Multiple platform build/check report for BioC 3.20 - CHECK results for graper on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4688
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4284
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4455
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4404
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 kjohnson3

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: 1.21.0

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_1.21.0.tar.gz

StartedAt: 2024-07-23 22:13:13 -0400 (Tue, 23 Jul 2024)

EndedAt: 2024-07-23 22:13:38 -0400 (Tue, 23 Jul 2024)

EllapsedTime: 25.3 seconds

RetCode: 0

Status: WARNINGS

CheckDir: graper.Rcheck

Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/graper.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.21.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... WARNING
Found the following significant warnings:
  /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
  #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/graper.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) predict.graper.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:23-24: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/graper.Rcheck/00check.log’
for details.

Installation output

graper.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘graper’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c fit_graper.cpp -o fit_graper.o
In file included from fit_graper.cpp:4:
In file included from ./graper_linear_dense_ff.h:2:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/digamma.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/math_fwd.hpp:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
#    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
     ^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-graper/00new/graper/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (graper)

Tests output

graper.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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=-849.784
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-595.781
ELB improved by 254.003

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-535.028
ELB improved by 60.7529

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-486.796
ELB improved by 48.2329

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.812
ELB improved by 24.9838

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.39
ELB improved by 10.4221

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.333
ELB improved by 6.05675

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.139
ELB improved by 5.19405

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.927
ELB improved by 5.21142

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.632
ELB improved by 5.29572

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.665
ELB improved by 4.96629

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.557
ELB improved by 4.10869

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.463
ELB improved by 3.09351

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.211
ELB improved by 2.25177

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.596
ELB improved by 1.61532

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.427
ELB improved by 1.16959

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.562
ELB improved by 0.864061

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.919
ELB improved by 0.643428

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.421
ELB improved by 0.498277

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.009
ELB improved by 0.411299

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.652
ELB improved by 0.357721

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.33
ELB improved by 0.321369

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.036
ELB improved by 0.294103

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.764
ELB improved by 0.271934

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.512
ELB improved by 0.252781

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.276
ELB improved by 0.235479

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.057
ELB improved by 0.219362

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.853
ELB improved by 0.204067

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.663
ELB improved by 0.189426

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.488
ELB improved by 0.175396

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.326
ELB improved by 0.162004

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.177
ELB improved by 0.149313

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.039
ELB improved by 0.137389

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.913
ELB improved by 0.126286

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.797
ELB improved by 0.116034

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.69
ELB improved by 0.10664

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.592
ELB improved by 0.0980889

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.502
ELB improved by 0.0903443

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.418
ELB improved by 0.083359

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.341
ELB improved by 0.0770768

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.27
ELB improved by 0.0714381

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.203
ELB improved by 0.0663828

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.142
ELB improved by 0.061853

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.084
ELB improved by 0.0577941

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.03
ELB improved by 0.0541562

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.979
ELB improved by 0.050894

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.931
ELB improved by 0.0479668

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.885
ELB improved by 0.0453388

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.843
ELB improved by 0.042978

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.802
ELB improved by 0.0408564

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.763
ELB improved by 0.0389493

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.725
ELB improved by 0.037235

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.69
ELB improved by 0.0356943

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.655
ELB improved by 0.0343103

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.622
ELB improved by 0.033068

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.59
ELB improved by 0.0319539

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.559
ELB improved by 0.030956

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.529
ELB improved by 0.0300636

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.5
ELB improved by 0.0292668

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.472
ELB improved by 0.0285566

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.444
ELB improved by 0.0279247

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.416
ELB improved by 0.0273634

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.389
ELB improved by 0.0268652

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.363
ELB improved by 0.0264233

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.337
ELB improved by 0.0260309

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.311
ELB improved by 0.0256814

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.286
ELB improved by 0.0253684

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.261
ELB improved by 0.0250854

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.236
ELB improved by 0.0248261

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.211
ELB improved by 0.024584

iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.187
ELB improved by 0.0243526

iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.163
ELB improved by 0.0241255

iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.139
ELB improved by 0.0238962

iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.115
ELB improved by 0.0236582

iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.092
ELB improved by 0.0234053

iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.069
ELB improved by 0.0231315

iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.046
ELB improved by 0.0228309

iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.024
ELB improved by 0.0224985

iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.001
ELB improved by 0.0221295

iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.98
ELB improved by 0.0217201

iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.958
ELB improved by 0.0212673

iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.938
ELB improved by 0.0207694

iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.917
ELB improved by 0.0202255

iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.898
ELB improved by 0.019636

iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.879
ELB improved by 0.0190027

iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.86
ELB improved by 0.0183284

iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.843
ELB improved by 0.0176172

iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.826
ELB improved by 0.016874

iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.81
ELB improved by 0.0161047

iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.795
ELB improved by 0.0153157

iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.78
ELB improved by 0.014514

iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.766
ELB improved by 0.0137064

iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.753
ELB improved by 0.0129001

iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.741
ELB improved by 0.0121017

iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.73
ELB improved by 0.0113174

iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.719
ELB improved by 0.0105528

iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.71
ELB improved by 0.00981278

