Multiple platform build/check report for BioC 3.9 - CHECK report for graper on merida2

Package: graper

Version: 0.99.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings graper_0.99.3.tar.gz

StartedAt: 2019-04-09 01:20:19 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:21:32 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 73.1 seconds

RetCode: 0

Status: OK

CheckDir: graper.Rcheck

Warnings: 0

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings graper_0.99.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/graper.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘0.99.3’
* package encoding: UTF-8
* 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 ‘graper’ 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 ... OK
* 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/graper.Rcheck/00check.log’
for details.

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL graper
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘graper’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c fit_graper.cpp -o fit_graper.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 graper.so RcppExports.o fit_graper.o -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/3.6/Resources/library/graper/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (graper)


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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.

> library(testthat)
> library(graper)
> 
> test_check("graper")
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-842.749
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-567.501
ELB improved by 275.249

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-510.354
ELB improved by 57.1464

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-474.819
ELB improved by 35.5349

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.775
ELB improved by 14.0441

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.01
ELB improved by 5.76582

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.378
ELB improved by 3.63188

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.386
ELB improved by 2.99197

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.676
ELB improved by 2.70969

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.132
ELB improved by 2.54369

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.735
ELB improved by 2.39727

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.513
ELB improved by 2.22226

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.519
ELB improved by 1.99336

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.811
ELB improved by 1.70813

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.418
ELB improved by 1.39341

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.324
ELB improved by 1.09378

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.48
ELB improved by 0.844445

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.824
ELB improved by 0.656019

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.303
ELB improved by 0.52056

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.879
ELB improved by 0.424089

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.525
ELB improved by 0.354115

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.223
ELB improved by 0.301678

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.962
ELB improved by 0.260929

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.734
ELB improved by 0.228194

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.533
ELB improved by 0.201179

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.354
ELB improved by 0.178434

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.195
ELB improved by 0.159011

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.053
ELB improved by 0.142262

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.925
ELB improved by 0.12772

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.81
ELB improved by 0.115028

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.707
ELB improved by 0.103906

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.612
ELB improved by 0.0941244

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.527
ELB improved by 0.0854934

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.449
ELB improved by 0.0778529

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.378
ELB improved by 0.0710677

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.313
ELB improved by 0.0650232

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.253
ELB improved by 0.0596223

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.199
ELB improved by 0.0547822

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.148
ELB improved by 0.0504324

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.102
ELB improved by 0.0465127

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.059
ELB improved by 0.0429716

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.019
ELB improved by 0.0397647

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.982
ELB improved by 0.0368538

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.948
ELB improved by 0.034206

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.916
ELB improved by 0.0317925

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.886
ELB improved by 0.0295885

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.859
ELB improved by 0.0275721

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.833
ELB improved by 0.0257243

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.809
ELB improved by 0.0240283

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.787
ELB improved by 0.0224693

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.766
ELB improved by 0.021034

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.746
ELB improved by 0.0197111

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.727
ELB improved by 0.01849

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.71
ELB improved by 0.0173616

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.694
ELB improved by 0.0163176

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.678
ELB improved by 0.0153507

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.664
ELB improved by 0.0144542

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.65
ELB improved by 0.0136221

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.637
ELB improved by 0.0128491

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.625
ELB improved by 0.0121304

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.614
ELB improved by 0.0114614

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.603
ELB improved by 0.0108383

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.593
ELB improved by 0.0102574

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.583
ELB improved by 0.00971537

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-868.26
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-567.534
ELB improved by 300.725

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-508.941
ELB improved by 58.5937

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.118
ELB improved by 38.8224

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.323
ELB improved by 15.7951

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.616
ELB improved by 5.70692

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.385
ELB improved by 3.23171

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.926
ELB improved by 2.45833

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.791
ELB improved by 2.1353

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.799
ELB improved by 1.99203

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.874
ELB improved by 1.92454

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.973
ELB improved by 1.90178

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.055
ELB improved by 1.91727

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.084
ELB improved by 1.97122

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.023
ELB improved by 2.06143

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.852
ELB improved by 2.17047

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.611
ELB improved by 2.2417

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.438
ELB improved by 2.1722

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.542
ELB improved by 1.89643

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.055
ELB improved by 1.48674

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.966
ELB improved by 1.08903

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.169
ELB improved by 0.797318

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.544
ELB improved by 0.62476

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.002
ELB improved by 0.542

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.496
ELB improved by 0.506531

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.015
ELB improved by 0.480519

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.558
ELB improved by 0.457272

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.105
ELB improved by 0.452572

