Multiple platform build/check report for BioC 3.21 - CHECK results for graper on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4752
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4466
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4420
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4375
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: 1.23.0

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_1.23.0.tar.gz

StartedAt: 2024-12-16 19:35:16 -0500 (Mon, 16 Dec 2024)

EndedAt: 2024-12-16 19:35:40 -0500 (Mon, 16 Dec 2024)

EllapsedTime: 24.3 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_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/graper.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.23.0’
* 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/4.5-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-3.21-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-3.21-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/4.5-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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -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/4.5-arm64/Resources/library/BH/include/boost/math/special_functions/digamma.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include/boost/math/special_functions/math_fwd.hpp:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11:
/Library/Frameworks/R.framework/Versions/4.5-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/4.5-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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
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=-854.28
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-572.635
ELB improved by 281.645

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-509.502
ELB improved by 63.1332

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.603
ELB improved by 40.8989

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.898
ELB improved by 16.7048

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.556
ELB improved by 7.34226

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.045
ELB improved by 4.51064

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.208
ELB improved by 3.83725

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.441
ELB improved by 3.76733

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.484
ELB improved by 3.95693

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.185
ELB improved by 4.29916

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.526
ELB improved by 4.659

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.776
ELB improved by 4.74987

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.535
ELB improved by 4.24126

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.315
ELB improved by 3.21983

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.117
ELB improved by 2.19834

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.617
ELB improved by 1.49905

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.524
ELB improved by 1.09343

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.688
ELB improved by 0.836343

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.048
ELB improved by 0.639853

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.556
ELB improved by 0.491631

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.167
ELB improved by 0.389375

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.844
ELB improved by 0.322607

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.564
ELB improved by 0.279906

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.312
ELB improved by 0.252557

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.077
ELB improved by 0.235013

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.853
ELB improved by 0.224127

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.634
ELB improved by 0.218251

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.418
ELB improved by 0.216632

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.199
ELB improved by 0.219031

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.973
ELB improved by 0.225356

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.738
ELB improved by 0.235018

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.492
ELB improved by 0.246043

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.237
ELB improved by 0.254945

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.978
ELB improved by 0.258892

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.72
ELB improved by 0.258482

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.463
ELB improved by 0.256822

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.207
ELB improved by 0.256402

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.949
ELB improved by 0.258188

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.686
ELB improved by 0.262489

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.416
ELB improved by 0.26958

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.137
ELB improved by 0.279805

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.843
ELB improved by 0.293501

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.532
ELB improved by 0.310904

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.2
ELB improved by 0.332025

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.844
ELB improved by 0.356444

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.461
ELB improved by 0.383001

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.051
ELB improved by 0.409388

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.62
ELB improved by 0.431845

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.174
ELB improved by 0.445315

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.73
ELB improved by 0.444441

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.304
ELB improved by 0.42542

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.916
ELB improved by 0.388005

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.58
ELB improved by 0.336358

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.302
ELB improved by 0.277807

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.082
ELB improved by 0.220091

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.913
ELB improved by 0.168886

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.786
ELB improved by 0.126881

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.692
ELB improved by 0.094301

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.622
ELB improved by 0.0699691

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.57
ELB improved by 0.0522227

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.53
ELB improved by 0.0394469

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.5
ELB improved by 0.0302965

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.476
ELB improved by 0.0237374

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.457
ELB improved by 0.0190101

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.442
ELB improved by 0.0155717

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.429
ELB improved by 0.0130396

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.418
ELB improved by 0.011147

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.408
ELB improved by 0.00970791

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-860.162
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-581.539
ELB improved by 278.622

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-518.289
ELB improved by 63.2502

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.666
ELB improved by 45.6233

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.128
ELB improved by 20.538

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.497
ELB improved by 7.63042

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.483
ELB improved by 4.01445

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.889
ELB improved by 2.59361

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.897
ELB improved by 1.99181

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.193
ELB improved by 1.70405

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.637
ELB improved by 1.5562

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.158
ELB improved by 1.47889

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.713
ELB improved by 1.44485

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.268
ELB improved by 1.44578

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.788
ELB improved by 1.47917

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.248
ELB improved by 1.54009

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.633
ELB improved by 1.61476

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.957
ELB improved by 1.67644

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.269
ELB improved by 1.68805

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.649
ELB improved by 1.61955

