- using R version 3.6.3 (2020-02-29)
- using platform: x86_64-w64-mingw32 (64-bit)
- using session charset: ISO8859-1
- checking for file 'gwsem/DESCRIPTION' ... OK
- checking extension type ... Package
- this is package 'gwsem' version '2.0.9'
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking whether package 'gwsem' can be installed ... OK
- checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
libs 4.0Mb
- checking package directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking R files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- loading checks for arch 'i386'
- checking whether the package can be loaded ... OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace can be unloaded cleanly ... OK
- checking loading without being on the library search path ... OK
- checking use of S3 registration ... OK
- loading checks for arch 'x64'
- checking whether the package can be loaded ... OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace can be unloaded cleanly ... OK
- checking loading without being on the library search path ... OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [7s] OK
- checking Rd files ... OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking compilation flags in Makevars ... OK
- checking for GNU extensions in Makefiles ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compiled code ... OK
- checking examples ...
- running examples for arch 'i386' ... ERROR
Running examples in 'gwsem-Ex.R' failed
The error most likely occurred in:
> ### Name: plot.gwsemResult
> ### Title: Creates a Manhattan plot
> ### Aliases: plot.gwsemResult
>
> ### ** Examples
>
> tdir <- tempdir()
> dir <- system.file("extdata", package = "gwsem")
> pheno <- data.frame(anxiety=rnorm(500))
> m1 <- buildItem(pheno, 'anxiety')
> GWAS(m1, file.path(dir,"example.bgen"),
+ file.path(tdir,"out.log"))
Running OneItem with 3 parameters
Done. See 'D:\temp\RtmpAh7Mvn/out.log' for results
> got <- loadResults(file.path(tdir,"out.log"), "snp_to_anxiety")
> plot(got)
Warning in data.matrix(x) : NAs introduced by coercion
Warning in data.matrix(x) : NAs introduced by coercion
Warning in data.matrix(x) : NAs introduced by coercion
Warning in data.matrix(x) : NAs introduced by coercion
Warning in data.matrix(x) : NAs introduced by coercion
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in plot.window(...) : need finite 'ylim' values
Calls: plot ... localPlot -> plot -> plot.default -> localWindow -> plot.window
Execution halted
- running examples for arch 'x64' ... ERROR
Running examples in 'gwsem-Ex.R' failed
The error most likely occurred in:
> ### Name: plot.gwsemResult
> ### Title: Creates a Manhattan plot
> ### Aliases: plot.gwsemResult
>
> ### ** Examples
>
> tdir <- tempdir()
> dir <- system.file("extdata", package = "gwsem")
> pheno <- data.frame(anxiety=rnorm(500))
> m1 <- buildItem(pheno, 'anxiety')
> GWAS(m1, file.path(dir,"example.bgen"),
+ file.path(tdir,"out.log"))
Running OneItem with 3 parameters
Done. See 'D:\temp\RtmpA5Bmg8/out.log' for results
> got <- loadResults(file.path(tdir,"out.log"), "snp_to_anxiety")
> plot(got)
Warning in data.matrix(x) : NAs introduced by coercion
Warning in data.matrix(x) : NAs introduced by coercion
Warning in data.matrix(x) : NAs introduced by coercion
Warning in data.matrix(x) : NAs introduced by coercion
Warning in data.matrix(x) : NAs introduced by coercion
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in plot.window(...) : need finite 'ylim' values
Calls: plot ... localPlot -> plot -> plot.default -> localWindow -> plot.window
Execution halted
- checking for unstated dependencies in 'tests' ... OK
- checking tests ...
- running tests for arch 'i386' ... [3s] OK
Running 'testthat.R' [3s]
- running tests for arch 'x64' ... [3s] OK
Running 'testthat.R' [2s]
- checking PDF version of manual ... OK
- DONE
Status: 2 ERRORs, 1 NOTE