Multiple platform build/check report for BioC 3.23 - CHECK results for graper on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4829
lconway	macOS 12.7.6 Monterey	x86_64	R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"	4602
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4566
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 lconway

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: 1.27.0

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_1.27.0.tar.gz

StartedAt: 2025-11-20 21:34:21 -0500 (Thu, 20 Nov 2025)

EndedAt: 2025-11-20 21:35:43 -0500 (Thu, 20 Nov 2025)

EllapsedTime: 81.7 seconds

RetCode: 0

Status: OK

CheckDir: graper.Rcheck

Warnings: 0

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_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.27.0’
* 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: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 ... 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-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/4.6-x86_64/Resources/library’
* installing *source* package ‘graper’ ...
** this is package ‘graper’ version ‘1.27.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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
clang++ -arch x86_64 -std=gnu++17 -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-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6-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 Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 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=-898.351
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-563.868
ELB improved by 334.483

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-505.63
ELB improved by 58.2385

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.33
ELB improved by 36.3

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.665
ELB improved by 17.6641

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.516
ELB improved by 8.14913

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.611
ELB improved by 4.90553

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.731
ELB improved by 3.88

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.074
ELB improved by 3.65665

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.264
ELB improved by 3.81043

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.025
ELB improved by 4.23906

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.198
ELB improved by 4.82694

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.982
ELB improved by 5.21529

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.069
ELB improved by 4.91331

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.13
ELB improved by 3.93875

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.233
ELB improved by 2.89743

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.045
ELB improved by 2.18816

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.269
ELB improved by 1.77595

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.749
ELB improved by 1.51938

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.419
ELB improved by 1.33058

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.245
ELB improved by 1.17344

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.209
ELB improved by 1.03642

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.292
ELB improved by 0.916473

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.48
ELB improved by 0.812612

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.756
ELB improved by 0.723808

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.107
ELB improved by 0.648627

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.522
ELB improved by 0.585286

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.99
ELB improved by 0.531715

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.505
ELB improved by 0.485606

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.06
ELB improved by 0.444558

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.654
ELB improved by 0.406408

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.284
ELB improved by 0.369676

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.95
ELB improved by 0.33383

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.651
ELB improved by 0.299193

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.385
ELB improved by 0.266553

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.148
ELB improved by 0.23677

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.937
ELB improved by 0.210558

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.749
ELB improved by 0.188505

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.577
ELB improved by 0.171289

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.417
ELB improved by 0.16016

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.259
ELB improved by 0.157929

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.089
ELB improved by 0.170761

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.88
ELB improved by 0.208969

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.607
ELB improved by 0.273151

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.29
ELB improved by 0.316256

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.993
ELB improved by 0.297194

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.707
ELB improved by 0.286276

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.345
ELB improved by 0.361989

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.829
ELB improved by 0.515461

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.309
ELB improved by 0.520078

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.974
ELB improved by 0.335034

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.786
ELB improved by 0.188642

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.675
ELB improved by 0.11038

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.606
ELB improved by 0.0687729

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.561
ELB improved by 0.0456828

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.528
ELB improved by 0.0322906

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.504
ELB improved by 0.0241694

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.485
ELB improved by 0.0190171

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.47
ELB improved by 0.0155966

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.456
ELB improved by 0.0132212

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.445
ELB improved by 0.0114981

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.435
ELB improved by 0.0101963

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.426
ELB improved by 0.00917609

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-900.311
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-614.728
ELB improved by 285.583

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-556.265
ELB improved by 58.4631

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-508.37
ELB improved by 47.8957

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-482.683
ELB improved by 25.6865

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.564
ELB improved by 10.119

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.816
ELB improved by 4.74774

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.395
ELB improved by 3.42142

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.18
ELB improved by 3.21546

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.799
ELB improved by 3.38031

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.072
ELB improved by 3.72773

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.972
ELB improved by 4.09927

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.729
ELB improved by 4.24339

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.828
ELB improved by 3.90051

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.734
ELB improved by 3.09401

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.592
ELB improved by 2.14194

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.219
ELB improved by 1.37312

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.334
ELB improved by 0.884841

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.718
ELB improved by 0.61663

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.23
ELB improved by 0.487887

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.784
ELB improved by 0.445551

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.333
ELB improved by 0.451196

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.887
ELB improved by 0.445834

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.502
ELB improved by 0.38547

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.193
ELB improved by 0.308483

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.935
ELB improved by 0.258203

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.7
ELB improved by 0.235459

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.471
ELB improved by 0.228775

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.241
ELB improved by 0.230374

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.004
ELB improved by 0.236501

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.759
ELB improved by 0.245414

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.503
ELB improved by 0.256208

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.234
ELB improved by 0.268322

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.953
ELB improved by 0.281364

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.658
ELB improved by 0.295067

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.348
ELB improved by 0.309287

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.024
ELB improved by 0.324014

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.685
ELB improved by 0.339373

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.329
ELB improved by 0.355614

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.956
ELB improved by 0.373078

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.564
ELB improved by 0.392154