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-914.312
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-567.867
ELB improved by 346.445

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-510.229
ELB improved by 57.6377

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-478.93
ELB improved by 31.2997

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.626
ELB improved by 12.304

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.946
ELB improved by 5.6802

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.441
ELB improved by 3.50436

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.763
ELB improved by 2.67831

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.391
ELB improved by 2.37233

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.111
ELB improved by 2.27917

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.843
ELB improved by 2.26848

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.567
ELB improved by 2.27618

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.31
ELB improved by 2.25716

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.149
ELB improved by 2.16065

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.203
ELB improved by 1.94555

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.569
ELB improved by 1.63452

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.254
ELB improved by 1.31512

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.202
ELB improved by 1.05169

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.358
ELB improved by 0.843971

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.675
ELB improved by 0.682592

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.109
ELB improved by 0.566949

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.623
ELB improved by 0.485657

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.199
ELB improved by 0.423611

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.826
ELB improved by 0.372877

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.495
ELB improved by 0.331687

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.196
ELB improved by 0.29902

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.923
ELB improved by 0.272877

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.672
ELB improved by 0.251245

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.439
ELB improved by 0.232747

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.222
ELB improved by 0.216609

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.02
ELB improved by 0.202414

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.83
ELB improved by 0.189934

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.651
ELB improved by 0.179025

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.481
ELB improved by 0.169597

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.32
ELB improved by 0.161589

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.165
ELB improved by 0.154983

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.015
ELB improved by 0.14981

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.869
ELB improved by 0.146172

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.724
ELB improved by 0.144272

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.58
ELB improved by 0.144442

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.433
ELB improved by 0.147148

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.28
ELB improved by 0.152886

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.118
ELB improved by 0.161818

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.945
ELB improved by 0.173015

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.761
ELB improved by 0.183813

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.571
ELB improved by 0.19075

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.378
ELB improved by 0.192416

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.187
ELB improved by 0.191041

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.996
ELB improved by 0.190913

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.799
ELB improved by 0.196763

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.585
ELB improved by 0.214435

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.332
ELB improved by 0.252698

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.01
ELB improved by 0.322074

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.591
ELB improved by 0.418711

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.094
ELB improved by 0.49698

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.583
ELB improved by 0.511952

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.101
ELB improved by 0.481134

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.671
ELB improved by 0.430239

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.301
ELB improved by 0.369747

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.994
ELB improved by 0.307695

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.743
ELB improved by 0.25038

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.542
ELB improved by 0.201033

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.382
ELB improved by 0.160333

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.254
ELB improved by 0.127503

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.153
ELB improved by 0.101262

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.073
ELB improved by 0.0803768

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.009
ELB improved by 0.0638348

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.958
ELB improved by 0.0508194

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.918
ELB improved by 0.0406491

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.885
ELB improved by 0.0327439

iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.858
ELB improved by 0.026616

iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.836
ELB improved by 0.0218665

iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.818
ELB improved by 0.0181777

iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.803
ELB improved by 0.0153018

iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.79
ELB improved by 0.0130483

iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.779
ELB improved by 0.0112716

iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.769
ELB improved by 0.00986085

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-862.251
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-601.009
ELB improved by 261.242

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-539.205
ELB improved by 61.8049

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-489.787
ELB improved by 49.4177

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.707
ELB improved by 26.0798

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.272
ELB improved by 10.4354

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.036
ELB improved by 5.2359

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.222
ELB improved by 3.81425

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.855
ELB improved by 3.36609

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.61
ELB improved by 3.245

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.344
ELB improved by 3.26628

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.976
ELB improved by 3.36808

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.471
ELB improved by 3.50553

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.89
ELB improved by 3.58102

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.457
ELB improved by 3.43213

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.499
ELB improved by 2.95884

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.23
ELB improved by 2.26888

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.634
ELB improved by 1.59545

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.546
ELB improved by 1.08776

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.789
ELB improved by 0.757627

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.233
ELB improved by 0.556131

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.798
ELB improved by 0.434488

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.438
ELB improved by 0.359901

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.125
ELB improved by 0.31289

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.843
ELB improved by 0.282347

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.581
ELB improved by 0.262025

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.333
ELB improved by 0.248423

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.093
ELB improved by 0.239579

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.859
ELB improved by 0.23437

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.627
ELB improved by 0.232068

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.395
ELB improved by 0.231991

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.161
ELB improved by 0.233213

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.927
ELB improved by 0.234481

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.692
ELB improved by 0.234559

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.459
ELB improved by 0.232896

