Build/check report for BioC 3.23 - CHECK results for graper on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4994
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 nebbiolo1

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: 1.28.0

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings graper_1.28.0.tar.gz

StartedAt: 2026-05-12 00:41:56 -0400 (Tue, 12 May 2026)

EndedAt: 2026-05-12 00:43:27 -0400 (Tue, 12 May 2026)

EllapsedTime: 91.1 seconds

RetCode: 0

Status: OK

CheckDir: graper.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings graper_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-12 04:41:56 UTC
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.28.0’
* 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 ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* 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 loading without being on the library search path ... 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 ... INFO
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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck/00check.log’
for details.

Installation output

graper.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL graper
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘graper’ ...
** this is package ‘graper’ version ‘1.28.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c fit_graper.cpp -o fit_graper.o
g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -llapack -L/home/biocbuild/bbs-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-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 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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=-850.599
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-559.737
ELB improved by 290.862

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-497.47
ELB improved by 62.2671

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.787
ELB improved by 40.6826

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.497
ELB improved by 16.2898

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.075
ELB improved by 6.42291

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.293
ELB improved by 3.78151

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.246
ELB improved by 3.04657

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.371
ELB improved by 2.87579

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.373
ELB improved by 2.99729

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.047
ELB improved by 3.32666

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.264
ELB improved by 3.78308

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.08
ELB improved by 4.18409

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.816
ELB improved by 4.26369

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.913
ELB improved by 3.90263

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.673
ELB improved by 3.24038

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.217
ELB improved by 2.45617

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.425
ELB improved by 1.79157

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.044
ELB improved by 1.38111

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.875
ELB improved by 1.16931

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.806
ELB improved by 1.06902

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.781
ELB improved by 1.02488

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.773
ELB improved by 1.00817

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.768
ELB improved by 1.00468

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.761
ELB improved by 1.00728

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.747
ELB improved by 1.01324

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.72
ELB improved by 1.02772

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.645
ELB improved by 1.07476

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.46
ELB improved by 1.18476

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.224
ELB improved by 1.23596

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.175
ELB improved by 1.04969

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.381
ELB improved by 0.794068

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.796
ELB improved by 0.584056

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.373
ELB improved by 0.423206

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.068
ELB improved by 0.305452

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.844
ELB improved by 0.223476

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.676
ELB improved by 0.16881

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.542
ELB improved by 0.133984

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.428
ELB improved by 0.113702

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.323
ELB improved by 0.104575

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.22
ELB improved by 0.103469

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.115
ELB improved by 0.104513

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.017
ELB improved by 0.098721

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.935
ELB improved by 0.0819668

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.874
ELB improved by 0.0607924

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.83
ELB improved by 0.0436058

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.797
ELB improved by 0.0328021

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.771
ELB improved by 0.0267615

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.747
ELB improved by 0.023401

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.726
ELB improved by 0.0213455

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.706
ELB improved by 0.0198372

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.688
ELB improved by 0.0184736

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.671
ELB improved by 0.0170584

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.655
ELB improved by 0.015539

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.641
ELB improved by 0.0139627

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.629
ELB improved by 0.012424

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.618
ELB improved by 0.0110119

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.608
ELB improved by 0.00977963

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-870.668
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-599.24
ELB improved by 271.427

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-542.035
ELB improved by 57.2054

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-495.072
ELB improved by 46.9635

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.803
ELB improved by 26.2686

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.219
ELB improved by 10.5841

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.725
ELB improved by 5.494

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.108
ELB improved by 4.6171

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.313
ELB improved by 4.79517

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.067
ELB improved by 5.24596

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.635
ELB improved by 5.4313

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.687
ELB improved by 4.94879

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.801
ELB improved by 3.88591

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.086
ELB improved by 2.7146

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.293
ELB improved by 1.79271

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.086
ELB improved by 1.20726

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.192
ELB improved by 0.894484

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.411
ELB improved by 0.78021

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.557
ELB improved by 0.854648

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.47
ELB improved by 1.08643

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.291
ELB improved by 1.17948

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.324
ELB improved by 0.967056

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.624
ELB improved by 0.699868

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.098
ELB improved by 0.525481

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.666
ELB improved by 0.432052

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.284
ELB improved by 0.382054

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.933
ELB improved by 0.351069

