Xiuwen Zheng
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/SAIGEgds |
| git_branch: RELEASE_3_14 |
| git_last_commit: 13e4275 |
| git_last_commit_date: 2022-03-29 03:49:02 -0400 (Tue, 29 Mar 2022) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:05:54 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1688/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SAIGEgds 1.8.1 (landing page) Xiuwen Zheng
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: SAIGEgds |
| Version: 1.8.1 |
| Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:SAIGEgds.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings SAIGEgds_1.8.1.tar.gz |
| StartedAt: 2022-04-12 09:11:21 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 09:13:37 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 135.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SAIGEgds.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:SAIGEgds.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings SAIGEgds_1.8.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/SAIGEgds.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.8.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SAIGEgds’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 11.0Mb
sub-directories of 1Mb or more:
libs 9.3Mb
* 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 6.397 0.020 6.416
seqAssocGLMM_spaACAT_V 6.007 0.023 6.031
seqAssocGLMM_spaBurden 5.926 0.032 5.958
seqAssocGLMM_spaACAT_O 5.468 0.011 5.480
seqAssocGLMM_SPA 5.014 0.012 5.026
* 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
‘/home/biocbuild/bbs-3.14-bioc/meat/SAIGEgds.Rcheck/00check.log’
for details.
SAIGEgds.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL SAIGEgds
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘SAIGEgds’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c SPATest.cpp -o SPATest.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c saige_fitnull.cpp -o saige_fitnull.o
saige_fitnull.cpp: In function ‘SEXPREC* saige_get_sparse(SEXP)’:
saige_fitnull.cpp:249:10: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_len_t’ {aka ‘int’} [-Wsign-compare]
249 | if (num > Rf_length(geno))
| ~~~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c saige_main.cpp -o saige_main.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c vectorization.cpp -o vectorization.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o SAIGEgds.so SPATest.o saige_fitnull.o saige_main.o vectorization.o -lm -L/home/biocbuild/bbs-3.14-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.14-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -lgcc -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/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)
SAIGEgds.Rcheck/tests/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, 0s
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:
Tue Apr 12 09:13:23 2022
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 ~ 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:
Tue Apr 12 09:13:27 2022
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
Tue Apr 12 09:13:28 2022
Done.
SAIGE association analysis:
Tue Apr 12 09:13:28 2022
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, 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:
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:
Tue Apr 12 09:13:33 2022
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
Tue Apr 12 09:13:33 2022
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, 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 -- Tue Apr 12 09:13:34 2022
***********************************************
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
22.711 0.325 23.020
SAIGEgds.Rcheck/SAIGEgds-Ex.timings
| name | user | system | elapsed | |
| SAIGEgds-package | 4.441 | 0.011 | 4.455 | |
| glmmHeritability | 4.399 | 0.029 | 4.427 | |
| pACAT | 0.003 | 0.000 | 0.003 | |
| seqAssocGLMM_SPA | 5.014 | 0.012 | 5.026 | |
| seqAssocGLMM_spaACAT_O | 5.468 | 0.011 | 5.480 | |
| seqAssocGLMM_spaACAT_V | 6.007 | 0.023 | 6.031 | |
| seqAssocGLMM_spaBurden | 5.926 | 0.032 | 5.958 | |
| seqFitNullGLMM_SPA | 4.144 | 0.016 | 4.160 | |
| seqGLMM_GxG_spa | 6.397 | 0.020 | 6.416 | |
| seqSAIGE_LoadPval | 0.038 | 0.004 | 0.042 | |