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.151
ELB improved by 0.41322

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.714
ELB improved by 0.43659

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.252
ELB improved by 0.462488

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.761
ELB improved by 0.491192

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.237
ELB improved by 0.523769

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.672
ELB improved by 0.564781

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.041
ELB improved by 0.631107

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.268
ELB improved by 0.772803

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.224
ELB improved by 1.04447

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.98
ELB improved by 1.24428

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.929
ELB improved by 1.05086

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.248
ELB improved by 0.680621

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.818
ELB improved by 0.429739

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.531
ELB improved by 0.287573

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.328
ELB improved by 0.202279

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.181
ELB improved by 0.147806

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.069
ELB improved by 0.111571

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.982
ELB improved by 0.0867393

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.913
ELB improved by 0.069265

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.856
ELB improved by 0.0566502

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.809
ELB improved by 0.0473152

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.769
ELB improved by 0.0402425

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.734
ELB improved by 0.0347648

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.704
ELB improved by 0.0304356

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.677
ELB improved by 0.0269505

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.653
ELB improved by 0.024098

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.631
ELB improved by 0.0217287

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.611
ELB improved by 0.0197352

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.593
ELB improved by 0.018039

iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.577
ELB improved by 0.016582

iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.561
ELB improved by 0.0153206

iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.547
ELB improved by 0.0142215

iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.534
ELB improved by 0.0132593

iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.521
ELB improved by 0.0124142

iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.51
ELB improved by 0.0116711

iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.499
ELB improved by 0.0110183

iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.488
ELB improved by 0.0104475

iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.478
ELB improved by 0.0099532

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-909.657
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-575.532
ELB improved by 334.125

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-515.452
ELB improved by 60.0801

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-479.309
ELB improved by 36.1423

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.54
ELB improved by 14.7693

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.855
ELB improved by 7.68487

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.867
ELB improved by 5.98795

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.882
ELB improved by 5.98511

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.272
ELB improved by 6.61048

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.112
ELB improved by 7.15961

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.307
ELB improved by 6.80492

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.031
ELB improved by 5.27656

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.591
ELB improved by 3.43978

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.462
ELB improved by 2.12915

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.112
ELB improved by 1.34963

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.227
ELB improved by 0.884999

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.611
ELB improved by 0.616218

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.146
ELB improved by 0.464742

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.766
ELB improved by 0.380404

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.431
ELB improved by 0.334456

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.123
ELB improved by 0.308667

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.834
ELB improved by 0.288424

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.571
ELB improved by 0.263013

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.34
ELB improved by 0.230726

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.143
ELB improved by 0.196926

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.977
ELB improved by 0.166079

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.838
ELB improved by 0.13947

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.721
ELB improved by 0.117176

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.622
ELB improved by 0.0990188

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.537
ELB improved by 0.0845385

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.464
ELB improved by 0.0730559

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.4
ELB improved by 0.0638718

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.344
ELB improved by 0.0564047

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.294
ELB improved by 0.050223

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.249
ELB improved by 0.0450223

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.208
ELB improved by 0.0405886

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.171
ELB improved by 0.0367694

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.138
ELB improved by 0.0334525

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.107
ELB improved by 0.0305527

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.079
ELB improved by 0.0280036

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.053
ELB improved by 0.0257523

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.03
ELB improved by 0.0237558

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.008
ELB improved by 0.0219788

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.987
ELB improved by 0.0203918

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.968
ELB improved by 0.0189702

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.951
ELB improved by 0.0176931

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.934
ELB improved by 0.0165427

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.919
ELB improved by 0.0155039

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.904
ELB improved by 0.0145636

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.89
ELB improved by 0.0137105

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.877
ELB improved by 0.0129349

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.865
ELB improved by 0.0122282

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.854
ELB improved by 0.0115831

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.843
ELB improved by 0.010993

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.832
ELB improved by 0.0104522

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.822
ELB improved by 0.00995562

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-816.884
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-586.361
ELB improved by 230.522

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-528.344
ELB improved by 58.0178

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-481.267
ELB improved by 47.0766

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453
ELB improved by 28.2668

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.357
ELB improved by 11.6429

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.62
ELB improved by 4.73741

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.798
ELB improved by 2.82157

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.618
ELB improved by 2.1803

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.677
ELB improved by 1.94141

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.805
ELB improved by 1.87142

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.927
ELB improved by 1.87795

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.013
ELB improved by 1.9143

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.067
ELB improved by 1.94555

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.126
ELB improved by 1.94129

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.243
ELB improved by 1.88282

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.473
ELB improved by 1.76991

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.862
ELB improved by 1.61187

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.451
ELB improved by 1.4108

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.283
ELB improved by 1.16778

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.374
ELB improved by 0.909054

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.695
ELB improved by 0.678835

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.188
ELB improved by 0.507534

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.791
ELB improved by 0.396734

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.46
ELB improved by 0.330749

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.167
ELB improved by 0.292669

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.897
ELB improved by 0.270356

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.641
ELB improved by 0.256306