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.605
ELB improved by 0.328284

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.295
ELB improved by 0.309837

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.001
ELB improved by 0.294609

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.718
ELB improved by 0.282516

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.444
ELB improved by 0.273969

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.174
ELB improved by 0.269794

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.903
ELB improved by 0.271424

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.621
ELB improved by 0.281373

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.317
ELB improved by 0.30406

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.971
ELB improved by 0.346693

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.553
ELB improved by 0.417949

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.033
ELB improved by 0.519651

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.393
ELB improved by 0.639612

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.618
ELB improved by 0.775017

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.683
ELB improved by 0.935548

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.622
ELB improved by 1.06088

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.557
ELB improved by 1.06471

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.579
ELB improved by 0.97848

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.72
ELB improved by 0.858378

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.993
ELB improved by 0.727601

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.394
ELB improved by 0.598693

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.912
ELB improved by 0.481683

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.529
ELB improved by 0.38378

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.224
ELB improved by 0.305129

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.984
ELB improved by 0.239811

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.8
ELB improved by 0.18348

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.663
ELB improved by 0.13683

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.562
ELB improved by 0.10135

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.486
ELB improved by 0.0760204

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.428
ELB improved by 0.0583968

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.381
ELB improved by 0.0462426

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.343
ELB improved by 0.0379875

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.311
ELB improved by 0.0326028

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.281
ELB improved by 0.0293907

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.254
ELB improved by 0.0277981

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.226
ELB improved by 0.0272586

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.199
ELB improved by 0.0270952

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.173
ELB improved by 0.0265723

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.148
ELB improved by 0.0251387

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.125
ELB improved by 0.0226998

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.105
ELB improved by 0.0196332

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.089
ELB improved by 0.0164992

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.075
ELB improved by 0.0137243

iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.064
ELB improved by 0.0114861

iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.054
ELB improved by 0.00977458

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-833.876
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-573.099
ELB improved by 260.777

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-512.428
ELB improved by 60.6713

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.525
ELB improved by 42.9032

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.833
ELB improved by 20.6918

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.216
ELB improved by 7.61695

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.511
ELB improved by 3.70445

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.905
ELB improved by 2.60646

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.672
ELB improved by 2.23244

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.539
ELB improved by 2.13349

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.401
ELB improved by 2.13815

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.233
ELB improved by 2.1683

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.062
ELB improved by 2.17077

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.967
ELB improved by 2.09433

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.065
ELB improved by 1.90256

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.463
ELB improved by 1.60235

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.211
ELB improved by 1.25185

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.284
ELB improved by 0.926353

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.611
ELB improved by 0.672991

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.114
ELB improved by 0.49729

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.733
ELB improved by 0.38103

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.43
ELB improved by 0.303319

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.18
ELB improved by 0.249783

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.968
ELB improved by 0.212262

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.782
ELB improved by 0.185941

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.614
ELB improved by 0.167525

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.46
ELB improved by 0.154637

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.314
ELB improved by 0.145644

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.174
ELB improved by 0.13951

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.039
ELB improved by 0.135664

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.905
ELB improved by 0.133908

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.77
ELB improved by 0.134415

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.633
ELB improved by 0.137856

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.487
ELB improved by 0.145754

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.326
ELB improved by 0.161259

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.135
ELB improved by 0.190553

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.891
ELB improved by 0.244085

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.559
ELB improved by 0.332034

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.116
ELB improved by 0.442491

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.594
ELB improved by 0.522405

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.057
ELB improved by 0.537334

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.532
ELB improved by 0.524311

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.011
ELB improved by 0.52133

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.475
ELB improved by 0.535731

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.911
ELB improved by 0.564288

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.308
ELB improved by 0.602887

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.661
ELB improved by 0.646849

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.972
ELB improved by 0.689647

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.249
ELB improved by 0.722489

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.513
ELB improved by 0.735714

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.791
ELB improved by 0.722146

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.11
ELB improved by 0.680955

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.491
ELB improved by 0.619241

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.942
ELB improved by 0.549379

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.459
ELB improved by 0.483049

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.033
ELB improved by 0.425621

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.658
ELB improved by 0.37497

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.332
ELB improved by 0.325633

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.058
ELB improved by 0.274414

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.834
ELB improved by 0.223467

