Multiple platform build/check report for BioC 3.19 - CHECK results for graper on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4763
palomino7	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4500
merida1	macOS 12.7.5 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4530
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4480
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*

CHECK results for graper on merida1

To the developers/maintainers of the graper package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: graper

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.20.0.tar.gz

StartedAt: 2024-10-17 06:19:43 -0400 (Thu, 17 Oct 2024)

EndedAt: 2024-10-17 06:21:52 -0400 (Thu, 17 Oct 2024)

EllapsedTime: 129.0 seconds

RetCode: 0

Status: WARNINGS

CheckDir: graper.Rcheck

Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/graper.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.20.0’
* 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 ... WARNING
Found the following significant warnings:
  /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
  #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
See ‘/Users/biocbuild/bbs-3.19-bioc/meat/graper.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 code 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 ... NOTE
checkRd: (-1) predict.graper.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:23-24: Lost braces in \itemize; meant \describe ?
* 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 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/graper.Rcheck/00check.log’
for details.

Installation output

graper.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL graper
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘graper’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c fit_graper.cpp -o fit_graper.o
In file included from fit_graper.cpp:4:
In file included from ./graper_linear_dense_ff.h:2:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/digamma.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/math_fwd.hpp:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
#    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
     ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-graper/00new/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 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 (graper)

Tests output

graper.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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=-875.877
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-565.575
ELB improved by 310.302

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-511.999
ELB improved by 53.5764

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-483.413
ELB improved by 28.5852

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.876
ELB improved by 11.5378

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.902
ELB improved by 4.9734

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.848
ELB improved by 3.05481

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.445
ELB improved by 2.40218

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.391
ELB improved by 2.05417

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.605
ELB improved by 1.78648

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.052
ELB improved by 1.55263

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.71
ELB improved by 1.34248

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.555
ELB improved by 1.1546

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.565
ELB improved by 0.989644

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.717
ELB improved by 0.848073

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.988
ELB improved by 0.729197

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.357
ELB improved by 0.630955

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.807
ELB improved by 0.550137

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.324
ELB improved by 0.48286

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.899
ELB improved by 0.42524

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.525
ELB improved by 0.374211

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.197
ELB improved by 0.328106

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.91
ELB improved by 0.286621

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.66
ELB improved by 0.25022

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.44
ELB improved by 0.219433

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.246
ELB improved by 0.19443

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.071
ELB improved by 0.17492

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.911
ELB improved by 0.160271

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.761
ELB improved by 0.149693

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.619
ELB improved by 0.142399

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.481
ELB improved by 0.137705

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.346
ELB improved by 0.135064

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.212
ELB improved by 0.134069

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.077
ELB improved by 0.134432

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.941
ELB improved by 0.13596

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.803
ELB improved by 0.138533

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.661
ELB improved by 0.14208

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.514
ELB improved by 0.146564

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.362
ELB improved by 0.151966

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.204
ELB improved by 0.158265

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.038
ELB improved by 0.165428

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.865
ELB improved by 0.173396

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.683
ELB improved by 0.182082

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.492
ELB improved by 0.191379

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.29
ELB improved by 0.201185

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.079
ELB improved by 0.21143

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.857
ELB improved by 0.222111

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.624
ELB improved by 0.233313

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.378
ELB improved by 0.245206

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.12
ELB improved by 0.25803

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.848
ELB improved by 0.272033

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.561
ELB improved by 0.287383

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.257
ELB improved by 0.304045

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.935
ELB improved by 0.32164

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.596
ELB improved by 0.33931

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.24
ELB improved by 0.355643

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.872
ELB improved by 0.368731

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.495
ELB improved by 0.37643

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.118
ELB improved by 0.376796

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.75
ELB improved by 0.368581

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.398
ELB improved by 0.351552

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.072
ELB improved by 0.326529

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.776
ELB improved by 0.295219

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.516
ELB improved by 0.26009

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.292
ELB improved by 0.224267

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.101
ELB improved by 0.191157

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.937
ELB improved by 0.163784

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.793
ELB improved by 0.144214

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.66
ELB improved by 0.133289

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.529
ELB improved by 0.130406

iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.396
ELB improved by 0.133102

iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.259
ELB improved by 0.13667

iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.125
ELB improved by 0.134827

iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.001
ELB improved by 0.123328

iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.897
ELB improved by 0.104508

iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.812
ELB improved by 0.0850586

iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.742
ELB improved by 0.0694484

iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.684
ELB improved by 0.0583236

iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.633
ELB improved by 0.0507088

iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.588
ELB improved by 0.0455855

iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.545
ELB improved by 0.0422796

iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.505
ELB improved by 0.0403858

iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.465
ELB improved by 0.0396234

iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.426
ELB improved by 0.0397158

iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.385
ELB improved by 0.0402988

iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.345
ELB improved by 0.0408697

iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.304
ELB improved by 0.040821

iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.264
ELB improved by 0.039596

iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.227
ELB improved by 0.0369192

iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.194
ELB improved by 0.0329446

iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.166
ELB improved by 0.0281884

iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.143
ELB improved by 0.0232894

iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.124
ELB improved by 0.0187711

iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.109
ELB improved by 0.0149313

iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.097
ELB improved by 0.011856

iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.088
ELB improved by 0.00949321