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.174
ELB improved by 1.47566

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.874
ELB improved by 1.29999

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.732
ELB improved by 1.14167

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.708
ELB improved by 1.02457

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.761
ELB improved by 0.946993

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.863
ELB improved by 0.897228

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411
ELB improved by 0.863138

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.165
ELB improved by 0.835168

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.357
ELB improved by 0.808187

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.575
ELB improved by 0.781516

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.818
ELB improved by 0.757017

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.081
ELB improved by 0.736951

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.358
ELB improved by 0.722915

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.642
ELB improved by 0.716043

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.925
ELB improved by 0.717715

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.196
ELB improved by 0.728969

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.45
ELB improved by 0.745239

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.702
ELB improved by 0.748228

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.985
ELB improved by 0.716966

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.327
ELB improved by 0.658261

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.724
ELB improved by 0.602968

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.136
ELB improved by 0.588415

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.477
ELB improved by 0.658907

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.697
ELB improved by 0.779495

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.974
ELB improved by 0.72283

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.454
ELB improved by 0.51998

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.091
ELB improved by 0.363371

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.817
ELB improved by 0.274277

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.584
ELB improved by 0.232392

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.358
ELB improved by 0.22601

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.116
ELB improved by 0.242457

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.869
ELB improved by 0.246641

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.665
ELB improved by 0.204223

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.523
ELB improved by 0.142152

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.424
ELB improved by 0.0988505

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.346
ELB improved by 0.0777982

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.274
ELB improved by 0.0720877

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.194
ELB improved by 0.0797973

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.089
ELB improved by 0.10574

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.933
ELB improved by 0.15572

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.725
ELB improved by 0.207511

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.523
ELB improved by 0.202511

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.377
ELB improved by 0.146108

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.283
ELB improved by 0.0936672

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.222
ELB improved by 0.0611296

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.18
ELB improved by 0.0423259

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.149
ELB improved by 0.0311273

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.124
ELB improved by 0.0241115

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.105
ELB improved by 0.0194901

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.089
ELB improved by 0.0162996

iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.075
ELB improved by 0.0139982

iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.062
ELB improved by 0.0122705

iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.051
ELB improved by 0.0109277

iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.042
ELB improved by 0.00985341

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-875.372
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-560.746
ELB improved by 314.626

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-497.684
ELB improved by 63.0621

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.368
ELB improved by 33.3153

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.42
ELB improved by 11.9483

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.744
ELB improved by 4.67639

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.033
ELB improved by 2.71098

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.834
ELB improved by 2.19883

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.685
ELB improved by 2.14894

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.342
ELB improved by 2.34327

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.611
ELB improved by 2.73042

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.314
ELB improved by 3.29705

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.333
ELB improved by 3.98107

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.749
ELB improved by 4.58439

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.989
ELB improved by 4.75986

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.744
ELB improved by 4.24474

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.428
ELB improved by 3.31587

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.903
ELB improved by 2.5256

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.873
ELB improved by 2.02979

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.174
ELB improved by 1.69876

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.72
ELB improved by 1.4546

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.443
ELB improved by 1.27655

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.303
ELB improved by 1.14007

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.277
ELB improved by 1.0261

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.351
ELB improved by 0.92558

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.517
ELB improved by 0.834516

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.766
ELB improved by 0.750778

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.093
ELB improved by 0.673023

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.493
ELB improved by 0.600461

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.96
ELB improved by 0.53276

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.49
ELB improved by 0.469919

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.078
ELB improved by 0.412109

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.718
ELB improved by 0.359497

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.406
ELB improved by 0.3121

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.136
ELB improved by 0.26973

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.904
ELB improved by 0.232045

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.706
ELB improved by 0.19866

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.536
ELB improved by 0.169241

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.393
ELB improved by 0.143536

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.272
ELB improved by 0.121328

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.169
ELB improved by 0.102388

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.083
ELB improved by 0.0864306

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.01
ELB improved by 0.0731271

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.948
ELB improved by 0.0621235

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.894
ELB improved by 0.0530711

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.849
ELB improved by 0.045648

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.809
ELB improved by 0.0395734

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.775
ELB improved by 0.0346122

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.744
ELB improved by 0.0305763

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.717
ELB improved by 0.0273233

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.692
ELB improved by 0.0247557

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.669
ELB improved by 0.0228246

