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CHECK report for SAIGEgds on tokay2

This page was generated on 2020-10-17 11:57:44 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE SAIGEgds PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1568/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SAIGEgds 1.2.3
Xiuwen Zheng
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/SAIGEgds
Branch: RELEASE_3_11
Last Commit: 7663323
Last Changed Date: 2020-09-18 22:33:13 -0400 (Fri, 18 Sep 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SAIGEgds
Version: 1.2.3
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SAIGEgds.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings SAIGEgds_1.2.3.tar.gz
StartedAt: 2020-10-17 07:55:43 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 07:59:18 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 215.0 seconds
RetCode: 0
Status:  OK  
CheckDir: SAIGEgds.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SAIGEgds.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings SAIGEgds_1.2.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/SAIGEgds.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SAIGEgds/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SAIGEgds' version '1.2.3'
* 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 'SAIGEgds' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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
* 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 dependencies in R code ... NOTE
':::' call which should be '::': 'SPAtest:::ScoreTest_wSaddleApprox_NULL_Model'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'SPAtest:::ScoreTest_wSaddleApprox_Get_X1' 'SeqArray:::.IsForking'
  'SeqArray:::.NumParallel' 'SeqArray:::.seqGet2bGeno'
  See the note in ?`:::` about the use of this operator.
* 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 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 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 ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/SAIGEgds/libs/i386/SAIGEgds.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/SAIGEgds/libs/x64/SAIGEgds.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
SAIGEgds-package   5.98   0.05    7.06
seqFitNullGLMM_SPA 5.04   0.00    5.05
seqAssocGLMM_SPA   5.00   0.02    5.02
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
SAIGEgds-package 5.44   0.05    8.52
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/SAIGEgds.Rcheck/00check.log'
for details.

Installation output

SAIGEgds.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/SAIGEgds_1.2.3.tar.gz && rm -rf SAIGEgds.buildbin-libdir && mkdir SAIGEgds.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SAIGEgds.buildbin-libdir SAIGEgds_1.2.3.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL SAIGEgds_1.2.3.zip && rm SAIGEgds_1.2.3.tar.gz SAIGEgds_1.2.3.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1396k  100 1396k    0     0  3064k      0 --:--:-- --:--:-- --:--:-- 3111k

install for i386

* installing *source* package 'SAIGEgds' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c SPATest.cpp -o SPATest.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c saige_fitnull.cpp -o saige_fitnull.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c saige_main.cpp -o saige_main.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c vectorization.cpp -o vectorization.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o SAIGEgds.dll tmp.def SPATest.o saige_fitnull.o saige_main.o vectorization.o -lm -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/lib/i386 -ltbb -ltbbmalloc -lgcc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/SAIGEgds.buildbin-libdir/00LOCK-SAIGEgds/00new/SAIGEgds/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SAIGEgds'
    finding HTML links ... done
    SAIGEgds-package                        html  
    seqAssocGLMM_SPA                        html  
    finding level-2 HTML links ... done

    seqFitNullGLMM_SPA                      html  
    seqSAIGE_LoadPval                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'SAIGEgds' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c SPATest.cpp -o SPATest.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c saige_fitnull.cpp -o saige_fitnull.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c saige_main.cpp -o saige_main.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c vectorization.cpp -o vectorization.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o SAIGEgds.dll tmp.def SPATest.o saige_fitnull.o saige_main.o vectorization.o -lm -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -lgcc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/SAIGEgds.buildbin-libdir/SAIGEgds/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SAIGEgds' as SAIGEgds_1.2.3.zip
* DONE (SAIGEgds)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'SAIGEgds' successfully unpacked and MD5 sums checked

Tests output

SAIGEgds.Rcheck/tests_i386/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("SAIGEgds")
SAIGE association analysis:
Sat Oct 17 07:58:38 2020
Filtering variants:

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
# of selected variants: 9,976
Fit the null model: y ~ x1 + x2 + var(GRM)
    # of samples: 1,000
    # of variants: 9,976
    using 1 thread
Transform on the design matrix with QR decomposition:
    new formula: y ~ x0 + x1 + x2 - 1
Start loading SNP genotypes:

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
    using 6.4M (sparse matrix)
Binary outcome: y
       y Number Proportion
       0    902      0.902
       1     98      0.098
Initial fixed-effect coefficients:
          x0         x1         x2
    2.520514 -0.7666948 -0.4557928
Initial variance component estimates, tau:
    Sigma_E: 1, Sigma_G: 0.499412
Iteration 1:
    tau: (1, 0.4994116)
    fixed coeff: (2.520514, -0.7666948, -0.4557928)
Iteration 2:
    tau: (1, 0.3287896)
    fixed coeff: (2.521231, -0.776603, -0.4592503)
Iteration 3:
    tau: (1, 0.2817812)
    fixed coeff: (2.525954, -0.7738757, -0.4579659)
Iteration 4:
    tau: (1, 0.3211452)
    fixed coeff: (2.525719, -0.7730823, -0.4577413)
Iteration 5:
    tau: (1, 0.3361534)
    fixed coeff: (2.527166, -0.7739766, -0.4579633)
Final tau: (1, 0.3322063)
    fixed coeff: (2.527666, -0.774237, -0.4580237)
Calculate the average ratio of variances:
Sat Oct 17 07:58:42 2020
     1, maf: 0.0775, mac: 155,	ratio: 0.9387 (var1: 0.0736, var2: 0.0785)
     2, maf: 0.0355, mac: 71,	ratio: 0.9362 (var1: 0.0671, var2: 0.0716)
     3, maf: 0.0730, mac: 146,	ratio: 0.9323 (var1: 0.0799, var2: 0.0857)
     4, maf: 0.0160, mac: 32,	ratio: 0.9481 (var1: 0.0653, var2: 0.0689)
     5, maf: 0.0585, mac: 117,	ratio: 0.9382 (var1: 0.0743, var2: 0.0791)
     6, maf: 0.0155, mac: 31,	ratio: 0.9388 (var1: 0.0754, var2: 0.0803)
     7, maf: 0.3075, mac: 615,	ratio: 0.9400 (var1: 0.0521, var2: 0.0554)
     8, maf: 0.0715, mac: 143,	ratio: 0.9416 (var1: 0.0714, var2: 0.0759)
     9, maf: 0.0115, mac: 23,	ratio: 0.9375 (var1: 0.0844, var2: 0.09)
    10, maf: 0.0470, mac: 94,	ratio: 0.9466 (var1: 0.0719, var2: 0.0759)
    11, maf: 0.0310, mac: 62,	ratio: 0.9335 (var1: 0.073, var2: 0.0782)
    12, maf: 0.1340, mac: 268,	ratio: 0.9381 (var1: 0.0633, var2: 0.0675)
    13, maf: 0.0855, mac: 171,	ratio: 0.9412 (var1: 0.0746, var2: 0.0792)
    14, maf: 0.1610, mac: 322,	ratio: 0.9379 (var1: 0.0647, var2: 0.069)
    15, maf: 0.0340, mac: 68,	ratio: 0.9471 (var1: 0.0685, var2: 0.0724)
    16, maf: 0.0215, mac: 43,	ratio: 0.9353 (var1: 0.0805, var2: 0.086)
    17, maf: 0.0600, mac: 120,	ratio: 0.9489 (var1: 0.0707, var2: 0.0745)
    18, maf: 0.0285, mac: 57,	ratio: 0.9455 (var1: 0.0732, var2: 0.0774)
    19, maf: 0.0145, mac: 29,	ratio: 0.9436 (var1: 0.0705, var2: 0.0747)
    20, maf: 0.0130, mac: 26,	ratio: 0.9454 (var1: 0.0688, var2: 0.0728)
    21, maf: 0.1350, mac: 270,	ratio: 0.9422 (var1: 0.0624, var2: 0.0663)
    22, maf: 0.0315, mac: 63,	ratio: 0.9342 (var1: 0.0699, var2: 0.0748)
    23, maf: 0.0475, mac: 95,	ratio: 0.9348 (var1: 0.0737, var2: 0.0788)
    24, maf: 0.2475, mac: 495,	ratio: 0.9360 (var1: 0.06, var2: 0.0641)
    25, maf: 0.0135, mac: 27,	ratio: 0.9523 (var1: 0.0622, var2: 0.0654)
    26, maf: 0.4915, mac: 983,	ratio: 0.9433 (var1: 0.0362, var2: 0.0383)
    27, maf: 0.0525, mac: 105,	ratio: 0.9366 (var1: 0.0734, var2: 0.0783)
    28, maf: 0.0195, mac: 39,	ratio: 0.9421 (var1: 0.0741, var2: 0.0787)
    29, maf: 0.0270, mac: 54,	ratio: 0.9502 (var1: 0.0718, var2: 0.0756)
    30, maf: 0.0380, mac: 76,	ratio: 0.9453 (var1: 0.0733, var2: 0.0776)
    ratio avg. is 0.9410507, sd: 0.005353982
Sat Oct 17 07:58:42 2020
Done.
SAIGE association analysis:
Sat Oct 17 07:58:42 2020
Filtering variants:

