAvsABandBB - g=
roup AA tested agains AB and BB, ABvsAAandBB - AB against AA and BB, BBvsAA=
andAB - BB against AA and AB. Only available for typed snps.
> -}
> -\details{
> -
> -The function var.test.gwaa tests for difference in genotypic variances. =
This difference points to presence of possible interaction between the test=
ed SNP
> -and some factor. In the case sqlm test the analysis consists of two stag=
e: firstly the regular GWA id done where regression analysis is performed w=
ith
> -covariates specified in the input parameter formula, in the second stage=
 the regression analysis is performed with using residuals from the first s=
tage and
> -a sno as a covariate.
> -}
> -
> -\value{
> - =A0 =A0 =A0 The ouput is a data.frame object. The table contains the ch=
isq of variance heterogeneity test (the name is chisq) the effects and stan=
dart errors of all covariates included into regression model,
> - =A0 =A0 =A0 main snp effect (the names are snp_eff and snp_se). In the =
case of sqlm test the columns snp_eff_dispertion and snp_se_dispertion cont=
ain
> - =A0 =A0 =A0 effect of a snp on squared vallues of a trait.
> -
> - =A0 =A0 =A0 }
> -
> -
> -%\references{ http://www.biomedcentral.com/1471-2156/11/92/abstract }
> -\author{Maksim Struchalin}
> -%\note{ ~~further notes~~
> -%}
> -\seealso{
> - =A0 =A0 =A0 \code{\link{var.meta}},
> -}
> -\examples{
> - =A0 =A0 =A0 library(GenABEL)
> - =A0 =A0 =A0 data(srdta)
> - =A0 =A0 =A0 result1 <- var.test.gwaa(bt~qt1+qt2, genodata=3Dsrdta at gtdat=
a, phenodata=3Dsrdta at phdata)
> -
> -#if there is no covariates needed:
> - =A0 =A0 =A0 result2 <- var.test.gwaa("bt", genodata=3Dsrdta at gtdata, phe=
nodata=3Dsrdta at phdata)
> -
> -}
> -% Add one or more standard keywords, see file 'KEYWORDS' in the
> -% R documentation directory.
> -\keyword{manip}
>
> Added: pkg/VariABEL/man/var_test_gwaa.Rd
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> --- pkg/VariABEL/man/var_test_gwaa.Rd =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=
 =A0 =A0 =A0 =A0 (rev 0)
> +++ pkg/VariABEL/man/var_test_gwaa.Rd =A0 2011-03-07 17:10:10 UTC (rev 68=
4)
> @@ -0,0 +1,52 @@
> +\name{var_test_gwaa}
> +\alias{var_test_gwaa}
> +\title{Function performs compariosn of genotypic variances.}
> +\description{
> +Presence of significant difference of genotypic variances points to poss=
ible
> + =A0 =A0 =A0 =A0 =A0 =A0 =A0 Significant variance difference points to p=
ossible presence of interaction between a tested SNP and a factor (or set o=
f factors).
> +}
> +\usage{
> +var_test_gwaa(formula, genodata, phenodata, genodata_info=3DNULL, testna=
me=3D"sqlm", analysis_type=3D"AAvsABvsBB")
> +}
> +\arguments{\item{formula}{Regression model used for analysis. In the fir=
st stage linear regression is run to exclude main snp effect. In this stage=
 adjustment for covariates is performed.}
> +\item{genodata}{The genotypes data in format of genabel or databel objec=
t.}
> +\item{phenodata}{The phenotypes data in format of data.frame object.}
> +\item{genodata_info}{The file with snp information (name, position). Use=
d if genodata is databel object.}
> +\item{testname}{Name of variance heterogeneity test to perform. sqlm (fo=
r imputed genotype data), levene, and bartlett test are supported.}
> +\item{analysis_type}{Type of analsysis to perform. AAvsABvsBB - additive=
 model where B allele additivly increase risk, AAvsABandBB - group AA teste=
d agains AB and BB, ABvsAAandBB - AB against AA and BB, BBvsAAandAB - BB ag=
ainst AA and AB. Only available for typed snps.}
> +}
> +\details{
> +
> +The function var_test_gwaa tests for difference in genotypic variances. =
This difference points to presence of possible interaction between the test=
ed SNP
> +and some factor. In the case sqlm test the analysis consists of two stag=
e: firstly the regular GWA id done where regression analysis is performed w=
ith
> +covariates specified in the input parameter formula, in the second stage=
 the regression analysis is performed with using residuals from the first s=
tage and
> +a sno as a covariate.
> +}
> +
> +\value{
> + =A0 =A0 =A0 The ouput is a data.frame object. The table contains the ch=
isq of variance heterogeneity test (the name is chisq) the effects and stan=
dart errors of all covariates included into regression model,
> + =A0 =A0 =A0 main snp effect (the names are snp_eff and snp_se). In the =
case of sqlm test the columns snp_eff_dispertion and snp_se_dispertion cont=
ain
> + =A0 =A0 =A0 effect of a snp on squared vallues of a trait.
> +
> + =A0 =A0 =A0 }
> +
> +
> +%\references{ http://www.biomedcentral.com/1471-2156/11/92/abstract }
> +\author{Maksim Struchalin}
> +%\note{ ~~further notes~~
> +%}
> +%\seealso{
> +% =A0 =A0 =A0\code{\link{var.meta}},
> +%}
> +\examples{
> + =A0 =A0 =A0 library(GenABEL)
> + =A0 =A0 =A0 data(srdta)
> + =A0 =A0 =A0 result1 <- var_test_gwaa(bt~qt1+qt2, genodata=3Dsrdta at gtdat=
a, phenodata=3Dsrdta at phdata)
> +
> +#if there is no covariates needed:
> + =A0 =A0 =A0 result2 <- var_test_gwaa("bt", genodata=3Dsrdta at gtdata, phe=
nodata=3Dsrdta at phdata)
> +
> +}
> +% Add one or more standard keywords, see file 'KEYWORDS' in the
> +% R documentation directory.
> +\keyword{manip}
>
> _______________________________________________
> Genabel-commits mailing list
> Genabel-commits at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-comm=
its
>