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This page was generated on 2021-10-15 15:06:51 -0400 (Fri, 15 Oct 2021).

CHECK results for SAIGEgds on machv2

To the developers/maintainers of the SAIGEgds package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SAIGEgds.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1664/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SAIGEgds 1.6.0  (landing page)
Xiuwen Zheng
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/SAIGEgds
git_branch: RELEASE_3_13
git_last_commit: bbfe3bd
git_last_commit_date: 2021-05-19 12:46:49 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    ERROR  skippedskipped
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SAIGEgds
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SAIGEgds.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SAIGEgds_1.6.0.tar.gz
StartedAt: 2021-10-14 23:31:16 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 23:34:08 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 172.2 seconds
RetCode: 0
Status:   OK  
CheckDir: SAIGEgds.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SAIGEgds.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SAIGEgds_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/SAIGEgds.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SAIGEgds/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SAIGEgds’ version ‘1.6.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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
* 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:::.file_split’
  ‘SeqArray:::.seqGet2bGeno’ ‘SeqArray:::.seqProgForward’
  ‘SeqArray:::.seqProgress’ ‘SeqArray:::process_index’
  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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
seqGLMM_GxG_spa        6.809  0.041   6.854
seqAssocGLMM_spaACAT_O 5.798  0.081   5.892
seqAssocGLMM_spaACAT_V 5.362  0.063   5.428
seqAssocGLMM_spaBurden 4.984  0.084   5.078
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/SAIGEgds.Rcheck/00check.log’
for details.

Installation output

SAIGEgds.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SAIGEgds
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘SAIGEgds’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c SPATest.cpp -o SPATest.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c saige_fitnull.cpp -o saige_fitnull.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c saige_main.cpp -o saige_main.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppParallel/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c vectorization.cpp -o vectorization.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o SAIGEgds.so SPATest.o saige_fitnull.o saige_main.o vectorization.o -lm -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-SAIGEgds/00new/SAIGEgds/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SAIGEgds)

Tests output

SAIGEgds.Rcheck/tests/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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")
Chromosome 1, # of units: 100
Chromosome 2, # of units: 3
# of units in total: 103
SAIGE ACAT-O analysis (combining burden & ACAT-V):
    # of samples: 1,000
    # of variants in total: 10,000
    # of units: 103
    avg. # of variants per unit: 193.2136
    min # of variants in a unit: 1
    max # of variants in a unit: 200
    sd  # of variants in a unit: 34.06529
    p-value threshold for SPA adjustment: 0.05
    variance ratio for approximation: 0.9410507
    variant weights: beta(1,1), beta(1,25)
    mac threshold for burden test: 10
    # of processes: 1
Calculating minor allele frequencies (MAF):

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 1s
    MAF: avg (0.08934), min (0.00200), max (0.50000), sd (0.12705)
Calculating p-values:

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 2s
Done.
SAIGE ACAT-V analysis:
    # of samples: 1,000
    # of variants in total: 10,000
    # of units: 103
    avg. # of variants per unit: 193.2136
    min # of variants in a unit: 1
    max # of variants in a unit: 200
    sd  # of variants in a unit: 34.06529
    p-value threshold for SPA adjustment: 0.05
    variance ratio for approximation: 0.9410507
    variant weights: beta(1,1), beta(1,25)
    mac threshold for burden test: 10
    # of processes: 1
Calculating minor allele frequencies (MAF):

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
    MAF: avg (0.08934), min (0.00200), max (0.50000), sd (0.12705)
Calculating p-values:

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 2s
Done.
SAIGE burden analysis:
    # of samples: 1,000
    # of variants in total: 10,000
    # of units: 103
    avg. # of variants per unit: 193.2136
    min # of variants in a unit: 1
    max # of variants in a unit: 200
    sd  # of variants in a unit: 34.06529
    p-value threshold for SPA adjustment: 0.05
    variance ratio for approximation: 0.9410507
    variant weights: beta(1,1), beta(1,25)
    # of processes: 1
Calculating minor allele frequencies (MAF):

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
    MAF: avg (0.08934), min (0.00200), max (0.50000), sd (0.12705)
Calculating p-values:

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 2s
Done.
SAIGE association analysis:
Thu Oct 14 23:33:49 2021
Filtering variants:

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 1s
# 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 ~ x_0 + x_1 + x_2 - 1
Start loading SNP genotypes:

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
    using 6.6M (sparse matrix)
Binary outcome: y
       y Number Proportion
       0    902      0.902
       1     98      0.098
Initial fixed-effect coefficients:
         x_0        x_1        x_2
    2.520514 -0.7666948 -0.4557928
Initial variance component estimates, tau:
    Sigma_E: 1, Sigma_G: 0.5
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:
Thu Oct 14 23:33:53 2021
     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
Thu Oct 14 23:33:53 2021
Done.
SAIGE association analysis:
Thu Oct 14 23:33:53 2021
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 ~ x_0 + x_1 + x_2 - 1
Start loading SNP genotypes:

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 1s
    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:
              x_0          x_1         x_2
    -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: (-6.28333e-17, -0.003167949, 0.001143224)
Calculate the average ratio of variances:
Thu Oct 14 23:33:59 2021
     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: 9.887242e-16
Thu Oct 14 23:33:59 2021
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: 0.9410507
    # of processes: 1

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


RUNIT TEST PROTOCOL -- Thu Oct 14 23:34:00 2021 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
SAIGEgds RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 22.874   0.629  23.550

Example timings

SAIGEgds.Rcheck/SAIGEgds-Ex.timings

nameusersystemelapsed
SAIGEgds-package4.8790.0724.962
glmmHeritability3.9360.0253.961
pACAT0.0030.0010.003
seqAssocGLMM_SPA3.7630.0333.797
seqAssocGLMM_spaACAT_O5.7980.0815.892
seqAssocGLMM_spaACAT_V5.3620.0635.428
seqAssocGLMM_spaBurden4.9840.0845.078
seqFitNullGLMM_SPA4.0600.0474.116
seqGLMM_GxG_spa6.8090.0416.854
seqSAIGE_LoadPval0.0920.0150.107