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
# of selected variants: 9,976
Fit the null model: yy ~ x1 + x2 + var(GRM)
    # of samples: 1,000
    # of variants: 9,976
    using 1 thread
Transform on the design matrix with QR decomposition:
    new formula: y ~ x0 + x1 + x2 - 1
Start loading SNP genotypes:

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
    using 6.4M (sparse matrix)
Quantitative outcome: yy
        mean        sd    min    max
    4.987525 0.9817471 1.6383 7.6701
Inverse normal transformation on residuals with standard deviation: 0.981695
Initial fixed-effect coefficients:
               x0           x1          x2
    -7.900429e-17 -0.003167949 0.001143224
Initial variance component estimates, tau:
    Sigma_E: 0.481718, Sigma_G: 0.481718
Iteration 1:
    tau: (0.5780754, 0.4791097)
    fixed coeff: (-7.900429e-17, -0.003167949, 0.001143224)
Iteration 2:
    tau: (0.7700948, 0.1571539)
    fixed coeff: (7.969752e-07, -0.01596609, -0.004398386)
Iteration 3:
    tau: (0.8649753, 0.0670912)
    fixed coeff: (3.558187e-07, -0.01030783, 3.137729e-05)
Iteration 4:
    tau: (0.9159832, 0.02884355)
    fixed coeff: (2.850052e-07, -0.006806145, 0.00088392)
Iteration 5:
    tau: (0.942882, 0)
    fixed coeff: (1.393627e-06, -0.004853796, 0.001081237)
Final tau: (0.9701727, 0)
    fixed coeff: (-6.282204e-17, -0.003167949, 0.001143224)
Calculate the average ratio of variances:
Sat Oct 17 07:58:48 2020
     1, maf: 0.0775, mac: 155,	ratio: 1.0307 (var1: 1.02, var2: 0.985)
     2, maf: 0.0355, mac: 71,	ratio: 1.0307 (var1: 0.955, var2: 0.927)
     3, maf: 0.0730, mac: 146,	ratio: 1.0307 (var1: 1, var2: 0.975)
     4, maf: 0.0160, mac: 32,	ratio: 1.0307 (var1: 0.994, var2: 0.964)
     5, maf: 0.0585, mac: 117,	ratio: 1.0307 (var1: 1.01, var2: 0.984)
     6, maf: 0.0155, mac: 31,	ratio: 1.0307 (var1: 0.998, var2: 0.968)
     7, maf: 0.3075, mac: 615,	ratio: 1.0307 (var1: 0.707, var2: 0.686)
     8, maf: 0.0715, mac: 143,	ratio: 1.0307 (var1: 0.969, var2: 0.94)
     9, maf: 0.0115, mac: 23,	ratio: 1.0307 (var1: 1, var2: 0.974)
    10, maf: 0.0470, mac: 94,	ratio: 1.0307 (var1: 0.999, var2: 0.969)
    11, maf: 0.0310, mac: 62,	ratio: 1.0307 (var1: 0.997, var2: 0.967)
    12, maf: 0.1340, mac: 268,	ratio: 1.0307 (var1: 0.882, var2: 0.855)
    13, maf: 0.0855, mac: 171,	ratio: 1.0307 (var1: 0.975, var2: 0.946)
    14, maf: 0.1610, mac: 322,	ratio: 1.0307 (var1: 0.878, var2: 0.851)
    15, maf: 0.0340, mac: 68,	ratio: 1.0307 (var1: 0.99, var2: 0.96)
    16, maf: 0.0215, mac: 43,	ratio: 1.0307 (var1: 0.986, var2: 0.957)