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-849.737
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-590.125
ELB improved by 259.612

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-528.204
ELB improved by 61.9213

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-487.374
ELB improved by 40.8292

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.9
ELB improved by 19.4748

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.74
ELB improved by 9.15951

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.788
ELB improved by 6.95227

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.594
ELB improved by 7.19386

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.179
ELB improved by 7.41464

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.588
ELB improved by 6.59168

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.69
ELB improved by 4.89766

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.396
ELB improved by 3.29352

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.148
ELB improved by 2.24833

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.495
ELB improved by 1.65286

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.219
ELB improved by 1.27625

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.208
ELB improved by 1.01118

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.348
ELB improved by 0.859835

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.545
ELB improved by 0.802873

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.752
ELB improved by 0.793237

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.96
ELB improved by 0.791447

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.158
ELB improved by 0.802497

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.307
ELB improved by 0.850784

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.364
ELB improved by 0.942809

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.287
ELB improved by 1.07748

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.041
ELB improved by 1.2462

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.635
ELB improved by 1.40513

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.111
ELB improved by 1.52496

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.478
ELB improved by 1.63236

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.759
ELB improved by 1.71894

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.026
ELB improved by 1.73363

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.388
ELB improved by 1.63786

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.944
ELB improved by 1.44373

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.736
ELB improved by 1.20789

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.74
ELB improved by 0.995966

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.891
ELB improved by 0.849594

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.131
ELB improved by 0.759186

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.486
ELB improved by 0.645601

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.017
ELB improved by 0.469004

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.712
ELB improved by 0.304379

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.516
ELB improved by 0.196446

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.383
ELB improved by 0.13311

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.287
ELB improved by 0.0954062

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.216
ELB improved by 0.0716168

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.16
ELB improved by 0.0556511

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.116
ELB improved by 0.0443886

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.08
ELB improved by 0.0361461

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.05
ELB improved by 0.0299447

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.024
ELB improved by 0.0251748

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.003
ELB improved by 0.0214362

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.985
ELB improved by 0.0184569

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.969
ELB improved by 0.016047

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.954
ELB improved by 0.0140715

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.942
ELB improved by 0.0124325

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.931
ELB improved by 0.0110582

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.921
ELB improved by 0.00989503

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-891.422
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-587.535
ELB improved by 303.887

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-530.89
ELB improved by 56.6445

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-493.412
ELB improved by 37.4785

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-475.377
ELB improved by 18.0354

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.102
ELB improved by 8.27403

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.839
ELB improved by 5.26302

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.127
ELB improved by 4.71253

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.354
ELB improved by 4.7729

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.355
ELB improved by 4.99857

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.147
ELB improved by 5.20852

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.969
ELB improved by 5.17759

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.378
ELB improved by 4.59138

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.903
ELB improved by 3.47503

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.558
ELB improved by 2.34483

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.029
ELB improved by 1.5294

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.99
ELB improved by 1.03846

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.213
ELB improved by 0.777462

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.57
ELB improved by 0.643026

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.999
ELB improved by 0.571059

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.467
ELB improved by 0.531387

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.956
ELB improved by 0.510825

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.452
ELB improved by 0.504123

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.942
ELB improved by 0.510349

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.411
ELB improved by 0.530652

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.847
ELB improved by 0.564283

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.242
ELB improved by 0.605501

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.582
ELB improved by 0.660067

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.803
ELB improved by 0.778376

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.833
ELB improved by 0.970237

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.747
ELB improved by 1.08619

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.475
ELB improved by 1.27145

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.947
ELB improved by 1.52837

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.429
ELB improved by 1.51777

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.955
ELB improved by 1.47381

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.456
ELB improved by 1.49968

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.907
ELB improved by 1.5488

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.339
ELB improved by 1.56765

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.829
ELB improved by 1.51055

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.468
ELB improved by 1.36075

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.328
ELB improved by 1.14022

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.434
ELB improved by 0.89416

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.768
ELB improved by 0.66556

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.289
ELB improved by 0.479413

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.947
ELB improved by 0.341313

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.703
ELB improved by 0.244248

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.526
ELB improved by 0.177186

