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This page was generated on 2026-05-12 11:33 -0400 (Tue, 12 May 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 RC (2026-04-17 r89917) -- "Because it was There" 4892
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

Package 930/2374HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
graper 1.29.0  (landing page)
Britta Velten
Snapshot Date: 2026-05-11 13:45 -0400 (Mon, 11 May 2026)
git_url: https://git.bioconductor.org/packages/graper
git_branch: devel
git_last_commit: ba611e2
git_last_commit_date: 2026-04-28 08:49:19 -0400 (Tue, 28 Apr 2026)
nebbiolo2Linux (Ubuntu 24.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
See other builds for graper in R Universe.

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: 1.29.0
Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings graper_1.29.0.tar.gz
StartedAt: 2026-05-12 00:26:10 -0400 (Tue, 12 May 2026)
EndedAt: 2026-05-12 00:27:46 -0400 (Tue, 12 May 2026)
EllapsedTime: 96.1 seconds
RetCode: 0
Status:   OK  
CheckDir: graper.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings graper_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/graper.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-12 04:26:10 UTC
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.29.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... INFO
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) predict.graper.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:23-24: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.24-bioc/meat/graper.Rcheck/00check.log’
for details.

Installation output

graper.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL graper
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘graper’ ...
** this is package ‘graper’ version ‘1.29.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c fit_graper.cpp -o fit_graper.o
g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.24-bioc/R/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -llapack -L/home/biocbuild/bbs-3.24-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.24-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.24-bioc/R/site-library/00LOCK-graper/00new/graper/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (graper)

Tests output

graper.Rcheck/tests/testthat.Rout


R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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

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

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

> library(testthat)
> library(graper)
> 
> test_check("graper")
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-831.176
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-581.308
ELB improved by 249.868

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-517.444
ELB improved by 63.8644

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.814
ELB improved by 47.6298

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.14
ELB improved by 22.6736

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.281
ELB improved by 9.8591

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.701
ELB improved by 5.5806

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.267
ELB improved by 4.43396

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.867
ELB improved by 4.3997

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.053
ELB improved by 4.81449

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.72
ELB improved by 5.33277

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.266
ELB improved by 5.4537

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.459
ELB improved by 4.80719

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.804
ELB improved by 3.65489

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.226
ELB improved by 2.5781

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.36
ELB improved by 1.86609

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.885
ELB improved by 1.47503

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.606
ELB improved by 1.2791

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.42
ELB improved by 1.1856

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.279
ELB improved by 1.14116

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.161
ELB improved by 1.11805

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.057
ELB improved by 1.10404

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.961
ELB improved by 1.09617

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.864
ELB improved by 1.09647

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.755
ELB improved by 1.10932

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.614
ELB improved by 1.14117

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.409
ELB improved by 1.20487

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.069
ELB improved by 1.34025

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.374
ELB improved by 1.6947

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.865
ELB improved by 2.50852

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.051
ELB improved by 2.81401

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.846
ELB improved by 2.20549

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.298
ELB improved by 1.54836

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.274
ELB improved by 1.02396

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.618
ELB improved by 0.655678

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.197
ELB improved by 0.421047

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.919
ELB improved by 0.278315

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.727
ELB improved by 0.191039

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.592
ELB improved by 0.135933

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.492
ELB improved by 0.0997737

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.417
ELB improved by 0.0751878

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.359
ELB improved by 0.0579554

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.313
ELB improved by 0.0455675

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.277
ELB improved by 0.0364717

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.247
ELB improved by 0.0296718

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.222
ELB improved by 0.0245085

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.202
ELB improved by 0.0205341

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.184
ELB improved by 0.0174375

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.169
ELB improved by 0.0149994

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.156
ELB improved by 0.0130624

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.145
ELB improved by 0.0115128

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.135
ELB improved by 0.0102675

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.125
ELB improved by 0.00926618

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-877.081
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-584.897
ELB improved by 292.184

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-523.064
ELB improved by 61.8332

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-484.588
ELB improved by 38.4759

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.419
ELB improved by 17.1692

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.096
ELB improved by 8.3232

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.6
ELB improved by 5.49581

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.673
ELB improved by 4.92643

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.602
ELB improved by 5.07164

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.153
ELB improved by 5.44836

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.416
ELB improved by 5.73693

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.967
ELB improved by 5.44973

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.591
ELB improved by 4.37606

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.607
ELB improved by 2.98343