    17, maf: 0.0600, mac: 120,	ratio: 1.0307 (var1: 0.987, var2: 0.958)
    18, maf: 0.0285, mac: 57,	ratio: 1.0307 (var1: 0.972, var2: 0.943)
    19, maf: 0.0145, mac: 29,	ratio: 1.0307 (var1: 1, var2: 0.97)
    20, maf: 0.0130, mac: 26,	ratio: 1.0307 (var1: 1, var2: 0.973)
    21, maf: 0.1350, mac: 270,	ratio: 1.0307 (var1: 0.866, var2: 0.84)
    22, maf: 0.0315, mac: 63,	ratio: 1.0307 (var1: 1.03, var2: 0.998)
    23, maf: 0.0475, mac: 95,	ratio: 1.0307 (var1: 0.954, var2: 0.925)
    24, maf: 0.2475, mac: 495,	ratio: 1.0307 (var1: 0.791, var2: 0.767)
    25, maf: 0.0135, mac: 27,	ratio: 1.0307 (var1: 0.999, var2: 0.969)
    26, maf: 0.4915, mac: 983,	ratio: 1.0307 (var1: 0.491, var2: 0.476)
    27, maf: 0.0525, mac: 105,	ratio: 1.0307 (var1: 0.98, var2: 0.951)
    28, maf: 0.0195, mac: 39,	ratio: 1.0307 (var1: 0.99, var2: 0.961)
    29, maf: 0.0270, mac: 54,	ratio: 1.0307 (var1: 0.972, var2: 0.943)
    30, maf: 0.0380, mac: 76,	ratio: 1.0307 (var1: 1.01, var2: 0.976)
    ratio avg. is 1.030744, sd: 9.84416e-16
Sat Oct 17 07:58:48 2020
Done.
SAIGE association analysis:
    # of samples: 1,000
    # of variants: 10,000
    MAF threshold: NaN
    MAC threshold: 4
    missing threshold for variants: 0.1
    p-value threshold for SPA adjustment: 0.05
    variance ratio for approximation: 0.9410486
    # of processes: 1

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
# of variants after filtering by MAF, MAC and missing thresholds: 10,000
Done.
SAIGE association analysis:
    # of samples: 1,000
    # of variants: 10,000
    MAF threshold: NaN
    MAC threshold: 4
    missing threshold for variants: 0.1
    p-value threshold for SPA adjustment: 0.05
    variance ratio for approximation: 1.030744
    # of processes: 1

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 1s
# of variants after filtering by MAF, MAC and missing thresholds: 10,000
Done.


RUNIT TEST PROTOCOL -- Sat Oct 17 07:58:50 2020 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
SAIGEgds RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  15.56    0.23   15.87

SAIGEgds.Rcheck/tests_x64/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("SAIGEgds")
SAIGE association analysis:
Sat Oct 17 07:58:56 2020
Filtering variants:

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
# of selected variants: 9,976
Fit the null model: y ~ x1 + x2 + var(GRM)
    # of samples: 1,000
    # of variants: 9,976
    using 1 thread
Transform on the design matrix with QR decomposition:
    new formula: y ~ x0 + x1 + x2 - 1
Start loading SNP genotypes:

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 1s
    using 6.6M (sparse matrix)
Binary outcome: y
       y Number Proportion
       0    902      0.902
       1     98      0.098
Initial fixed-effect coefficients:
          x0         x1         x2
    2.520514 -0.7666948 -0.4557928
Initial variance component estimates, tau:
    Sigma_E: 1, Sigma_G: 0.499412
Iteration 1:
    tau: (1, 0.4994116)
    fixed coeff: (2.520514, -0.7666948, -0.4557928)
Iteration 2:
    tau: (1, 0.3287896)
    fixed coeff: (2.521231, -0.776603, -0.4592503)
Iteration 3:
    tau: (1, 0.2817812)
    fixed coeff: (2.525954, -0.7738757, -0.4579659)
Iteration 4:
    tau: (1, 0.3211452)
    fixed coeff: (2.525719, -0.7730823, -0.4577413)
Iteration 5:
    tau: (1, 0.3361534)
    fixed coeff: (2.527166, -0.7739766, -0.4579633)
Final tau: (1, 0.3322063)
    fixed coeff: (2.527666, -0.774237, -0.4580237)
Calculate the average ratio of variances:
Sat Oct 17 07:59:02 2020
     1, maf: 0.0775, mac: 155,	ratio: 0.9387 (var1: 0.0736, var2: 0.0785)
     2, maf: 0.0355, mac: 71,	ratio: 0.9362 (var1: 0.0671, var2: 0.0716)
     3, maf: 0.0730, mac: 146,	ratio: 0.9323 (var1: 0.0799, var2: 0.0857)
     4, maf: 0.0160, mac: 32,	ratio: 0.9481 (var1: 0.0653, var2: 0.0689)
     5, maf: 0.0585, mac: 117,	ratio: 0.9382 (var1: 0.0743, var2: 0.0791)
     6, maf: 0.0155, mac: 31,	ratio: 0.9388 (var1: 0.0754, var2: 0.0803)
     7, maf: 0.3075, mac: 615,	ratio: 0.9400 (var1: 0.0521, var2: 0.0554)
     8, maf: 0.0715, mac: 143,	ratio: 0.9416 (var1: 0.0714, var2: 0.0759)
     9, maf: 0.0115, mac: 23,	ratio: 0.9375 (var1: 0.0844, var2: 0.09)
    10, maf: 0.0470, mac: 94,	ratio: 0.9466 (var1: 0.0719, var2: 0.0759)
    11, maf: 0.0310, mac: 62,	ratio: 0.9335 (var1: 0.073, var2: 0.0782)
    12, maf: 0.1340, mac: 268,	ratio: 0.9381 (var1: 0.0633, var2: 0.0675)
    13, maf: 0.0855, mac: 171,	ratio: 0.9412 (var1: 0.0746, var2: 0.0792)
    14, maf: 0.1610, mac: 322,	ratio: 0.9379 (var1: 0.0647, var2: 0.069)
    15, maf: 0.0340, mac: 68,	ratio: 0.9471 (var1: 0.0685, var2: 0.0724)
    16, maf: 0.0215, mac: 43,	ratio: 0.9353 (var1: 0.0805, var2: 0.086)
    17, maf: 0.0600, mac: 120,	ratio: 0.9489 (var1: 0.0707, var2: 0.0745)
    18, maf: 0.0285, mac: 57,	ratio: 0.9455 (var1: 0.0732, var2: 0.0774)
    19, maf: 0.0145, mac: 29,	ratio: 0.9436 (var1: 0.0705, var2: 0.0747)
    20, maf: 0.0130, mac: 26,	ratio: 0.9454 (var1: 0.0688, var2: 0.0728)
    21, maf: 0.1350, mac: 270,	ratio: 0.9422 (var1: 0.0624, var2: 0.0663)
    22, maf: 0.0315, mac: 63,	ratio: 0.9342 (var1: 0.0699, var2: 0.0748)
    23, maf: 0.0475, mac: 95,	ratio: 0.9348 (var1: 0.0737, var2: 0.0788)
    24, maf: 0.2475, mac: 495,	ratio: 0.9360 (var1: 0.06, var2: 0.0641)
    25, maf: 0.0135, mac: 27,	ratio: 0.9523 (var1: 0.0622, var2: 0.0654)
    26, maf: 0.4915, mac: 983,	ratio: 0.9433 (var1: 0.0362, var2: 0.0383)
    27, maf: 0.0525, mac: 105,	ratio: 0.9366 (var1: 0.0734, var2: 0.0783)
    28, maf: 0.0195, mac: 39,	ratio: 0.9421 (var1: 0.0741, var2: 0.0787)
    29, maf: 0.0270, mac: 54,	ratio: 0.9502 (var1: 0.0718, var2: 0.0756)
    30, maf: 0.0380, mac: 76,	ratio: 0.9453 (var1: 0.0733, var2: 0.0776)
    ratio avg. is 0.9410507, sd: 0.005353982
Sat Oct 17 07:59:02 2020
Done.
SAIGE association analysis:
Sat Oct 17 07:59:02 2020
Filtering variants:

