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CHECK report for SAIGEgds on celaya2

This page was generated on 2020-01-16 13:55:32 -0500 (Thu, 16 Jan 2020).

Package 1504/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SAIGEgds 1.1.0
Xiuwen Zheng
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/SAIGEgds
Branch: master
Last Commit: 0e203e8
Last Changed Date: 2019-10-29 13:43:44 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: SAIGEgds
Version: 1.1.0
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_1.1.0.tar.gz
StartedAt: 2020-01-16 08:32:47 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 08:35:50 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 183.5 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_1.1.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/SAIGEgds.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.1.0’
* 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 ... 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 ... 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:::.pretty_size’
  ‘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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
SAIGEgds-package   5.599  0.132   5.836
seqAssocGLMM_SPA   5.453  0.039   5.496
seqFitNullGLMM_SPA 4.994  0.037   5.033
* 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: 3 NOTEs
See
  ‘/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:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SAIGEgds
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘SAIGEgds’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c SPATest.cpp -o SPATest.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c saige_fitnull.cpp -o saige_fitnull.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c saige_main.cpp -o saige_main.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c vectorization.cpp -o vectorization.o
clang++ -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-darwin15/6.1.0 -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/4.0/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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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")
SAIGE association analysis:
Thu Jan 16 08:35:28 2020
Filtering variants:

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
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 6.6M (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:
Thu Jan 16 08:35:32 2020
     1, maf: 0.0775, var1: 0.0736, var2: 0.0785, ratio: 0.93873
     2, maf: 0.0355, var1: 0.0671, var2: 0.0716, ratio: 0.93625
     3, maf: 0.0730, var1: 0.0799, var2: 0.0857, ratio: 0.93230
     4, maf: 0.0160, var1: 0.0653, var2: 0.0689, ratio: 0.94814
     5, maf: 0.0585, var1: 0.0743, var2: 0.0791, ratio: 0.93824
     6, maf: 0.0155, var1: 0.0754, var2: 0.0803, ratio: 0.93875
     7, maf: 0.3075, var1: 0.0521, var2: 0.0554, ratio: 0.93998
     8, maf: 0.0715, var1: 0.0714, var2: 0.0759, ratio: 0.94163
     9, maf: 0.0115, var1: 0.0844, var2: 0.09, ratio: 0.93752
    10, maf: 0.0470, var1: 0.0719, var2: 0.0759, ratio: 0.94660
    11, maf: 0.0310, var1: 0.073, var2: 0.0782, ratio: 0.93352
    12, maf: 0.1340, var1: 0.0633, var2: 0.0675, ratio: 0.93814
    13, maf: 0.0855, var1: 0.0746, var2: 0.0792, ratio: 0.94122
    14, maf: 0.1610, var1: 0.0647, var2: 0.069, ratio: 0.93786
    15, maf: 0.0340, var1: 0.0685, var2: 0.0724, ratio: 0.94707
    16, maf: 0.0215, var1: 0.0805, var2: 0.086, ratio: 0.93530
    17, maf: 0.0600, var1: 0.0707, var2: 0.0745, ratio: 0.94890
    18, maf: 0.0285, var1: 0.0732, var2: 0.0774, ratio: 0.94549
    19, maf: 0.0145, var1: 0.0705, var2: 0.0747, ratio: 0.94357
    20, maf: 0.0130, var1: 0.0688, var2: 0.0728, ratio: 0.94542
    21, maf: 0.1350, var1: 0.0624, var2: 0.0663, ratio: 0.94215
    22, maf: 0.0315, var1: 0.0699, var2: 0.0748, ratio: 0.93419
    23, maf: 0.0475, var1: 0.0737, var2: 0.0788, ratio: 0.93482
    24, maf: 0.2475, var1: 0.06, var2: 0.0641, ratio: 0.93597
    25, maf: 0.0135, var1: 0.0622, var2: 0.0654, ratio: 0.95229
    26, maf: 0.4915, var1: 0.0362, var2: 0.0383, ratio: 0.94335
    27, maf: 0.0525, var1: 0.0734, var2: 0.0783, ratio: 0.93658
    28, maf: 0.0195, var1: 0.0741, var2: 0.0787, ratio: 0.94208
    29, maf: 0.0270, var1: 0.0718, var2: 0.0756, ratio: 0.95017
    30, maf: 0.0380, var1: 0.0733, var2: 0.0776, ratio: 0.94530
    ratio avg. is 0.9410507, sd: 0.005353982
Thu Jan 16 08:35:32 2020
Done.
SAIGE association analysis:
Thu Jan 16 08:35:32 2020
Filtering variants:

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
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, 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:
               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: (-7.557369e-17, -0.003167949, 0.001143224)
Calculate the average ratio of variances:
Thu Jan 16 08:35:39 2020
     1, maf: 0.0775, var1: 1.02, var2: 0.985, ratio: 1.03074
     2, maf: 0.0355, var1: 0.955, var2: 0.927, ratio: 1.03074
     3, maf: 0.0730, var1: 1, var2: 0.975, ratio: 1.03074
     4, maf: 0.0160, var1: 0.994, var2: 0.964, ratio: 1.03074
     5, maf: 0.0585, var1: 1.01, var2: 0.984, ratio: 1.03074
     6, maf: 0.0155, var1: 0.998, var2: 0.968, ratio: 1.03074
     7, maf: 0.3075, var1: 0.707, var2: 0.686, ratio: 1.03074
     8, maf: 0.0715, var1: 0.969, var2: 0.94, ratio: 1.03074
     9, maf: 0.0115, var1: 1, var2: 0.974, ratio: 1.03074
    10, maf: 0.0470, var1: 0.999, var2: 0.969, ratio: 1.03074
    11, maf: 0.0310, var1: 0.997, var2: 0.967, ratio: 1.03074
    12, maf: 0.1340, var1: 0.882, var2: 0.855, ratio: 1.03074
    13, maf: 0.0855, var1: 0.975, var2: 0.946, ratio: 1.03074
    14, maf: 0.1610, var1: 0.878, var2: 0.851, ratio: 1.03074
    15, maf: 0.0340, var1: 0.99, var2: 0.96, ratio: 1.03074
    16, maf: 0.0215, var1: 0.986, var2: 0.957, ratio: 1.03074
    17, maf: 0.0600, var1: 0.987, var2: 0.958, ratio: 1.03074
    18, maf: 0.0285, var1: 0.972, var2: 0.943, ratio: 1.03074
    19, maf: 0.0145, var1: 1, var2: 0.97, ratio: 1.03074
    20, maf: 0.0130, var1: 1, var2: 0.973, ratio: 1.03074
    21, maf: 0.1350, var1: 0.866, var2: 0.84, ratio: 1.03074
    22, maf: 0.0315, var1: 1.03, var2: 0.998, ratio: 1.03074
    23, maf: 0.0475, var1: 0.954, var2: 0.925, ratio: 1.03074
    24, maf: 0.2475, var1: 0.791, var2: 0.767, ratio: 1.03074
    25, maf: 0.0135, var1: 0.999, var2: 0.969, ratio: 1.03074
    26, maf: 0.4915, var1: 0.491, var2: 0.476, ratio: 1.03074
    27, maf: 0.0525, var1: 0.98, var2: 0.951, ratio: 1.03074
    28, maf: 0.0195, var1: 0.99, var2: 0.961, ratio: 1.03074
    29, maf: 0.0270, var1: 0.972, var2: 0.943, ratio: 1.03074
    30, maf: 0.0380, var1: 1.01, var2: 0.976, ratio: 1.03074
    ratio avg. is 1.030744, sd: 8.717561e-16
Thu Jan 16 08:35:39 2020
Done.
SAIGE association analysis:
    # of samples: 1,000
    # of variants: 10,000
    p-value threshold for SPA adjustment: 0.05
    variance ratio for approximation: 0.9410486

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

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


RUNIT TEST PROTOCOL -- Thu Jan 16 08:35:40 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 
 17.926   0.854  18.818

Example timings

SAIGEgds.Rcheck/SAIGEgds-Ex.timings

nameusersystemelapsed
SAIGEgds-package5.5990.1325.836
seqAssocGLMM_SPA5.4530.0395.496
seqFitNullGLMM_SPA4.9940.0375.033
seqSAIGE_LoadPval0.0660.0080.075