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: 2026-05-13 00:44:57 -0400 (Wed, 13 May 2026)

EndedAt: 2026-05-13 00:46:34 -0400 (Wed, 13 May 2026)

EllapsedTime: 97.2 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: 2026-05-13 04:44:57 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
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
predict.graper 3.672  0.511   5.472
* 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=-873.398
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-586.075
ELB improved by 287.323

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-526.679
ELB improved by 59.3958

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-488.465
ELB improved by 38.2141

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.729
ELB improved by 15.736

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.014
ELB improved by 5.71515

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.834
ELB improved by 3.17919

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.36
ELB improved by 2.47458

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.117
ELB improved by 2.24313

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.916
ELB improved by 2.20031

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.671
ELB improved by 2.24556

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.348
ELB improved by 2.32297

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.98
ELB improved by 2.36818

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.666
ELB improved by 2.31335

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.547
ELB improved by 2.11964

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.744
ELB improved by 1.80247

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.319
ELB improved by 1.42554

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.254
ELB improved by 1.0643

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.483
ELB improved by 0.771719

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.918
ELB improved by 0.565023

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.485
ELB improved by 0.432223

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.135
ELB improved by 0.350509

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.835
ELB improved by 0.300118

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.567
ELB improved by 0.268063

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.32
ELB improved by 0.246777

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.088
ELB improved by 0.23201

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.867
ELB improved by 0.221333

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.653
ELB improved by 0.213285

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.446
ELB improved by 0.206925

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.245
ELB improved by 0.201604

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.048
ELB improved by 0.196851

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.856
ELB improved by 0.192327

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.668
ELB improved by 0.18779

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.485
ELB improved by 0.183087

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.307
ELB improved by 0.17814

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.134
ELB improved by 0.172937

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.966
ELB improved by 0.167512

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.804
ELB improved by 0.161936

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.648
ELB improved by 0.1563

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.497
ELB improved by 0.150697

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.352
ELB improved by 0.145215

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.212
ELB improved by 0.139931

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.077
ELB improved by 0.134902

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.947
ELB improved by 0.130171

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.821
ELB improved by 0.125759

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.7
ELB improved by 0.121674

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.582
ELB improved by 0.117911

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.467
ELB improved by 0.11445

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.356
ELB improved by 0.111267

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.248
ELB improved by 0.108329

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.142
ELB improved by 0.1056

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.039
ELB improved by 0.103042

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.938
ELB improved by 0.100614

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.84
ELB improved by 0.0982822

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.744
ELB improved by 0.0960122

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.65
ELB improved by 0.093777

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.559
ELB improved by 0.0915564

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.469
ELB improved by 0.089339

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.382
ELB improved by 0.0871236

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.297
ELB improved by 0.0849207

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.215
ELB improved by 0.0827535

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.134
ELB improved by 0.0806592

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.055
ELB improved by 0.0786903

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.978
ELB improved by 0.0769152

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.903
ELB improved by 0.0754188

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.829
ELB improved by 0.074301

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.755
ELB improved by 0.0736732

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.681
ELB improved by 0.0736501

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.607
ELB improved by 0.0743367

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.531
ELB improved by 0.0758125

iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.453
ELB improved by 0.0781165

iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.372
ELB improved by 0.0812461

iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.287
ELB improved by 0.0851743

iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.197
ELB improved by 0.0898839

iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.101
ELB improved by 0.0953964

iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432
ELB improved by 0.101773

iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.89
ELB improved by 0.109079

iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.773
ELB improved by 0.117321

iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.647
ELB improved by 0.126374

iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.511
ELB improved by 0.135912

iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.366
ELB improved by 0.145324

iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.212
ELB improved by 0.153516

iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.054
ELB improved by 0.158529

iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.896
ELB improved by 0.157415

iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.749
ELB improved by 0.147588

iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.619
ELB improved by 0.129501

iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.512
ELB improved by 0.107274

iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.426
ELB improved by 0.0857128

iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.359
ELB improved by 0.0675

iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.305
ELB improved by 0.0531172

iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.263
ELB improved by 0.0420235

iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.23
ELB improved by 0.0334893

iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.203
ELB improved by 0.0268957

iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.181
ELB improved by 0.0217747

iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.163
ELB improved by 0.0177799

iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.149
ELB improved by 0.0146523

iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.137
ELB improved by 0.0121961

iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.126
ELB improved by 0.0102611

iteration 99
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.118
ELB improved by 0.00873168