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
# of selected variants: 9,976
Fit the null model: yy ~ x1 + x2 + var(GRM)
    # of samples: 1,000
    # of variants: 9,976
    using 1 thread
Transform on the design matrix with QR decomposition:
    new formula: y ~ x0 + x1 + x2 - 1
Start loading SNP genotypes:

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
    using 6.6M (sparse matrix)
Quantitative outcome: yy
        mean        sd    min    max
    4.987525 0.9817471 1.6383 7.6701
Inverse normal transformation on residuals with standard deviation: 0.981695
Initial fixed-effect coefficients:
               x0           x1          x2
    -7.900429e-17 -0.003167949 0.001143224
Initial variance component estimates, tau:
    Sigma_E: 0.481718, Sigma_G: 0.481718
Iteration 1:
    tau: (0.5780754, 0.4791097)
    fixed coeff: (-7.900429e-17, -0.003167949, 0.001143224)
Iteration 2:
    tau: (0.7700948, 0.1571539)
    fixed coeff: (7.969752e-07, -0.01596609, -0.004398386)
Iteration 3:
    tau: (0.8649753, 0.0670912)
    fixed coeff: (3.558187e-07, -0.01030783, 3.137729e-05)
Iteration 4:
    tau: (0.9159832, 0.02884355)
    fixed coeff: (2.850052e-07, -0.006806145, 0.00088392)
Iteration 5:
    tau: (0.942882, 0)
    fixed coeff: (1.393627e-06, -0.004853796, 0.001081237)
Final tau: (0.9701727, 0)
    fixed coeff: (-6.282204e-17, -0.003167949, 0.001143224)
Calculate the average ratio of variances:
Sat Oct 17 07:59:09 2020
     1, maf: 0.0775, mac: 155,	ratio: 1.0307 (var1: 1.02, var2: 0.985)
     2, maf: 0.0355, mac: 71,	ratio: 1.0307 (var1: 0.955, var2: 0.927)
     3, maf: 0.0730, mac: 146,	ratio: 1.0307 (var1: 1, var2: 0.975)
     4, maf: 0.0160, mac: 32,	ratio: 1.0307 (var1: 0.994, var2: 0.964)
     5, maf: 0.0585, mac: 117,	ratio: 1.0307 (var1: 1.01, var2: 0.984)
     6, maf: 0.0155, mac: 31,	ratio: 1.0307 (var1: 0.998, var2: 0.968)
     7, maf: 0.3075, mac: 615,	ratio: 1.0307 (var1: 0.707, var2: 0.686)
     8, maf: 0.0715, mac: 143,	ratio: 1.0307 (var1: 0.969, var2: 0.94)
     9, maf: 0.0115, mac: 23,	ratio: 1.0307 (var1: 1, var2: 0.974)
    10, maf: 0.0470, mac: 94,	ratio: 1.0307 (var1: 0.999, var2: 0.969)
    11, maf: 0.0310, mac: 62,	ratio: 1.0307 (var1: 0.997, var2: 0.967)
    12, maf: 0.1340, mac: 268,	ratio: 1.0307 (var1: 0.882, var2: 0.855)
    13, maf: 0.0855, mac: 171,	ratio: 1.0307 (var1: 0.975, var2: 0.946)
    14, maf: 0.1610, mac: 322,	ratio: 1.0307 (var1: 0.878, var2: 0.851)
    15, maf: 0.0340, mac: 68,	ratio: 1.0307 (var1: 0.99, var2: 0.96)
    16, maf: 0.0215, mac: 43,	ratio: 1.0307 (var1: 0.986, var2: 0.957)
    17, maf: 0.0600, mac: 120,	ratio: 1.0307 (var1: 0.987, var2: 0.958)
    18, maf: 0.0285, mac: 57,	ratio: 1.0307 (var1: 0.972, var2: 0.943)
    19, maf: 0.0145, mac: 29,	ratio: 1.0307 (var1: 1, var2: 0.97)
    20, maf: 0.0130, mac: 26,	ratio: 1.0307 (var1: 1, var2: 0.973)
    21, maf: 0.1350, mac: 270,	ratio: 1.0307 (var1: 0.866, var2: 0.84)
    22, maf: 0.0315, mac: 63,	ratio: 1.0307 (var1: 1.03, var2: 0.998)
    23, maf: 0.0475, mac: 95,	ratio: 1.0307 (var1: 0.954, var2: 0.925)
    24, maf: 0.2475, mac: 495,	ratio: 1.0307 (var1: 0.791, var2: 0.767)
    25, maf: 0.0135, mac: 27,	ratio: 1.0307 (var1: 0.999, var2: 0.969)
    26, maf: 0.4915, mac: 983,	ratio: 1.0307 (var1: 0.491, var2: 0.476)
    27, maf: 0.0525, mac: 105,	ratio: 1.0307 (var1: 0.98, var2: 0.951)
    28, maf: 0.0195, mac: 39,	ratio: 1.0307 (var1: 0.99, var2: 0.961)
    29, maf: 0.0270, mac: 54,	ratio: 1.0307 (var1: 0.972, var2: 0.943)
    30, maf: 0.0380, mac: 76,	ratio: 1.0307 (var1: 1.01, var2: 0.976)
    ratio avg. is 1.030744, sd: 9.84416e-16
Sat Oct 17 07:59:09 2020
Done.
SAIGE association analysis:
    # of samples: 1,000
    # of variants: 10,000
    MAF threshold: NaN
    MAC threshold: 4
    missing threshold for variants: 0.1
    p-value threshold for SPA adjustment: 0.05
    variance ratio for approximation: 0.9410486
    # of processes: 1

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
# of variants after filtering by MAF, MAC and missing thresholds: 10,000
Done.
SAIGE association analysis:
    # of samples: 1,000
    # of variants: 10,000
    MAF threshold: NaN
    MAC threshold: 4
    missing threshold for variants: 0.1
    p-value threshold for SPA adjustment: 0.05
    variance ratio for approximation: 1.030744
    # of processes: 1

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 1s
# of variants after filtering by MAF, MAC and missing thresholds: 10,000
Done.


RUNIT TEST PROTOCOL -- Sat Oct 17 07:59:10 2020 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
SAIGEgds RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  19.12    0.31   19.43

Example timings

SAIGEgds.Rcheck/examples_i386/SAIGEgds-Ex.timings

nameusersystemelapsed
SAIGEgds-package5.980.057.06
seqAssocGLMM_SPA5.000.025.02
seqFitNullGLMM_SPA5.040.005.05
seqSAIGE_LoadPval0.070.000.17

SAIGEgds.Rcheck/examples_x64/SAIGEgds-Ex.timings

nameusersystemelapsed
SAIGEgds-package5.440.058.52
seqAssocGLMM_SPA4.450.014.47
seqFitNullGLMM_SPA4.900.024.93
seqSAIGE_LoadPval0.070.010.07