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.632
ELB improved by 0.472692

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.119
ELB improved by 0.513623

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.548
ELB improved by 0.571066

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.904
ELB improved by 0.643409

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.173
ELB improved by 0.731131

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.338
ELB improved by 0.835097

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.384
ELB improved by 0.954

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.303
ELB improved by 1.08141

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.099
ELB improved by 1.20385

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.797
ELB improved by 1.30178

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.442
ELB improved by 1.35496

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.089
ELB improved by 1.35313

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.785
ELB improved by 1.30423

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.573
ELB improved by 1.21148

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.531
ELB improved by 1.0428

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.701
ELB improved by 0.829378

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.027
ELB improved by 0.673999

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.434
ELB improved by 0.593261

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.911
ELB improved by 0.522512

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.492
ELB improved by 0.419208

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.182
ELB improved by 0.310311

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.952
ELB improved by 0.229981

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.769
ELB improved by 0.183276

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.605
ELB improved by 0.16359

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.438
ELB improved by 0.1673

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.242
ELB improved by 0.195607

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.996
ELB improved by 0.246281

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.7
ELB improved by 0.295677

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.396
ELB improved by 0.30376

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.133
ELB improved by 0.263194

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.931
ELB improved by 0.202532

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.783
ELB improved by 0.148113

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.671
ELB improved by 0.111413

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.582
ELB improved by 0.0891818

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.509
ELB improved by 0.0734292

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.449
ELB improved by 0.0593536

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.403
ELB improved by 0.0461683

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.368
ELB improved by 0.0348847

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.342
ELB improved by 0.0262603

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.322
ELB improved by 0.0201983

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.306
ELB improved by 0.0161118

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.292
ELB improved by 0.0133656

iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.281
ELB improved by 0.0114723

iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.271
ELB improved by 0.0101111

iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.262
ELB improved by 0.00908609

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-895.907
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-574.485
ELB improved by 321.422

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-514.112
ELB improved by 60.3733

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-475.259
ELB improved by 38.8527

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.253
ELB improved by 17.0059

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.385
ELB improved by 6.86756

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.066
ELB improved by 4.31941

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.467
ELB improved by 3.59942

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.039
ELB improved by 3.42753

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.527
ELB improved by 3.51221

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.793
ELB improved by 3.73365

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.82
ELB improved by 3.97293

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.792
ELB improved by 4.0287

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.066
ELB improved by 3.7252

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.936
ELB improved by 3.13073

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.466
ELB improved by 2.4699

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.646
ELB improved by 1.81976

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.39
ELB improved by 1.25559

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.51
ELB improved by 0.880828

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.842
ELB improved by 0.667564

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.294
ELB improved by 0.548003

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.817
ELB improved by 0.476682

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.388
ELB improved by 0.429645

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.993
ELB improved by 0.395053

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.625
ELB improved by 0.367189

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.282
ELB improved by 0.343447

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.959
ELB improved by 0.322884

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.654
ELB improved by 0.305573

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.361
ELB improved by 0.292374

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.076
ELB improved by 0.285074

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.789
ELB improved by 0.2868

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.487
ELB improved by 0.302219

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.152
ELB improved by 0.334875

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.775
ELB improved by 0.377367

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.369
ELB improved by 0.406317

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.959
ELB improved by 0.409858

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.557
ELB improved by 0.401801

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.164
ELB improved by 0.3933

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.779
ELB improved by 0.38497

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.404
ELB improved by 0.374661

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.044
ELB improved by 0.360454

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.702
ELB improved by 0.341073

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.386
ELB improved by 0.316136

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.1
ELB improved by 0.286339

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.847
ELB improved by 0.253365

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.627
ELB improved by 0.219476

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.44
ELB improved by 0.186948

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.283
ELB improved by 0.15757

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.15
ELB improved by 0.132389

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.039
ELB improved by 0.111698

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.943
ELB improved by 0.0952103

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.861
ELB improved by 0.0822935

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.789
ELB improved by 0.0721798

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.725
ELB improved by 0.0641215

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.667
ELB improved by 0.0574848

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.615
ELB improved by 0.0517916

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.569
ELB improved by 0.046724

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.527
ELB improved by 0.0421004

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.489
ELB improved by 0.0378393

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.455
ELB improved by 0.0339193

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.425
ELB improved by 0.0303459

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.397
ELB improved by 0.0271273

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.373
ELB improved by 0.0242626

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.351
ELB improved by 0.0217374

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.332
ELB improved by 0.0195264

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.314
ELB improved by 0.0175975

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.298
ELB improved by 0.015916