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-874.758
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-602.75
ELB improved by 272.009

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-540.41
ELB improved by 62.3394

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-493.989
ELB improved by 46.4211

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.718
ELB improved by 23.2711

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.197
ELB improved by 9.52051

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.391
ELB improved by 4.80591

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.833
ELB improved by 3.5585

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.614
ELB improved by 3.21877

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.559
ELB improved by 3.05523

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.694
ELB improved by 2.86475

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.121
ELB improved by 2.5737

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.937
ELB improved by 2.18381

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.186
ELB improved by 1.75063

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.84
ELB improved by 1.34559

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.825
ELB improved by 1.01589

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.054
ELB improved by 0.770815

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.458
ELB improved by 0.59589

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.987
ELB improved by 0.47134

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.605
ELB improved by 0.381093

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.291
ELB improved by 0.314113

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.028
ELB improved by 0.263172

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.805
ELB improved by 0.223544

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.613
ELB improved by 0.192085

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.446
ELB improved by 0.166668

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.3
ELB improved by 0.14582

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.172
ELB improved by 0.128493

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.058
ELB improved by 0.113933

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.956
ELB improved by 0.101577

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.865
ELB improved by 0.0910026

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.783
ELB improved by 0.0818863

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.709
ELB improved by 0.073975

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.642
ELB improved by 0.0670692

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.581
ELB improved by 0.0610093

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.525
ELB improved by 0.0556664

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.475
ELB improved by 0.0509353

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.428
ELB improved by 0.0467295

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.385
ELB improved by 0.0429771

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.345
ELB improved by 0.0396183

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.309
ELB improved by 0.0366026

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.275
ELB improved by 0.0338873

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.243
ELB improved by 0.031436

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.214
ELB improved by 0.0292178

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.187
ELB improved by 0.0272058

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.161
ELB improved by 0.0253771

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.138
ELB improved by 0.0237117

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.116
ELB improved by 0.0221921

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.095
ELB improved by 0.0208031

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.075
ELB improved by 0.0195314

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.057
ELB improved by 0.0183653

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.04
ELB improved by 0.0172943

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.023
ELB improved by 0.0163092

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.008
ELB improved by 0.0154021

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.993
ELB improved by 0.0145655

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.979
ELB improved by 0.013793

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.966
ELB improved by 0.0130788

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.954
ELB improved by 0.0124178

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.942
ELB improved by 0.0118052

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.931
ELB improved by 0.0112369

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.92
ELB improved by 0.0107091

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.91
ELB improved by 0.0102183

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.9
ELB improved by 0.00976154

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-916.067
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-567.473
ELB improved by 348.594

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-504.712
ELB improved by 62.7606

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.838
ELB improved by 35.8744

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.752
ELB improved by 15.0852

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.56
ELB improved by 8.19202

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.906
ELB improved by 6.65394

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.298
ELB improved by 6.60838

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.061
ELB improved by 7.23673

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.14
ELB improved by 7.92144

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.327
ELB improved by 7.81262

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.912
ELB improved by 6.41511

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.49
ELB improved by 4.42175

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.678
ELB improved by 2.81238

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.894
ELB improved by 1.78452

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.719
ELB improved by 1.17503

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.88
ELB improved by 0.838898

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.218
ELB improved by 0.661296

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.654
ELB improved by 0.564366

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.156
ELB improved by 0.498349

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.717
ELB improved by 0.438969

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.328
ELB improved by 0.389011

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.969
ELB improved by 0.358577

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.625
ELB improved by 0.343961

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.304
ELB improved by 0.320666

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.039
ELB improved by 0.265054

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.846
ELB improved by 0.193108

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.709
ELB improved by 0.13732

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.604
ELB improved by 0.10458

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.518
ELB improved by 0.0859101

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.445
ELB improved by 0.0738082

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.38
ELB improved by 0.0647987

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.322
ELB improved by 0.0575111

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.271
ELB improved by 0.0513792

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.225
ELB improved by 0.0461231

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.183
ELB improved by 0.0415723

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.146
ELB improved by 0.0376063

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.112
ELB improved by 0.034132

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.08
ELB improved by 0.031075

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.052
ELB improved by 0.0283745

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.026
ELB improved by 0.0259801

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.002
ELB improved by 0.0238498

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.98
ELB improved by 0.0219485

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.96
ELB improved by 0.0202463

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.941
ELB improved by 0.0187182

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.924
ELB improved by 0.0173427

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.908
ELB improved by 0.0161014

