Multiple platform build/check report for BioC 3.22 - CHECK results for graper on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4901
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4691
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4637
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 nebbiolo2

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: 1.26.0

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings graper_1.26.0.tar.gz

StartedAt: 2025-10-30 06:35:00 -0400 (Thu, 30 Oct 2025)

EndedAt: 2025-10-30 06:36:31 -0400 (Thu, 30 Oct 2025)

EllapsedTime: 91.1 seconds

RetCode: 0

Status: OK

CheckDir: graper.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings graper_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.26.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) predict.graper.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:23-24: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck/00check.log’
for details.

Installation output

graper.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL graper
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘graper’ ...
** this is package ‘graper’ version ‘1.26.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c fit_graper.cpp -o fit_graper.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -llapack -L/home/biocbuild/bbs-3.22-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-graper/00new/graper/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (graper)

Tests output

graper.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(graper)
> 
> test_check("graper")
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-886.583
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-580.788
ELB improved by 305.794

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-522.506
ELB improved by 58.2826

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-483.843
ELB improved by 38.6624

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.347
ELB improved by 18.4969

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.775
ELB improved by 8.57194

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.638
ELB improved by 5.13664

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.161
ELB improved by 4.47742

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.421
ELB improved by 4.73904

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.107
ELB improved by 5.31423

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.412
ELB improved by 5.69494

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.134
ELB improved by 5.27856

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.133
ELB improved by 4.0011

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.538
ELB improved by 2.59435

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.842
ELB improved by 1.69622

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.542
ELB improved by 1.29965

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.496
ELB improved by 1.04643

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.738
ELB improved by 0.7584

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.199
ELB improved by 0.538243

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.786
ELB improved by 0.413577

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.442
ELB improved by 0.343862

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.142
ELB improved by 0.299761

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.874
ELB improved by 0.268343

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.629
ELB improved by 0.24433

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.404
ELB improved by 0.225559

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.193
ELB improved by 0.211327

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.991
ELB improved by 0.201873

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.792
ELB improved by 0.19837

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.589
ELB improved by 0.203151

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.37
ELB improved by 0.21934

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.123
ELB improved by 0.247083

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.848
ELB improved by 0.27441

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.568
ELB improved by 0.280178

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.304
ELB improved by 0.263789

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.059
ELB improved by 0.244951

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.824
ELB improved by 0.23535

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.588
ELB improved by 0.235687

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.351
ELB improved by 0.237749

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.123
ELB improved by 0.227806

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.918
ELB improved by 0.204655

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.736
ELB improved by 0.182195

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.565
ELB improved by 0.171417

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.386
ELB improved by 0.178514

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.172
ELB improved by 0.213972

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.881
ELB improved by 0.291088

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.498
ELB improved by 0.382727

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.081
ELB improved by 0.416999

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.654
ELB improved by 0.427626

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.234
ELB improved by 0.420089

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.884
ELB improved by 0.349489

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.602
ELB improved by 0.282219

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.349
ELB improved by 0.25287

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.098
ELB improved by 0.250801

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.834
ELB improved by 0.264487

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.546
ELB improved by 0.287293

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.232
ELB improved by 0.314602

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.89
ELB improved by 0.341874

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.526
ELB improved by 0.364012

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.151
ELB improved by 0.375379

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.781
ELB improved by 0.369497

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.442
ELB improved by 0.339318

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.158
ELB improved by 0.283381

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.944
ELB improved by 0.214825

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.79
ELB improved by 0.153394

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.682
ELB improved by 0.108376

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.604
ELB improved by 0.0780708

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.546
ELB improved by 0.0578445

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.502
ELB improved by 0.0440422

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.467
ELB improved by 0.0343639

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.44
ELB improved by 0.0274144

iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.418
ELB improved by 0.0223271

iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.399
ELB improved by 0.0185426

iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.383
ELB improved by 0.0156872

iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.37
ELB improved by 0.0135035

iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.358
ELB improved by 0.0118108

iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.348
ELB improved by 0.0104798

iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.338
ELB improved by 0.00941745

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-851.662
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-585.973
ELB improved by 265.689

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-524.102
ELB improved by 61.8718

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-481.85
ELB improved by 42.2515

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.522
ELB improved by 19.328

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.986
ELB improved by 8.53607

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.314
ELB improved by 5.67229

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.863
ELB improved by 5.45029

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.11
ELB improved by 5.7534

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.319
ELB improved by 5.79155

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.214
ELB improved by 5.10454

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.421
ELB improved by 3.79327

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.944
ELB improved by 2.47672

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.38
ELB improved by 1.56356

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.344
ELB improved by 1.03592

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.602
ELB improved by 0.742441