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.284
ELB improved by 0.0144485

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.271
ELB improved by 0.0131645

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.259
ELB improved by 0.0120375

iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.248
ELB improved by 0.0110448

iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.237
ELB improved by 0.0101676

iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.228
ELB improved by 0.00938981

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-846.533
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-570.97
ELB improved by 275.563

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-504.668
ELB improved by 66.3026

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.743
ELB improved by 43.9247

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.631
ELB improved by 19.1121

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.6
ELB improved by 8.03068

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.66
ELB improved by 4.93996

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.72
ELB improved by 3.93999

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.111
ELB improved by 3.60967

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.6
ELB improved by 3.51031

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.157
ELB improved by 3.44289

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.848
ELB improved by 3.3098

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.796
ELB improved by 3.05113

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.145
ELB improved by 2.65188

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.979
ELB improved by 2.16537

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.291
ELB improved by 1.68828

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.992
ELB improved by 1.29862

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.975
ELB improved by 1.01774

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.155
ELB improved by 0.819544

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.488
ELB improved by 0.667368

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.945
ELB improved by 0.542892

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.5
ELB improved by 0.444368

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.129
ELB improved by 0.371549

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.809
ELB improved by 0.320324

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.524
ELB improved by 0.284985

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.263
ELB improved by 0.260567

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.02
ELB improved by 0.243482

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.788
ELB improved by 0.231308

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.566
ELB improved by 0.222407

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.35
ELB improved by 0.215654

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.14
ELB improved by 0.21026

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.934
ELB improved by 0.205665

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.733
ELB improved by 0.201481

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.535
ELB improved by 0.197454

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.342
ELB improved by 0.193446

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.152
ELB improved by 0.189414

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.967
ELB improved by 0.185393

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.786
ELB improved by 0.181478

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.608
ELB improved by 0.177795

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.433
ELB improved by 0.174481

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.262
ELB improved by 0.171662

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.092
ELB improved by 0.169434

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.924
ELB improved by 0.167856

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.757
ELB improved by 0.166945

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.591
ELB improved by 0.166676

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.424
ELB improved by 0.166991

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.256
ELB improved by 0.167799

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.087
ELB improved by 0.168991

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.917
ELB improved by 0.170436

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.745
ELB improved by 0.171998

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.571
ELB improved by 0.173533

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.396
ELB improved by 0.174905

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.22
ELB improved by 0.176003

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.043
ELB improved by 0.176764

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.866
ELB improved by 0.177217

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.689
ELB improved by 0.177522

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.511
ELB improved by 0.178

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.331
ELB improved by 0.179114

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.15
ELB improved by 0.18133

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.965
ELB improved by 0.184771

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.777
ELB improved by 0.188649

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.586
ELB improved by 0.190864

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.397
ELB improved by 0.188608

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.217
ELB improved by 0.180235

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.05
ELB improved by 0.166635

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.9
ELB improved by 0.150386

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.766
ELB improved by 0.133881

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.648
ELB improved by 0.118455

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.543
ELB improved by 0.104606

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.451
ELB improved by 0.0924268

iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.369
ELB improved by 0.0818627

iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.296
ELB improved by 0.0728055

iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.231
ELB improved by 0.0651269

iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.172
ELB improved by 0.0586888

iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.119
ELB improved by 0.05334

iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.07
ELB improved by 0.0489039

iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.025
ELB improved by 0.045164

iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.983
ELB improved by 0.0418567

iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.944
ELB improved by 0.038689

iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.909
ELB improved by 0.0353921

iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.877
ELB improved by 0.031805

iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.849
ELB improved by 0.027941

iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.825
ELB improved by 0.0239814

iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.805
ELB improved by 0.0201867

iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.788
ELB improved by 0.0167822

iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.774
ELB improved by 0.0138902

iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.763
ELB improved by 0.0115271

iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.753
ELB improved by 0.00964018

ELB converged
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 24 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  2.741   0.245   3.130

name	user	system	elapsed
coef.graper	0.082	0.017	0.100
getPIPs	0.065	0.011	0.076
graper	0.112	0.019	0.133
makeExampleData	0.016	0.002	0.019
makeExampleDataWithUnequalGroups	0.016	0.003	0.018
plotELBO	0.223	0.020	0.242
plotGroupPenalties	0.986	0.038	1.031
plotPosterior	0.900	0.021	0.939
predict.graper	2.959	0.055	3.050
print.graper	0.06	0.01	0.07

CHECK report for graper on merida2

Summary

Command output

Installation output

Tests output

Example timings