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bitwise.ia() degraded performance on windows #234

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zkamvar opened this issue Jan 31, 2021 · 1 comment · Fixed by #235
Closed

bitwise.ia() degraded performance on windows #234

zkamvar opened this issue Jan 31, 2021 · 1 comment · Fixed by #235
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bug 🐛 ☠️ C-level 🔩

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@zkamvar
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zkamvar commented Jan 31, 2021

It appears that bitwise.ia() is not performing well on Windows as it seems to overflow the stack too early. This test in particular fails on both windows flavors:

poppr/tests/testthat/test-values.R

Lines 340 to 347 in 0ab416f

test_that("bitwise.ia can handle large samples", {
skip_on_cran()
set.seed(999)
x <- glSim(n.ind = 200, n.snp.nonstruc = 2e3, ploidy = 2, parallel = FALSE)
position(x) <- sort(sample(1e4, 2e3))
res <- bitwise.ia(x[, snps], thread = 1L)
expect_equal(res, 8.6296328853274e-06)
})

here's the error summary:

== 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
R CMD check output on winbuilder 
* 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 <zkamvar@gmail.com>'

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 ... [46s] 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' ... [48s] OK
** running examples for arch 'x64' ... [58s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ... [24s] ERROR
  Running 'test-all.R' [24s]
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 (186)
  
  == 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 186 | PASS 364 ]
  Error: Test failures
  Execution halted
** running tests for arch 'x64' ... [25s] ERROR
  Running 'test-all.R' [25s]
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 (186)
  
  == 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 186 | PASS 364 ]
  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 ... [26s] OK
* checking PDF version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 ERRORs, 1 WARNING
@zkamvar
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zkamvar commented Feb 2, 2021

N.B. I realized that I never tested bitwise.ia() on Windows because the NOT_CRAN was never assigned on Appveyor and so those tests were never run. Luckily, this one test with bitwise.ia() is the only one that fails. Here are the results after I comment out the not_cran() from bitwise.ia() tests:

== 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 ]
R CMD check output on winbuilder 
* 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 <zkamvar@gmail.com>'

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

zkamvar added a commit that referenced this issue Feb 4, 2021
@zkamvar
update denominator for bitwise.ia to be int64_t
e9d4769 
Windows machines apparently do not treat long int the same way that UNIX
machines do and caused integer overflows for people who were performing
bitwise.ia() on sample sizes of more than 2000 loci x 200 individuals.
This wasn't caught earlier because I had skipped these tests on CRAN and
appveyor didn't run them either. This fixes the problem and adds a news
item.

This addresses #234
@zkamvar zkamvar mentioned this issue Feb 4, 2021
Merged
@zkamvar zkamvar mentioned this issue Sep 28, 2021
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update denominator for bitwise.ia to be int64_t grunwaldlab/poppr
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