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.735
ELB improved by 1.87249

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.531
ELB improved by 1.20333

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.686
ELB improved by 0.845738

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.028
ELB improved by 0.657672

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.473
ELB improved by 0.554781

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.98
ELB improved by 0.493014

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.532
ELB improved by 0.448634

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.123
ELB improved by 0.408927

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.753
ELB improved by 0.369611

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.421
ELB improved by 0.332187

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.122
ELB improved by 0.299272

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.85
ELB improved by 0.271834

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.6
ELB improved by 0.249724

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.367
ELB improved by 0.232933

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.145
ELB improved by 0.221771

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.929
ELB improved by 0.21639

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.712
ELB improved by 0.216603

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.49
ELB improved by 0.222092

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.258
ELB improved by 0.232694

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.009
ELB improved by 0.248563

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.739
ELB improved by 0.270212

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.44
ELB improved by 0.298519

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.105
ELB improved by 0.334747

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.725
ELB improved by 0.38066

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.286
ELB improved by 0.438813

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.773
ELB improved by 0.513073

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.164
ELB improved by 0.609256

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.429
ELB improved by 0.73463

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.54
ELB improved by 0.889024

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.505
ELB improved by 1.03526

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.402
ELB improved by 1.10264

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.315
ELB improved by 1.08751

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.282
ELB improved by 1.03268

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.331
ELB improved by 0.951224

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.483
ELB improved by 0.847978

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.748
ELB improved by 0.734653

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.122
ELB improved by 0.625694

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.59
ELB improved by 0.532386

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.13
ELB improved by 0.460035

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.724
ELB improved by 0.405856

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.365
ELB improved by 0.359273

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.054
ELB improved by 0.311104

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.791
ELB improved by 0.262787

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.571
ELB improved by 0.220216

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.385
ELB improved by 0.185386

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.228
ELB improved by 0.157718

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.091
ELB improved by 0.1369

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.968
ELB improved by 0.122953

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.853
ELB improved by 0.115093

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.742
ELB improved by 0.110835

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.635
ELB improved by 0.106367

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.536
ELB improved by 0.0991

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.446
ELB improved by 0.0902442

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.363
ELB improved by 0.0835505

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.281
ELB improved by 0.081902

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.194
ELB improved by 0.0862528

iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.097
ELB improved by 0.0973534

iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.977
ELB improved by 0.119572

iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.81
ELB improved by 0.167894

iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.543
ELB improved by 0.266987

iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.157
ELB improved by 0.385159

iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.777
ELB improved by 0.380423

iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.54
ELB improved by 0.236629

iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.435
ELB improved by 0.105034

iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.393
ELB improved by 0.0420776

iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.375
ELB improved by 0.0179778

iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.366
ELB improved by 0.00907313

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-889.309
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-559.714
ELB improved by 329.596

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-500.76
ELB improved by 58.9534

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.985
ELB improved by 29.7757

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.024
ELB improved by 9.96071

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.473
ELB improved by 4.55084

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.251
ELB improved by 3.22223

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.345
ELB improved by 2.90588

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.313
ELB improved by 3.0319

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.875
ELB improved by 3.43842

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.861
ELB improved by 4.01345

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.314
ELB improved by 4.54774

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.631
ELB improved by 4.68272

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.487
ELB improved by 4.1442

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.378
ELB improved by 3.10865

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.294
ELB improved by 2.08372

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.904
ELB improved by 1.39075

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.884
ELB improved by 1.01921

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.04
ELB improved by 0.844225

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.271
ELB improved by 0.768778

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.532
ELB improved by 0.739013

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.805
ELB improved by 0.727765

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.083
ELB improved by 0.72184

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.368
ELB improved by 0.715153

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.662
ELB improved by 0.70511

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.972
ELB improved by 0.690704

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.3
ELB improved by 0.67165

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.652
ELB improved by 0.648087

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.032
ELB improved by 0.62046

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.442
ELB improved by 0.589332

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.887
ELB improved by 0.555167

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.369
ELB improved by 0.518196

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.89
ELB improved by 0.478513

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.454
ELB improved by 0.436406

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.061
ELB improved by 0.392754

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.712
ELB improved by 0.349241

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.404
ELB improved by 0.308189

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.132
ELB improved by 0.272049

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.889
ELB improved by 0.242711

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.668
ELB improved by 0.220689

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.464
ELB improved by 0.203845

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.278
ELB improved by 0.186073

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.118
ELB improved by 0.159994

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.993
ELB improved by 0.125768

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.9
ELB improved by 0.0925944

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.832
ELB improved by 0.0675559

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.782
ELB improved by 0.0507878

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.742
ELB improved by 0.0396681

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.71
ELB improved by 0.0319969

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.684
ELB improved by 0.0264659

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.661
ELB improved by 0.0223383

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.642
ELB improved by 0.0191777

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.625
ELB improved by 0.0167067

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.611
ELB improved by 0.0147394

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.597
ELB improved by 0.0131469

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.586
ELB improved by 0.0118374

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.575
ELB improved by 0.0107451

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.565
ELB improved by 0.00982152

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-888.354
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-567.53
ELB improved by 320.825

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-506.958
ELB improved by 60.5722

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.031
ELB improved by 35.9269

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.46
ELB improved by 14.571

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.402
ELB improved by 6.05803

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.78
ELB improved by 3.62221

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.058
ELB improved by 2.72159

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.736
ELB improved by 2.32188

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.62
ELB improved by 2.11596

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.63
ELB improved by 1.99057

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.727
ELB improved by 1.90225

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.906
ELB improved by 1.82175

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.189
ELB improved by 1.71645

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.63
ELB improved by 1.55878

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.284
ELB improved by 1.3459

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.178
ELB improved by 1.10642

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.296
ELB improved by 0.881528

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.597
ELB improved by 0.699315

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.031
ELB improved by 0.566201

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.556
ELB improved by 0.47485

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.142
ELB improved by 0.414089

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.768
ELB improved by 0.373904

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.421
ELB improved by 0.346696

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.094
ELB improved by 0.327162

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.782
ELB improved by 0.311874

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.483
ELB improved by 0.298852

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.196
ELB improved by 0.287171

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.92
ELB improved by 0.276649

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.652
ELB improved by 0.267611

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.391
ELB improved by 0.260733

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.134
ELB improved by 0.256993

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.877
ELB improved by 0.257704

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.612
ELB improved by 0.264557

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.333
ELB improved by 0.279332

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.03
ELB improved by 0.302501

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.7
ELB improved by 0.330526

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.344
ELB improved by 0.355542

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.972
ELB improved by 0.371937

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.59
ELB improved by 0.381751

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.2
ELB improved by 0.390718

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.796
ELB improved by 0.403495

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.373
ELB improved by 0.423153

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.922
ELB improved by 0.451036

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.439
ELB improved by 0.482859

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.936
ELB improved by 0.503268

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.44
ELB improved by 0.496354

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.971
ELB improved by 0.468774

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.528
ELB improved by 0.442413

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.096
ELB improved by 0.432358

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.657
ELB improved by 0.439513

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.211
ELB improved by 0.445722

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.784
ELB improved by 0.426462

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.4
ELB improved by 0.383879

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.064
ELB improved by 0.336109

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.778
ELB improved by 0.286441

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.545
ELB improved by 0.23271

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.362
ELB improved by 0.183275

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.214
ELB improved by 0.147765

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.086
ELB improved by 0.127718

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.966
ELB improved by 0.120111

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.846
ELB improved by 0.12057

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.723
ELB improved by 0.122405

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.606
ELB improved by 0.11747

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.503
ELB improved by 0.102749

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.42
ELB improved by 0.0831995

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.355
ELB improved by 0.0649703

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.305
ELB improved by 0.0504755

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.265
ELB improved by 0.0395315

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.234
ELB improved by 0.0313459

iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.208
ELB improved by 0.0252457

iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.188
ELB improved by 0.0207292

iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.17
ELB improved by 0.0174007

iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.155
ELB improved by 0.0149393

iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.142
ELB improved by 0.0130931

iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.131
ELB improved by 0.0116751

iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.12
ELB improved by 0.0105536

iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.11
ELB improved by 0.00964007

ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
> 
> proc.time()
   user  system elapsed 
  2.439   0.167   2.596

Example timings

graper.Rcheck/graper-Ex.timings

nameusersystemelapsed
coef.graper0.0550.0100.065
getPIPs0.0730.0230.096
graper0.0810.0040.085
makeExampleData0.0090.0010.010
makeExampleDataWithUnequalGroups0.0120.0000.012
plotELBO0.3080.0220.330
plotGroupPenalties0.9410.0020.943
plotPosterior0.6640.0010.665
predict.graper2.0580.0182.076
print.graper0.0500.0030.053