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.03
ELB improved by 0.572257

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.563
ELB improved by 0.467156

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.164
ELB improved by 0.398676

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.812
ELB improved by 0.352255

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.492
ELB improved by 0.319463

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.198
ELB improved by 0.294659

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.923
ELB improved by 0.274138

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.667
ELB improved by 0.256526

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.424
ELB improved by 0.242836

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.189
ELB improved by 0.235468

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.952
ELB improved by 0.236953

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.703
ELB improved by 0.248651

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.435
ELB improved by 0.26807

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.149
ELB improved by 0.285597

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.86
ELB improved by 0.288873

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.585
ELB improved by 0.275963

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.328
ELB improved by 0.25602

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.092
ELB improved by 0.236518

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.873
ELB improved by 0.218962

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.671
ELB improved by 0.202491

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.484
ELB improved by 0.186458

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.313
ELB improved by 0.170834

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.157
ELB improved by 0.155908

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.015
ELB improved by 0.142009

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.886
ELB improved by 0.129379

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.768
ELB improved by 0.118146

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.659
ELB improved by 0.108345

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.559
ELB improved by 0.0999623

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.467
ELB improved by 0.0929685

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.379
ELB improved by 0.0873534

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.296
ELB improved by 0.083152

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.216
ELB improved by 0.0804644

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.136
ELB improved by 0.079456

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.056
ELB improved by 0.0803072

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.973
ELB improved by 0.0830494

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.885
ELB improved by 0.0872273

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.794
ELB improved by 0.0915084

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.7
ELB improved by 0.093776

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.608
ELB improved by 0.0922429

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.521
ELB improved by 0.0868188

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.442
ELB improved by 0.0790362

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.371
ELB improved by 0.0706814

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.309
ELB improved by 0.0628394

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.253
ELB improved by 0.0558891

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.203
ELB improved by 0.0498429

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.158
ELB improved by 0.0445949

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.118
ELB improved by 0.0400263

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.082
ELB improved by 0.0360348

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.05
ELB improved by 0.0325365

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.02
ELB improved by 0.0294624

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.993
ELB improved by 0.0267548

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.969
ELB improved by 0.0243645

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.947
ELB improved by 0.0222494

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.926
ELB improved by 0.0203734

iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.908
ELB improved by 0.0187055

iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.891
ELB improved by 0.0172191

iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.875
ELB improved by 0.0158914

iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.86
ELB improved by 0.0147028

iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.846
ELB improved by 0.0136365

iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.834
ELB improved by 0.0126782

iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.822
ELB improved by 0.0118154

iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.811
ELB improved by 0.0110377

iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.8
ELB improved by 0.0103357

iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.791
ELB improved by 0.00970177

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-848.554
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-564.164
ELB improved by 284.39

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-505.517
ELB improved by 58.647

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.21
ELB improved by 33.3077

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.237
ELB improved by 13.9724

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.386
ELB improved by 6.85103

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.011
ELB improved by 5.37575

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.325
ELB improved by 5.68503

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.607
ELB improved by 6.71886

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.741
ELB improved by 7.86552

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.808
ELB improved by 7.93351

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.526
ELB improved by 6.28174

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.384
ELB improved by 4.14227

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.709
ELB improved by 2.67423

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.851
ELB improved by 1.85825

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.432
ELB improved by 1.41955

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.245
ELB improved by 1.18684

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.188
ELB improved by 1.05712

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.216
ELB improved by 0.971613

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.316
ELB improved by 0.900054

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.486
ELB improved by 0.829526

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.729
ELB improved by 0.75706

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.045
ELB improved by 0.684529

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.43
ELB improved by 0.615263

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.877
ELB improved by 0.552341

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.379
ELB improved by 0.498308

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.923
ELB improved by 0.4559

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.493
ELB improved by 0.429685

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.065
ELB improved by 0.428614

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.599
ELB improved by 0.465269

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.069
ELB improved by 0.530188

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.517
ELB improved by 0.551735

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.023
ELB improved by 0.494934

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.602
ELB improved by 0.421033

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.241
ELB improved by 0.36093

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.928
ELB improved by 0.312099

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.658
ELB improved by 0.270154

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.425
ELB improved by 0.233174

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.225
ELB improved by 0.200554

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.053
ELB improved by 0.172111

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.905
ELB improved by 0.147656

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.778
ELB improved by 0.126873

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.669
ELB improved by 0.109347

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.574
ELB improved by 0.0946306

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.492
ELB improved by 0.0822925

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.42
ELB improved by 0.0719427

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.357
ELB improved by 0.0632393

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.301
ELB improved by 0.0558888

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.251
ELB improved by 0.0496454

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.207
ELB improved by 0.0443085