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.229
ELB improved by 0.23001

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.002
ELB improved by 0.227153

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.777
ELB improved by 0.225733

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.55
ELB improved by 0.227068

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.317
ELB improved by 0.232542

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.073
ELB improved by 0.243912

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.81
ELB improved by 0.263565

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.515
ELB improved by 0.294396

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.177
ELB improved by 0.338503

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.782
ELB improved by 0.394295

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.327
ELB improved by 0.45549

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.809
ELB improved by 0.517718

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.224
ELB improved by 0.584915

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.564
ELB improved by 0.660388

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.838
ELB improved by 0.725933

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.095
ELB improved by 0.742997

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.391
ELB improved by 0.704342

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.747
ELB improved by 0.643799

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.156
ELB improved by 0.590347

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.609
ELB improved by 0.54733

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.12
ELB improved by 0.489474

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.723
ELB improved by 0.396584

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.43
ELB improved by 0.29272

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.221
ELB improved by 0.209302

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.068
ELB improved by 0.152688

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.953
ELB improved by 0.115201

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.865
ELB improved by 0.0885232

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.797
ELB improved by 0.0680527

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.744
ELB improved by 0.0522063

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.704
ELB improved by 0.0404203

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.672
ELB improved by 0.0320193

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.646
ELB improved by 0.0261406

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.624
ELB improved by 0.0219831

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.605
ELB improved by 0.0189463

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.588
ELB improved by 0.0166339

iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.573
ELB improved by 0.0148011

iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.56
ELB improved by 0.0133005

iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.548
ELB improved by 0.0120421

iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.537
ELB improved by 0.0109688

iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.527
ELB improved by 0.0100424

iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.518
ELB improved by 0.00923578

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-841.35
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-563.191
ELB improved by 278.159

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-503.973
ELB improved by 59.218

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.1
ELB improved by 36.8727

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.792
ELB improved by 16.308

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.275
ELB improved by 6.51705

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.314
ELB improved by 2.96103

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.455
ELB improved by 1.85966

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.967
ELB improved by 1.48793

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.613
ELB improved by 1.3532

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.304
ELB improved by 1.30944

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.006
ELB improved by 1.2976

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.718
ELB improved by 1.28826

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.454
ELB improved by 1.26463

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.233
ELB improved by 1.2201

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.073
ELB improved by 1.16088

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.965
ELB improved by 1.10717

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.877
ELB improved by 1.08864

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.745
ELB improved by 1.13187

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.506
ELB improved by 1.23931

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.131
ELB improved by 1.37453

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.645
ELB improved by 1.48647

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.093
ELB improved by 1.55208

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.51
ELB improved by 1.58261

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.904
ELB improved by 1.60556

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.26
ELB improved by 1.64427

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.54
ELB improved by 1.72017

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.679
ELB improved by 1.86103

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.632
ELB improved by 2.04656

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.49
ELB improved by 2.1419

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.34
ELB improved by 2.15032

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.207
ELB improved by 2.13313

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.025
ELB improved by 2.18243

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.884
ELB improved by 2.14098

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.095
ELB improved by 1.78876

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.809
ELB improved by 1.28617

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.905
ELB improved by 0.904091

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.226
ELB improved by 0.678869

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.69
ELB improved by 0.535926

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.244
ELB improved by 0.445623

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.816
ELB improved by 0.427894

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.323
ELB improved by 0.493642

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.718
ELB improved by 0.604782

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.056
ELB improved by 0.662273

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.449
ELB improved by 0.606908

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.981
ELB improved by 0.467581

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.684
ELB improved by 0.297482

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.516
ELB improved by 0.167205

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.42
ELB improved by 0.0960975

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.358
ELB improved by 0.0617477

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.314
ELB improved by 0.0445616

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.279
ELB improved by 0.034866

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.25
ELB improved by 0.0285791

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.226
ELB improved by 0.0240284

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.206
ELB improved by 0.0205007

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.188
ELB improved by 0.0176605

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.173
ELB improved by 0.0153272

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.16
ELB improved by 0.0133882

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.148
ELB improved by 0.0117655

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.137
ELB improved by 0.0104007

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.128
ELB improved by 0.00924827

ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
> 
> proc.time()
   user  system elapsed 
  0.900   0.066   0.963

Example timings

graper.Rcheck/graper-Ex.timings

name	user	system	elapsed
coef.graper	0.030	0.005	0.034
getPIPs	0.028	0.004	0.032
graper	0.046	0.006	0.051
makeExampleData	0.004	0.000	0.004
makeExampleDataWithUnequalGroups	0.013	0.001	0.013
plotELBO	0.084	0.005	0.089
plotGroupPenalties	0.232	0.006	0.239
plotPosterior	0.187	0.006	0.193
predict.graper	1.024	0.021	1.044
print.graper	0.025	0.003	0.028