CRAN Package Check Results for Package lfmm

Last updated on 2021-05-27 12:54:15 CEST.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	1.0	44.07	154.45	198.52	ERROR
r-devel-linux-x86_64-debian-gcc	1.0	32.32	115.25	147.57	ERROR
r-devel-linux-x86_64-fedora-clang	1.0			275.91	ERROR
r-devel-linux-x86_64-fedora-gcc	1.0			251.54	ERROR
r-devel-windows-x86_64	1.0	53.00	242.00	295.00	OK
r-devel-windows-x86_64-gcc10-UCRT	1.0				NOTE
r-patched-linux-x86_64	1.0	36.55	179.58	216.13	OK
r-patched-solaris-x86	1.0			593.20	NOTE
r-release-linux-x86_64	1.0	38.24	176.55	214.79	OK
r-release-windows-ix86+x86_64	1.0	64.00	339.00	403.00	OK
r-oldrel-macos-x86_64	1.0				NOTE
r-oldrel-windows-ix86+x86_64	1.0	68.00	282.00	350.00	OK

Check Details

Version: 1.0
Check: examples
Result: ERROR
    Running examples in 'lfmm-Ex.R' failed
    The error most likely occurred in:

    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: effect_size
    > ### Title: Direct effect sizes estimated from latent factor models
    > ### Aliases: effect_size
    >
    > ### ** Examples
    >
    > library(lfmm)
    >
    > ## Simulation of 1000 genotypes for 100 individuals (y)
    > u <- matrix(rnorm(300, sd = 1), nrow = 100, ncol = 2)
    Error in matrix(rnorm(300, sd = 1), nrow = 100, ncol = 2) :
     data length differs from size of matrix: [300 != 100 x 2]
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'lfmm.Rmd' using rmarkdown
    It = 1/100, err2 = 0.163976365842701
    It = 2/100, err2 = 0.150909974059673
    It = 3/100, err2 = 0.150916204324368
    === lambda = 0.140473176172564, no zero B proportion = 0.000445384701035519
    It = 1/100, err2 = 0.150916343641328
    It = 2/100, err2 = 0.15091547425753
    === lambda = 0.134088453517907, no zero B proportion = 0.00103923096908288
    It = 1/100, err2 = 0.150915412709902
    It = 2/100, err2 = 0.150913975701532
    === lambda = 0.12799392636169, no zero B proportion = 0.00196711576290688
    It = 1/100, err2 = 0.150913871462829
    It = 2/100, err2 = 0.150911733598199
    It = 3/100, err2 = 0.150911574423684
    === lambda = 0.12217640487064, no zero B proportion = 0.00300634673198976
    It = 1/100, err2 = 0.150911562286119
    It = 2/100, err2 = 0.150908693359628
    It = 3/100, err2 = 0.150908471900049
    === lambda = 0.11662329870976, no zero B proportion = 0.00456519318561407
    It = 1/100, err2 = 0.150908454358739
    It = 2/100, err2 = 0.150904858480187
    It = 3/100, err2 = 0.150904571937453
    === lambda = 0.111322589794214, no zero B proportion = 0.00627250120625023
    It = 1/100, err2 = 0.15090454848927
    It = 2/100, err2 = 0.150900036019481
    It = 3/100, err2 = 0.150899664398152
    === lambda = 0.106262806279665, no zero B proportion = 0.00868500167019263
    It = 1/100, err2 = 0.150899632925778
    It = 2/100, err2 = 0.150894188051447
    It = 3/100, err2 = 0.150893724548089
    === lambda = 0.10143299773481, no zero B proportion = 0.0117284637939353
    Quitting from lines 241-254 (lfmm.Rmd)
    Error: processing vignette 'lfmm.Rmd' failed with diagnostics:
    data length differs from size of matrix: [300 != 100 x 2]
    --- failed re-building 'lfmm.Rmd'

    SUMMARY: processing the following file failed:
     'lfmm.Rmd'

    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.0
Check: installed package size
Result: NOTE
     installed size is 12.0Mb
     sub-directories of 1Mb or more:
     data 1.8Mb
     libs 9.7Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-oldrel-macos-x86_64

Version: 1.0
Check: dependencies in R code
Result: NOTE
    Namespaces in Imports field not imported from:
     ‘ggplot2’ ‘knitr’ ‘purrr’ ‘rmarkdown’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-gcc10-UCRT, r-patched-solaris-x86, r-oldrel-macos-x86_64

Version: 1.0
Check: examples
Result: ERROR
    Running examples in ‘lfmm-Ex.R’ failed
    The error most likely occurred in:

    > ### Name: effect_size
    > ### Title: Direct effect sizes estimated from latent factor models
    > ### Aliases: effect_size
    >
    > ### ** Examples
    >
    > library(lfmm)
    >
    > ## Simulation of 1000 genotypes for 100 individuals (y)
    > u <- matrix(rnorm(300, sd = 1), nrow = 100, ncol = 2)
    Error in matrix(rnorm(300, sd = 1), nrow = 100, ncol = 2) :
     data length differs from size of matrix: [300 != 100 x 2]
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘lfmm.Rmd’ using rmarkdown
    It = 1/100, err2 = 0.163976365842701
    It = 2/100, err2 = 0.150909974059673
    It = 3/100, err2 = 0.150916204324368
    === lambda = 0.140473176172564, no zero B proportion = 0.000445384701035519
    It = 1/100, err2 = 0.150916343641328
    It = 2/100, err2 = 0.15091547425753
    === lambda = 0.134088453517907, no zero B proportion = 0.00103923096908288
    It = 1/100, err2 = 0.150915412709902
    It = 2/100, err2 = 0.150913975701532
    === lambda = 0.12799392636169, no zero B proportion = 0.00196711576290688
    It = 1/100, err2 = 0.150913871462829
    It = 2/100, err2 = 0.150911733598199
    It = 3/100, err2 = 0.150911574423684
    === lambda = 0.12217640487064, no zero B proportion = 0.00300634673198976
    It = 1/100, err2 = 0.150911562286119
    It = 2/100, err2 = 0.150908693359628
    It = 3/100, err2 = 0.150908471900049
    === lambda = 0.11662329870976, no zero B proportion = 0.00456519318561407
    It = 1/100, err2 = 0.150908454358739
    It = 2/100, err2 = 0.150904858480187
    It = 3/100, err2 = 0.150904571937453
    === lambda = 0.111322589794214, no zero B proportion = 0.00627250120625023
    It = 1/100, err2 = 0.15090454848927
    It = 2/100, err2 = 0.150900036019481
    It = 3/100, err2 = 0.150899664398152
    === lambda = 0.106262806279665, no zero B proportion = 0.00868500167019263
    It = 1/100, err2 = 0.150899632925778
    It = 2/100, err2 = 0.150894188051447
    It = 3/100, err2 = 0.150893724548089
    === lambda = 0.10143299773481, no zero B proportion = 0.0117284637939353
    Quitting from lines 241-254 (lfmm.Rmd)
    Error: processing vignette 'lfmm.Rmd' failed with diagnostics:
    data length differs from size of matrix: [300 != 100 x 2]
    --- failed re-building ‘lfmm.Rmd’

    SUMMARY: processing the following file failed:
     ‘lfmm.Rmd’

    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc