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 12:07:17 -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: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SAIGEgds.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SAIGEgds_1.8.1.tar.gz |
| StartedAt: 2022-04-13 02:12:30 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 02:16:56 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 265.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SAIGEgds.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SAIGEgds.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SAIGEgds_1.8.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/SAIGEgds.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.8.1'
* 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 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:::.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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-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-3.14-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
seqGLMM_GxG_spa 6.47 0.01 6.50
seqAssocGLMM_spaACAT_O 5.70 0.06 5.76
seqAssocGLMM_spaACAT_V 5.48 0.08 5.58
SAIGEgds-package 4.83 0.06 12.60
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
seqGLMM_GxG_spa 6.22 0.00 6.22
seqAssocGLMM_spaACAT_V 6.11 0.02 6.13
seqAssocGLMM_spaACAT_O 5.47 0.00 5.47
* 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-3.14-bioc/meat/SAIGEgds.Rcheck/00check.log'
for details.
SAIGEgds.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/SAIGEgds_1.8.1.tar.gz && rm -rf SAIGEgds.buildbin-libdir && mkdir SAIGEgds.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SAIGEgds.buildbin-libdir SAIGEgds_1.8.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL SAIGEgds_1.8.1.zip && rm SAIGEgds_1.8.1.tar.gz SAIGEgds_1.8.1.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
31 1502k 31 466k 0 0 543k 0 0:00:02 --:--:-- 0:00:02 543k
100 1502k 100 1502k 0 0 916k 0 0:00:01 0:00:01 --:--:-- 917k
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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=0 -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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=0 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c saige_fitnull.cpp -o saige_fitnull.o
saige_fitnull.cpp: In function 'SEXPREC* saige_store_2b_geno(SEXP, SEXP, SEXP, SEXP, SEXP)':
saige_fitnull.cpp:71:13: warning: unused variable 'th_idx' [-Wunused-variable]
const int th_idx = 0; \
^~~~~~
saige_fitnull.cpp:71:13: note: in definition of macro 'PARALLEL_FOR'
const int th_idx = 0; \
^~~~~~
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 unsigned int'} and 'R_len_t' {aka 'int'} [-Wsign-compare]
if (num > Rf_length(geno))
~~~~^~~~~~~~~~~~~~~~~
saige_fitnull.cpp: In function 'SEXPREC* saige_store_sp_geno(SEXP, SEXP, SEXP, SEXP, SEXP)':
saige_fitnull.cpp:71:13: warning: unused variable 'th_idx' [-Wunused-variable]
const int th_idx = 0; \
^~~~~~
saige_fitnull.cpp:71:13: note: in definition of macro 'PARALLEL_FOR'
const int th_idx = 0; \
^~~~~~
saige_fitnull.cpp: In function 'void get_crossprod_b_grm(const dcolvec&, arma::dvec&)':
saige_fitnull.cpp:75:13: warning: unused variable 'th_idx' [-Wunused-variable]
const int th_idx = 0; \
^~~~~~
saige_fitnull.cpp:75:13: note: in definition of macro 'PARALLEL_RANGE'
const int th_idx = 0; \
^~~~~~
saige_fitnull.cpp: In function 'void get_diag_sigma(const dvec&, const dvec&, arma::dvec&)':
saige_fitnull.cpp:75:13: warning: unused variable 'th_idx' [-Wunused-variable]
const int th_idx = 0; \
^~~~~~
saige_fitnull.cpp:75:13: note: in definition of macro 'PARALLEL_RANGE'
const int th_idx = 0; \
^~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=0 -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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=0 -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-3~1.14-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/lib/i386 -ltbb -ltbbmalloc -lgcc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-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
glmmHeritability html
pACAT html
seqAssocGLMM_SPA html
finding level-2 HTML links ... done
seqAssocGLMM_spaACAT_O html
seqAssocGLMM_spaACAT_V html
seqAssocGLMM_spaBurden html
seqFitNullGLMM_SPA html
seqGLMM_GxG_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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=0 -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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=0 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c saige_fitnull.cpp -o saige_fitnull.o
saige_fitnull.cpp: In function 'SEXPREC* saige_store_2b_geno(SEXP, SEXP, SEXP, SEXP, SEXP)':
saige_fitnull.cpp:71:13: warning: unused variable 'th_idx' [-Wunused-variable]
const int th_idx = 0; \
^~~~~~
saige_fitnull.cpp:71:13: note: in definition of macro 'PARALLEL_FOR'
const int th_idx = 0; \
^~~~~~
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 long unsigned int'} and 'R_len_t' {aka 'int'} [-Wsign-compare]
if (num > Rf_length(geno))
~~~~^~~~~~~~~~~~~~~~~
saige_fitnull.cpp: In function 'SEXPREC* saige_store_sp_geno(SEXP, SEXP, SEXP, SEXP, SEXP)':
saige_fitnull.cpp:71:13: warning: unused variable 'th_idx' [-Wunused-variable]
const int th_idx = 0; \
^~~~~~
saige_fitnull.cpp:71:13: note: in definition of macro 'PARALLEL_FOR'
const int th_idx = 0; \
^~~~~~
saige_fitnull.cpp: In function 'void get_crossprod_b_grm(const dcolvec&, arma::dvec&)':
saige_fitnull.cpp:75:13: warning: unused variable 'th_idx' [-Wunused-variable]
const int th_idx = 0; \
^~~~~~
saige_fitnull.cpp:75:13: note: in definition of macro 'PARALLEL_RANGE'
const int th_idx = 0; \
^~~~~~
saige_fitnull.cpp: In function 'void get_diag_sigma(const dvec&, const dvec&, arma::dvec&)':
saige_fitnull.cpp:75:13: warning: unused variable 'th_idx' [-Wunused-variable]
const int th_idx = 0; \
^~~~~~
saige_fitnull.cpp:75:13: note: in definition of macro 'PARALLEL_RANGE'
const int th_idx = 0; \
^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=0 -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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=0 -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-3~1.14-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -lgcc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/SAIGEgds.buildbin-libdir/SAIGEgds/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SAIGEgds' as SAIGEgds_1.8.1.zip
* DONE (SAIGEgds)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'SAIGEgds' successfully unpacked and MD5 sums checked
|
SAIGEgds.Rcheck/tests_i386/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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")
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, 3s
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, 3s
Done.
SAIGE association analysis:
Wed Apr 13 02:16:15 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 6.4M (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:
Wed Apr 13 02:16:20 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
Wed Apr 13 02:16:20 2022
Done.
SAIGE association analysis:
Wed Apr 13 02:16:20 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 6.4M (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:
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: (-6.282204e-17, -0.003167949, 0.001143224)
Calculate the average ratio of variances:
Wed Apr 13 02:16:25 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: 9.84416e-16
Wed Apr 13 02:16:25 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, 0s
# of variants after filtering by MAF, MAC and missing thresholds: 10,000
Done.
RUNIT TEST PROTOCOL -- Wed Apr 13 02:16:26 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
23.20 0.48 23.73
|
SAIGEgds.Rcheck/tests_x64/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-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")
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, 3s
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:
Wed Apr 13 02:16:38 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:
Wed Apr 13 02:16:41 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
Wed Apr 13 02:16:42 2022
Done.
SAIGE association analysis:
Wed Apr 13 02:16:42 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: (-6.282204e-17, -0.003167949, 0.001143224)
Calculate the average ratio of variances:
Wed Apr 13 02:16:46 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: 9.84416e-16
Wed Apr 13 02:16:46 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, 0s
# of variants after filtering by MAF, MAC and missing thresholds: 10,000
Done.
RUNIT TEST PROTOCOL -- Wed Apr 13 02:16:47 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
19.96 0.48 20.43
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SAIGEgds.Rcheck/examples_i386/SAIGEgds-Ex.timings
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SAIGEgds.Rcheck/examples_x64/SAIGEgds-Ex.timings
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