* using log directory 'd:/RCompile/CRANincoming/R-devel/smer.Rcheck'
* using R Under development (unstable) (2025-01-13 r87564 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'smer/DESCRIPTION' ... OK
* this is package 'smer' version '0.0.1'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Julian Stamp <julian.d.stamp@gmail.com>'

New submission

Possibly misspelled words in DESCRIPTION:
  Epistasis (2:24)
  al (13:14)
  epistasis (12:47)
  et (13:11)

Found the following (possibly) invalid file URIs:
  URI: articles/tutorial-memory-optimization.html
    From: inst/doc/smer.html
  URI: articles/tutorial-simulate-traits.html
    From: inst/doc/smer.html
  URI: articles/tutorial-create-mask-file.html
    From: inst/doc/study-erythroid-differentiation-data.html
  URI: articles/study-erythroid-differentiation-data.html
    From: inst/doc/tutorial-memory-optimization.html
  URI: articles/tutorial-memory-optimization.html
    From: README.md
* 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 'smer' can be installed ... OK
* used C++ compiler: 'g++.exe (GCC) 13.3.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Unknown package 'sme' in Rd xrefs
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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 use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... ERROR
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(smer)
  > 
  > test_check("smer")
  HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
    #000: C:/rtools40/tmp/CMake-hdf5-1.10.7/hdf5-1.10.7/src/H5F.c line 429 in H5Fopen(): unable to open file
      major: File accessibility
      minor: Unable to open file
    #001: C:/rtools40/tmp/CMake-hdf5-1.10.7/hdf5-1.10.7/src/H5Fint.c line 1644 in H5F_open(): unable to open file: time = Tue Jan 14 18:08:29 2025
  , name = '../../smer/testdata/test.h5', tent_flags = 0
      major: File accessibility
      minor: Unable to open file
    #002: C:/rtools40/tmp/CMake-hdf5-1.10.7/hdf5-1.10.7/src/H5FD.c line 741 in H5FD_open(): open failed
      major: Virtual File Layer
      minor: Unable to initialize object
    #003: C:/rtools40/tmp/CMake-hdf5-1.10.7/hdf5-1.10.7/src/H5FDsec2.c line 360 in H5FD__sec2_open(): unable to open file: name = '../../smer/testdata/test.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0
      major: File accessibility
      minor: Unable to open file
  HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
    #000: C:/rtools40/tmp/CMake-hdf5-1.10.7/hdf5-1.10.7/src/H5F.c line 429 in H5Fopen(): unable to open file
      major: File accessibility
      minor: Unable to open file
    #001: C:/rtools40/tmp/CMake-hdf5-1.10.7/hdf5-1.10.7/src/H5Fint.c line 1644 in H5F_open(): unable to open file: time = Tue Jan 14 18:08:29 2025
  , name = '../../smer/testdata/test.h5', tent_flags = 0
      major: File accessibility
      minor: Unable to open file
    #002: C:/rtools40/tmp/CMake-hdf5-1.10.7/hdf5-1.10.7/src/H5FD.c line 741 in H5FD_open(): open failed
      major: Virtual File Layer
      minor: Unable to initialize object
    #003: C:/rtools40/tmp/CMake-hdf5-1.10.7/hdf5-1.10.7/src/H5FDsec2.c line 360 in H5FD__sec2_open(): unable to open file: name = '../../smer/testdata/test.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0
      major: File accessibility
      minor: Unable to open file
  HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
    #000: C:/rtools40/tmp/CMake-hdf5-1.10.7/hdf5-1.10.7/src/H5F.c line 429 in H5Fopen(): unable to open file
      major: File accessibility
      minor: Unable to open file
    #001: C:/rtools40/tmp/CMake-hdf5-1.10.7/hdf5-1.10.7/src/H5Fint.c line 1644 in H5F_open(): unable to open file: time = Tue Jan 14 18:08:29 2025
  , name = '../../smer/testdata/test_ld.h5', tent_flags = 0
      major: File accessibility
      minor: Unable to open file
    #002: C:/rtools40/tmp/CMake-hdf5-1.10.7/hdf5-1.10.7/src/H5FD.c line 741 in H5FD_open(): open failed
      major: Virtual File Layer
      minor: Unable to initialize object
    #003: C:/rtools40/tmp/CMake-hdf5-1.10.7/hdf5-1.10.7/src/H5FDsec2.c line 360 in H5FD__sec2_open(): unable to open file: name = '../../smer/testdata/test_ld.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0
      major: File accessibility
      minor: Unable to open file
  HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
    #000: C:/rtools40/tmp/CMake-hdf5-1.10.7/hdf5-1.10.7/src/H5F.c line 429 in H5Fopen(): unable to open file
      major: File accessibility
      minor: Unable to open file
    #001: C:/rtools40/tmp/CMake-hdf5-1.10.7/hdf5-1.10.7/src/H5Fint.c line 1644 in H5F_open(): unable to open file: time = Tue Jan 14 18:08:29 2025
  , name = '../../smer/testdata/test_ld.h5', tent_flags = 0
      major: File accessibility
      minor: Unable to open file
    #002: C:/rtools40/tmp/CMake-hdf5-1.10.7/hdf5-1.10.7/src/H5FD.c line 741 in H5FD_open(): open failed
      major: Virtual File Layer
      minor: Unable to initialize object
    #003: C:/rtools40/tmp/CMake-hdf5-1.10.7/hdf5-1.10.7/src/H5FDsec2.c line 360 in H5FD__sec2_open(): unable to open file: name = '../../smer/testdata/test_ld.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0
      major: File accessibility
      minor: Unable to open file
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [13s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 3 NOTEs