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.395
ELB improved by 0.246166

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.157
ELB improved by 0.237492

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.928
ELB improved by 0.228973

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.708
ELB improved by 0.219979

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.498
ELB improved by 0.210293

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.298
ELB improved by 0.199946

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.109
ELB improved by 0.189104

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.931
ELB improved by 0.177991

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.764
ELB improved by 0.166837

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.608
ELB improved by 0.155851

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.463
ELB improved by 0.145207

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.328
ELB improved by 0.135035

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.202
ELB improved by 0.125426

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.086
ELB improved by 0.116436

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.978
ELB improved by 0.108092

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.878
ELB improved by 0.100398

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.784
ELB improved by 0.0933432

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.697
ELB improved by 0.0869033

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.616
ELB improved by 0.0810478

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.54
ELB improved by 0.0757418

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.47
ELB improved by 0.070949

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.403
ELB improved by 0.0666332

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.34
ELB improved by 0.0627598

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.281
ELB improved by 0.0592965

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.225
ELB improved by 0.0562138

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.171
ELB improved by 0.0534856

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.12
ELB improved by 0.0510891

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.071
ELB improved by 0.0490047

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.024
ELB improved by 0.0472166

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.978
ELB improved by 0.0457126

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.934
ELB improved by 0.044484

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.89
ELB improved by 0.0435259

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.847
ELB improved by 0.0428373

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.805
ELB improved by 0.0424214

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.763
ELB improved by 0.0422861

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.72
ELB improved by 0.0424442

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.677
ELB improved by 0.0429143

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.633
ELB improved by 0.0437215

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.589
ELB improved by 0.0448981

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.542
ELB improved by 0.0464854

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.494
ELB improved by 0.048534

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.442
ELB improved by 0.0511059

iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.388
ELB improved by 0.0542757

iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.33
ELB improved by 0.0581309

iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.267
ELB improved by 0.0627723

iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.199
ELB improved by 0.0683126

iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.124
ELB improved by 0.074871

iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.042
ELB improved by 0.0825655

iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.95
ELB improved by 0.0914979

iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.848
ELB improved by 0.101734

iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.735
ELB improved by 0.113282

iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.609
ELB improved by 0.12608

iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.469
ELB improved by 0.140015

iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.314
ELB improved by 0.15502

iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.143
ELB improved by 0.171298

iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.953
ELB improved by 0.189739

iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.74
ELB improved by 0.212557

iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.496
ELB improved by 0.243954

iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.206
ELB improved by 0.289954

iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.852
ELB improved by 0.354534

iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.428
ELB improved by 0.424033

iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.983
ELB improved by 0.444708

iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.603
ELB improved by 0.380556

iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.313
ELB improved by 0.28949

iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.09
ELB improved by 0.222651

iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.91
ELB improved by 0.180704

iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.758
ELB improved by 0.151934

iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.63
ELB improved by 0.127647

iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.526
ELB improved by 0.104187

iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.444
ELB improved by 0.0823038

iteration 99
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.38
ELB improved by 0.0641167

iteration 100
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.329
ELB improved by 0.0504668

iteration 101
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.288
ELB improved by 0.0407489

iteration 102
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.254
ELB improved by 0.0338836

iteration 103
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.225
ELB improved by 0.02896

iteration 104
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.2
ELB improved by 0.0253896

iteration 105
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.177
ELB improved by 0.022849

iteration 106
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.156
ELB improved by 0.0211967

iteration 107
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.136
ELB improved by 0.0204254

iteration 108
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.115
ELB improved by 0.0206678

iteration 109
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.093
ELB improved by 0.0222692

iteration 110
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.067
ELB improved by 0.0259618

iteration 111
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.034
ELB improved by 0.033204

iteration 112
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.987
ELB improved by 0.0466542

iteration 113
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.917
ELB improved by 0.0699529

iteration 114
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.814
ELB improved by 0.103323

iteration 115
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.681
ELB improved by 0.132593

iteration 116
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.547
ELB improved by 0.134332

iteration 117
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.436
ELB improved by 0.110462

iteration 118
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.355
ELB improved by 0.0816048

iteration 119
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.298
ELB improved by 0.0567955

iteration 120
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.261
ELB improved by 0.0371397

iteration 121
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.238
ELB improved by 0.0230635

iteration 122
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.223
ELB improved by 0.0141226

iteration 123
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.215
ELB improved by 0.00894584

ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
> 
> proc.time()
   user  system elapsed 
  2.854   0.307   3.193

Example timings

graper.Rcheck/graper-Ex.timings

name	user	system	elapsed
coef.graper	0.051	0.016	0.068
getPIPs	0.044	0.013	0.057
graper	0.091	0.019	0.110
makeExampleData	0.008	0.001	0.008
makeExampleDataWithUnequalGroups	0.011	0.001	0.012
plotELBO	0.312	0.018	0.332
plotGroupPenalties	1.320	0.042	1.370
plotPosterior	0.731	0.035	0.771
predict.graper	1.867	0.083	1.960
print.graper	0.045	0.010	0.054