bitwise.ia() degraded performance on windows about poppr HOT 1 CLOSED

* using log directory 'd:/RCompile/CRANguest/R-release/poppr.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'poppr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'poppr' version '2.8.7'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... WARNING
Maintainer: 'Zhian N. Kamvar <[email protected]>'

Insufficient package version (submitted: 2.8.7, existing: 2.8.7)
* 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 serialization versions ... OK
* checking whether package 'poppr' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' 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 ... [25s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... 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 compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [28s] OK
** running examples for arch 'x64' ... [32s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ... [12s] ERROR
  Running 'test-all.R' [11s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > options(poppr.debug = TRUE)
  > test_check("poppr")
  Loading required package: poppr
  Loading required package: adegenet
  Loading required package: ade4
  
     /// adegenet 2.1.3 is loaded ////////////
  
     > overview: '?adegenet'
     > tutorials/doc/questions: 'adegenetWeb()' 
     > bug reports/feature requests: adegenetIssues()
  
  
  This is poppr version 2.8.7. To get started, type package?poppr
  OMP parallel support: available
  == Skipped tests ===============================================================
  * On CRAN (182)
  
  == Warnings ====================================================================
  -- Warning (test-values.R:345:3): bitwise.ia can handle large samples ----------
  
  An integer overflow has occured and the resulting index will not be accurate.
  Please consider using a smaller sample.
  Backtrace:
   1. poppr::bitwise.ia(x[, snps], thread = 1L) test-values.R:345:2
  
  == Failed tests ================================================================
  -- Failure (test-values.R:346:3): bitwise.ia can handle large samples ----------
  `res` not equal to 8.6296328853274e-06.
  1/1 mismatches
  [1] -2.21 - 8.63e-06 == -2.21
  
  [ FAIL 1 | WARN 1 | SKIP 182 | PASS 376 ]
  Error: Test failures
  Execution halted
** running tests for arch 'x64' ... [13s] ERROR
  Running 'test-all.R' [12s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > options(poppr.debug = TRUE)
  > test_check("poppr")
  Loading required package: poppr
  Loading required package: adegenet
  Loading required package: ade4
  
     /// adegenet 2.1.3 is loaded ////////////
  
     > overview: '?adegenet'
     > tutorials/doc/questions: 'adegenetWeb()' 
     > bug reports/feature requests: adegenetIssues()
  
  
  This is poppr version 2.8.7. To get started, type package?poppr
  OMP parallel support: available
  == Skipped tests ===============================================================
  * On CRAN (182)
  
  == Warnings ====================================================================
  -- Warning (test-values.R:345:3): bitwise.ia can handle large samples ----------
  
  An integer overflow has occured and the resulting index will not be accurate.
  Please consider using a smaller sample.
  Backtrace:
   1. poppr::bitwise.ia(x[, snps], thread = 1L) test-values.R:345:2
  
  == Failed tests ================================================================
  -- Failure (test-values.R:346:3): bitwise.ia can handle large samples ----------
  `res` not equal to 8.6296328853274e-06.
  1/1 mismatches
  [1] -2.21 - 8.63e-06 == -2.21
  
  [ FAIL 1 | WARN 1 | SKIP 182 | PASS 376 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... [15s] OK
* checking PDF version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 ERRORs, 1 WARNING