CRAN Package Check Results for Package gwsem

Last updated on 2021-05-09 18:46:46 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.1.0 140.75 446.35 587.10 NOTE
r-devel-linux-x86_64-debian-gcc 2.1.0 97.55 330.26 427.81 NOTE
r-devel-linux-x86_64-fedora-clang 2.1.0 580.85 NOTE
r-devel-linux-x86_64-fedora-gcc 2.1.0 595.06 NOTE
r-devel-windows-ix86+x86_64 2.1.0 244.00 174.00 418.00 NOTE
r-devel-windows-x86_64-gcc10-UCRT 2.1.0 NOTE
r-patched-linux-x86_64 2.1.0 112.89 385.79 498.68 NOTE
r-patched-solaris-x86 2.1.0 268.20 OK
r-release-linux-x86_64 2.1.0 111.57 386.66 498.23 OK
r-release-macos-x86_64 2.1.0 ERROR
r-release-windows-ix86+x86_64 2.1.0 230.00 138.00 368.00 NOTE
r-oldrel-macos-x86_64 2.1.0 ERROR
r-oldrel-windows-ix86+x86_64 2.1.0 256.00 159.00 415.00 ERROR

Additional issues

M1mac

Check Details

Version: 2.1.0
Check: LazyData
Result: NOTE
     'LazyData' is specified without a 'data' directory
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-x86_64-gcc10-UCRT, r-patched-linux-x86_64

Version: 2.1.0
Check: installed package size
Result: NOTE
     installed size is 11.7Mb
     sub-directories of 1Mb or more:
     libs 10.4Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.1.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [47s/47s]
    Running the tests in ‘tests/testthat.R’ failed.
    Last 13 lines of output:
    
     >
     > test_check("gwsem")
     ══ Skipped tests ═══════════════════════════════════════════════════════════════
     • On Mac (1)
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Failure (test-formats.R:115:1): (code run outside of `test_that()`) ─────────
     rmse(bgen$snp_to_F, pgen$snp_to_F) not equal to 0.
     1/1 mismatches
     [1] 1.76 - 0 == 1.76
    
     [ FAIL 1 | WARN 7 | SKIP 1 | PASS 188 ]
     Error: Test failures
     Execution halted
Flavor: r-release-macos-x86_64

Version: 2.1.0
Check: examples
Result: 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 '/tmp/RtmpdasUxT/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
Flavor: r-oldrel-macos-x86_64

Version: 2.1.0
Check: running examples for arch ‘i386’
Result: 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\Rtmpa8xXBF/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
Flavor: r-oldrel-windows-ix86+x86_64

Version: 2.1.0
Check: running examples for arch ‘x64’
Result: 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\RtmpyCMd8M/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
Flavor: r-oldrel-windows-ix86+x86_64