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.167
ELB improved by 0.0397174

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.131
ELB improved by 0.035745

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.099
ELB improved by 0.0322906

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.07
ELB improved by 0.0292732

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.043
ELB improved by 0.0266265

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.019
ELB improved by 0.0242957

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.996
ELB improved by 0.0222347

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.976
ELB improved by 0.0204049

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.957
ELB improved by 0.0187737

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.94
ELB improved by 0.0173138

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.924
ELB improved by 0.0160023

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.909
ELB improved by 0.0148203

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.895
ELB improved by 0.0137517

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.883
ELB improved by 0.0127831

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.871
ELB improved by 0.0119032

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.86
ELB improved by 0.0111024

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.849
ELB improved by 0.0103724

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.84
ELB improved by 0.00970614

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-883.717
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-613.28
ELB improved by 270.437

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-551.646
ELB improved by 61.634

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-503.755
ELB improved by 47.8911

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-478.088
ELB improved by 25.6676

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.319
ELB improved by 11.7682

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.998
ELB improved by 7.32113

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.358
ELB improved by 6.64009

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.602
ELB improved by 6.75614

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.21
ELB improved by 6.39164

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.154
ELB improved by 5.05594

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.778
ELB improved by 3.37624

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.67
ELB improved by 2.10851

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.318
ELB improved by 1.35208

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.389
ELB improved by 0.92834

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.7
ELB improved by 0.689361

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.149
ELB improved by 0.550544

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.682
ELB improved by 0.467877

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.262
ELB improved by 0.419693

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.866
ELB improved by 0.395888

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.474
ELB improved by 0.391606

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.072
ELB improved by 0.40211

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.654
ELB improved by 0.417992

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.228
ELB improved by 0.425891

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.81
ELB improved by 0.417975

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.413
ELB improved by 0.397499

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.041
ELB improved by 0.372129

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.694
ELB improved by 0.346598

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.372
ELB improved by 0.32233

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.072
ELB improved by 0.299611

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.794
ELB improved by 0.278646

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.534
ELB improved by 0.259658

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.291
ELB improved by 0.242787

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.063
ELB improved by 0.228039

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.848
ELB improved by 0.215289

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.643
ELB improved by 0.204323

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.449
ELB improved by 0.194875

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.262
ELB improved by 0.186656

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.083
ELB improved by 0.179376

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.91
ELB improved by 0.172754

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.743
ELB improved by 0.166535

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.583
ELB improved by 0.160495

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.428
ELB improved by 0.154462

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.28
ELB improved by 0.148323

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.138
ELB improved by 0.142054

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.002
ELB improved by 0.135745

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.873
ELB improved by 0.129636

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.748
ELB improved by 0.124188

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.628
ELB improved by 0.120182

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.509
ELB improved by 0.11883

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.388
ELB improved by 0.121587

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.259
ELB improved by 0.128578

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.125
ELB improved by 0.13444

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.997
ELB improved by 0.127504

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.893
ELB improved by 0.104606

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.813
ELB improved by 0.0795488

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.75
ELB improved by 0.0627926

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.697
ELB improved by 0.0533201

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.649
ELB improved by 0.0477957

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.605
ELB improved by 0.0444848

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.562
ELB improved by 0.0426816

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.52
ELB improved by 0.042015

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.478
ELB improved by 0.042142

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.435
ELB improved by 0.0425973

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.393
ELB improved by 0.0427465

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.351
ELB improved by 0.0419114

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.311
ELB improved by 0.0396713

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.275
ELB improved by 0.0361333

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.243
ELB improved by 0.0318754

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.215
ELB improved by 0.0275827

iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.192
ELB improved by 0.0237206

iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.171
ELB improved by 0.0204627

iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.153
ELB improved by 0.0177921

iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.138
ELB improved by 0.015618

iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.124
ELB improved by 0.0138415

iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.112
ELB improved by 0.0123789

iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.1
ELB improved by 0.0111646

iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.09
ELB improved by 0.0101488

iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.081
ELB improved by 0.00929311

ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
> 
> proc.time()
   user  system elapsed 
  2.179   0.191   2.358

Example timings

graper.Rcheck/graper-Ex.timings

name	user	system	elapsed
coef.graper	0.049	0.003	0.054
getPIPs	0.052	0.000	0.052
graper	0.075	0.010	0.085
makeExampleData	0.011	0.000	0.010
makeExampleDataWithUnequalGroups	0.011	0.001	0.012
plotELBO	0.322	0.026	0.348
plotGroupPenalties	1.135	0.058	1.192
plotPosterior	0.691	0.012	0.703
predict.graper	2.068	0.019	2.086
print.graper	0.048	0.005	0.052