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.395
ELB improved by 0.130648

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.297
ELB improved by 0.0981005

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.222
ELB improved by 0.0752359

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.163
ELB improved by 0.0590865

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.115
ELB improved by 0.047543

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.076
ELB improved by 0.0391246

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.043
ELB improved by 0.032826

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.015
ELB improved by 0.0279841

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.991
ELB improved by 0.024167

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.97
ELB improved by 0.0210926

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.951
ELB improved by 0.0185733

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.935
ELB improved by 0.0164808

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.92
ELB improved by 0.0147247

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.907
ELB improved by 0.0132388

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.895
ELB improved by 0.0119736

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.884
ELB improved by 0.0108909

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.874
ELB improved by 0.0099604

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-906.67
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-577.465
ELB improved by 329.205

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-519.733
ELB improved by 57.7317

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-488.541
ELB improved by 31.1926

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.835
ELB improved by 14.7061

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.225
ELB improved by 7.60965

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.985
ELB improved by 5.23996

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.205
ELB improved by 4.78038

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.167
ELB improved by 5.03772

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.824
ELB improved by 5.34306

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.678
ELB improved by 5.1461

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.422
ELB improved by 4.2562

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.367
ELB improved by 3.05491

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.335
ELB improved by 2.03205

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.992
ELB improved by 1.34253

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.075
ELB improved by 0.916879

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.418
ELB improved by 0.656855

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.924
ELB improved by 0.494314

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.535
ELB improved by 0.389132

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.217
ELB improved by 0.318335

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.948
ELB improved by 0.268598

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.716
ELB improved by 0.232133

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.511
ELB improved by 0.204362

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.329
ELB improved by 0.18255

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.164
ELB improved by 0.165003

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.013
ELB improved by 0.150631

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.875
ELB improved by 0.138704

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.746
ELB improved by 0.128719

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.626
ELB improved by 0.120331

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.512
ELB improved by 0.113311

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.405
ELB improved by 0.107527

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.302
ELB improved by 0.102949

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.202
ELB improved by 0.099654

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.104
ELB improved by 0.097864

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.006
ELB improved by 0.0979886

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.906
ELB improved by 0.10067

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.799
ELB improved by 0.106773

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.682
ELB improved by 0.117221

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.549
ELB improved by 0.132634

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.396
ELB improved by 0.152986

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.218
ELB improved by 0.177463

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.015
ELB improved by 0.203584

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.789
ELB improved by 0.225742

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.552
ELB improved by 0.237382

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.314
ELB improved by 0.237595

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.081
ELB improved by 0.232676

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.852
ELB improved by 0.229201

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.623
ELB improved by 0.229633

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.389
ELB improved by 0.233979

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.147
ELB improved by 0.241967

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.893
ELB improved by 0.253727

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.623
ELB improved by 0.269733

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.333
ELB improved by 0.290673

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.015
ELB improved by 0.317423

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.664
ELB improved by 0.351196

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.27
ELB improved by 0.393819

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.822
ELB improved by 0.447863

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.307
ELB improved by 0.515579

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.712
ELB improved by 0.594673

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.041
ELB improved by 0.670672

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.331
ELB improved by 0.710795

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.653
ELB improved by 0.678057

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.074
ELB improved by 0.578725

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.615
ELB improved by 0.459126

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.265
ELB improved by 0.349407

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.008
ELB improved by 0.257645

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.822
ELB improved by 0.18596

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.688
ELB improved by 0.133629

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.591
ELB improved by 0.0970118

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.519
ELB improved by 0.0716775

iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.465
ELB improved by 0.0540019

iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.424
ELB improved by 0.0414685

iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.391
ELB improved by 0.0324308

iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.366
ELB improved by 0.0258252

iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.345
ELB improved by 0.0209568

iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.327
ELB improved by 0.0173576

iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.313
ELB improved by 0.0146986

iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.3
ELB improved by 0.0127378

iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.289
ELB improved by 0.0112907

iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.278
ELB improved by 0.0102142

iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.269
ELB improved by 0.00939662

ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
> 
> proc.time()
   user  system elapsed 
  4.591   0.447   5.557

Example timings

graper.Rcheck/graper-Ex.timings

name	user	system	elapsed
coef.graper	0.085	0.044	0.144
getPIPs	0.074	0.038	0.114
graper	0.128	0.056	0.197
makeExampleData	0.018	0.002	0.021
makeExampleDataWithUnequalGroups	0.046	0.006	0.054
plotELBO	0.416	0.042	0.490
plotGroupPenalties	1.694	0.067	1.919
plotPosterior	1.221	0.046	1.384
predict.graper	3.136	0.204	3.959
print.graper	0.075	0.030	0.120