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.648
ELB improved by 0.0215402

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.627
ELB improved by 0.0209977

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.605
ELB improved by 0.0214331

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.582
ELB improved by 0.0233413

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.554
ELB improved by 0.0277285

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.517
ELB improved by 0.0366578

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.463
ELB improved by 0.0543896

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.374
ELB improved by 0.0893883

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.218
ELB improved by 0.155293

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.96
ELB improved by 0.258179

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.598
ELB improved by 0.362161

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.149
ELB improved by 0.449445

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.503
ELB improved by 0.64519

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.485
ELB improved by 1.01843

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.252
ELB improved by 1.23272

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.173
ELB improved by 1.07903

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.391
ELB improved by 0.782588

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.874
ELB improved by 0.516484

iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.547
ELB improved by 0.327675

iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.342
ELB improved by 0.20465

iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.215
ELB improved by 0.127347

iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.135
ELB improved by 0.0798067

iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.084
ELB improved by 0.0509527

iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.05
ELB improved by 0.0335355

iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.027
ELB improved by 0.0229989

iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.011
ELB improved by 0.0165636

iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.998
ELB improved by 0.0125661

iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.988
ELB improved by 0.0100215

iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.98
ELB improved by 0.00834927

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-808.544
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-565.513
ELB improved by 243.03

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-502.133
ELB improved by 63.3798

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.016
ELB improved by 44.1175

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.373
ELB improved by 21.643

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.561
ELB improved by 8.81203

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.5
ELB improved by 4.0612

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.974
ELB improved by 2.52581

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.047
ELB improved by 1.92655

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.35
ELB improved by 1.69684

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.72
ELB improved by 1.63034

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.073
ELB improved by 1.64731

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.356
ELB improved by 1.71706

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.535
ELB improved by 1.82105

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.601
ELB improved by 1.93378

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.587
ELB improved by 2.01408

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.572
ELB improved by 2.01449

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.661
ELB improved by 1.9116

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.934
ELB improved by 1.72643

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.424
ELB improved by 1.51027

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.112
ELB improved by 1.3125

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.947
ELB improved by 1.16466

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.854
ELB improved by 1.0926

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.745
ELB improved by 1.10893

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.572
ELB improved by 1.17298

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.343
ELB improved by 1.22902

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.037
ELB improved by 1.30601

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.582
ELB improved by 1.45531

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.912
ELB improved by 1.67036

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.03
ELB improved by 1.88131

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.981
ELB improved by 2.04944

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.834
ELB improved by 2.14682

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.717
ELB improved by 2.11759

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.774
ELB improved by 1.94305

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.122
ELB improved by 1.65109

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.82
ELB improved by 1.30252

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.822
ELB improved by 0.99745

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.004
ELB improved by 0.818941

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.204
ELB improved by 0.799869

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.348
ELB improved by 0.855382

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.629
ELB improved by 0.718849

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.182
ELB improved by 0.447577

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.922
ELB improved by 0.259874

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.761
ELB improved by 0.160515

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.654
ELB improved by 0.107706

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.576
ELB improved by 0.0775257

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.517
ELB improved by 0.0588636

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.471
ELB improved by 0.046512

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.433
ELB improved by 0.037864

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.401
ELB improved by 0.0315217

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.375
ELB improved by 0.0266925

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.352
ELB improved by 0.0229061

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.332
ELB improved by 0.0198708

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.315
ELB improved by 0.0173986

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.299
ELB improved by 0.0153627

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.286
ELB improved by 0.0136749

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.273
ELB improved by 0.0122716

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.262
ELB improved by 0.0111062

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.252
ELB improved by 0.0101445

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.243
ELB improved by 0.00936167

ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
> 
> proc.time()
   user  system elapsed 
  0.820   0.075   0.895

Example timings

graper.Rcheck/graper-Ex.timings

name	user	system	elapsed
coef.graper	0.029	0.006	0.036
getPIPs	0.027	0.004	0.031
graper	0.044	0.007	0.051
makeExampleData	0.004	0.001	0.005
makeExampleDataWithUnequalGroups	0.012	0.001	0.013
plotELBO	0.081	0.007	0.088
plotGroupPenalties	0.226	0.006	0.236
plotPosterior	0.182	0.007	0.192
predict.graper	1.031	0.047	1.100
print.graper	0.028	0.005	0.033