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.893
ELB improved by 0.0149786

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.879
ELB improved by 0.0139607

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.866
ELB improved by 0.013036

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.854
ELB improved by 0.0121942

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.842
ELB improved by 0.0114264

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.832
ELB improved by 0.0107247

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.821
ELB improved by 0.0100825

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.812
ELB improved by 0.0094935

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-881.56
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-594.961
ELB improved by 286.599

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-532.555
ELB improved by 62.4058

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-486.559
ELB improved by 45.9963

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.655
ELB improved by 22.9041

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.082
ELB improved by 9.57225

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.113
ELB improved by 4.96924

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.54
ELB improved by 3.57353

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.444
ELB improved by 3.0953

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.542
ELB improved by 2.90248

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.749
ELB improved by 2.79235

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.052
ELB improved by 2.69706

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.474
ELB improved by 2.57874

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.06
ELB improved by 2.41327

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.862
ELB improved by 2.19836

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.932
ELB improved by 1.92983

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.347
ELB improved by 1.58527

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.147
ELB improved by 1.19998

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.286
ELB improved by 0.860925

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.671
ELB improved by 0.614904

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.213
ELB improved by 0.457751

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.849
ELB improved by 0.36444

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.538
ELB improved by 0.310585

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.259
ELB improved by 0.279369

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.998
ELB improved by 0.260776

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.749
ELB improved by 0.249159

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.508
ELB improved by 0.241363

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.272
ELB improved by 0.235604

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.041
ELB improved by 0.230868

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.815
ELB improved by 0.226594

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.592
ELB improved by 0.222507

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.374
ELB improved by 0.21852

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.159
ELB improved by 0.214669

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.948
ELB improved by 0.211069

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.74
ELB improved by 0.207873

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.535
ELB improved by 0.205246

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.331
ELB improved by 0.203354

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.129
ELB improved by 0.202348

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.927
ELB improved by 0.202373

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.723
ELB improved by 0.203573

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.517
ELB improved by 0.206109

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.307
ELB improved by 0.21019

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.091
ELB improved by 0.216115

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.866
ELB improved by 0.224341

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.631
ELB improved by 0.235593

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.38
ELB improved by 0.251014

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.107
ELB improved by 0.272359

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.805
ELB improved by 0.302064

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.463
ELB improved by 0.342718

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.068
ELB improved by 0.395034

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.612
ELB improved by 0.455042

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.096
ELB improved by 0.516838

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.51
ELB improved by 0.585152

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.828
ELB improved by 0.682285

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.008
ELB improved by 0.819766

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.087
ELB improved by 0.921149

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.211
ELB improved by 0.875939

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.502
ELB improved by 0.709829

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.969
ELB improved by 0.532303

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.568
ELB improved by 0.401399

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.254
ELB improved by 0.313621

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.997
ELB improved by 0.257595

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.76
ELB improved by 0.237025

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.495
ELB improved by 0.264246

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.154
ELB improved by 0.341758

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.722
ELB improved by 0.431946

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.261
ELB improved by 0.460313

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.862
ELB improved by 0.39909

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.554
ELB improved by 0.308517

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.309
ELB improved by 0.244873

iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.106
ELB improved by 0.202431

iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.946
ELB improved by 0.160378

iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.831
ELB improved by 0.11531

iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.754
ELB improved by 0.0765711

iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.704
ELB improved by 0.0501881

iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.669
ELB improved by 0.03463

iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.643
ELB improved by 0.0258584

iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.623
ELB improved by 0.020742

iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.605
ELB improved by 0.0175057

iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.59
ELB improved by 0.0152591

iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.576
ELB improved by 0.01357

iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.564
ELB improved by 0.0122243

iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.553
ELB improved by 0.0111109

iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.543
ELB improved by 0.0101671

iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.534
ELB improved by 0.00935488

ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
> 
> proc.time()
   user  system elapsed 
  2.401   0.209   2.600

Example timings

graper.Rcheck/graper-Ex.timings

name	user	system	elapsed
coef.graper	0.051	0.020	0.072
getPIPs	0.076	0.023	0.099
graper	0.084	0.016	0.100
makeExampleData	0.009	0.000	0.009
makeExampleDataWithUnequalGroups	0.011	0.000	0.012
plotELBO	0.305	0.020	0.327
plotGroupPenalties	0.955	0.014	0.969
plotPosterior	0.663	0.011	0.673
predict.graper	3.672	0.511	5.472
print.graper	0.311	0.086	0.396