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.656
ELB improved by 0.178259

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.514
ELB improved by 0.142602

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.397
ELB improved by 0.117018

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.296
ELB improved by 0.100197

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.206
ELB improved by 0.090345

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.121
ELB improved by 0.0854495

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.038
ELB improved by 0.0828264

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.959
ELB improved by 0.078946

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.888
ELB improved by 0.0708522

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.829
ELB improved by 0.0585852

iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.784
ELB improved by 0.0451731

iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.751
ELB improved by 0.0336519

iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.725
ELB improved by 0.0251186

iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.706
ELB improved by 0.0192198

iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.691
ELB improved by 0.0152011

iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.679
ELB improved by 0.0124215

iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.668
ELB improved by 0.0104475

iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.659
ELB improved by 0.00900764

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-880.954
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-559.004
ELB improved by 321.95

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-501.364
ELB improved by 57.6398

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.85
ELB improved by 31.5145

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.022
ELB improved by 13.828

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.206
ELB improved by 6.81572

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.597
ELB improved by 4.60933

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.661
ELB improved by 3.93606

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.983
ELB improved by 3.67807

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.508
ELB improved by 3.47521

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.3
ELB improved by 3.20729

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.48
ELB improved by 2.8204

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.194
ELB improved by 2.28618

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.505
ELB improved by 1.68875

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.325
ELB improved by 1.17965

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.498
ELB improved by 0.826892

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.891
ELB improved by 0.607149

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.423
ELB improved by 0.468568

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.047
ELB improved by 0.375312

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.735
ELB improved by 0.312592

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.462
ELB improved by 0.27315

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.211
ELB improved by 0.250747

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.971
ELB improved by 0.240377

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.732
ELB improved by 0.238731

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.488
ELB improved by 0.243765

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.234
ELB improved by 0.254113

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.965
ELB improved by 0.268858

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.677
ELB improved by 0.287731

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.366
ELB improved by 0.311365

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.025
ELB improved by 0.34119

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.646
ELB improved by 0.378904

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.22
ELB improved by 0.425551

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.741
ELB improved by 0.479759

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.205
ELB improved by 0.535596

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.621
ELB improved by 0.583834

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.002
ELB improved by 0.618859

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.361
ELB improved by 0.64173

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.706
ELB improved by 0.654191

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.052
ELB improved by 0.654441

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.413
ELB improved by 0.638724

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.809
ELB improved by 0.604596

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.255
ELB improved by 0.553676

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.763
ELB improved by 0.492353

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.333
ELB improved by 0.429366

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.961
ELB improved by 0.371763

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.639
ELB improved by 0.322406

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.358
ELB improved by 0.280739

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.113
ELB improved by 0.245387

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.897
ELB improved by 0.215935

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.704
ELB improved by 0.193092

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.526
ELB improved by 0.178223

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.353
ELB improved by 0.172696

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.177
ELB improved by 0.176135

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.994
ELB improved by 0.182588

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.815
ELB improved by 0.179504

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.655
ELB improved by 0.159872

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.523
ELB improved by 0.132195

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.416
ELB improved by 0.106443

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.332
ELB improved by 0.0841347

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.268
ELB improved by 0.064359

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.22
ELB improved by 0.047768

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.185
ELB improved by 0.0352561

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.158
ELB improved by 0.0266304

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.137
ELB improved by 0.0209297

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.12
ELB improved by 0.0171416

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.106
ELB improved by 0.0145292

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.093
ELB improved by 0.0126371

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.082
ELB improved by 0.0112012

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.072
ELB improved by 0.0100688

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.062
ELB improved by 0.00914841

ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
> 
> proc.time()
   user  system elapsed 
  2.381   0.192   2.557

Example timings

graper.Rcheck/graper-Ex.timings

name	user	system	elapsed
coef.graper	0.045	0.032	0.077
getPIPs	0.074	0.031	0.105
graper	0.079	0.020	0.101
makeExampleData	0.009	0.001	0.011
makeExampleDataWithUnequalGroups	0.011	0.000	0.012
plotELBO	0.299	0.026	0.325
plotGroupPenalties	0.931	0.015	0.944
plotPosterior	0.635	0.013	0.649
predict.graper	2.060	0.081	2.141
print.graper	0.054	0.010	0.064