• 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