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This page was generated on 2025-10-16 11:40 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 915/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
graper 1.24.2  (landing page)
Britta Velten
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/graper
git_branch: RELEASE_3_21
git_last_commit: fb5f237
git_last_commit_date: 2025-06-24 03:18:49 -0400 (Tue, 24 Jun 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for graper on kjohnson1

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: 1.24.2
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_1.24.2.tar.gz
StartedAt: 2025-10-14 23:47:15 -0400 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 23:48:33 -0400 (Tue, 14 Oct 2025)
EllapsedTime: 78.1 seconds
RetCode: 0
Status:   OK  
CheckDir: graper.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.24.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/graper.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.24.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) predict.graper.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:23-24: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... 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: 2 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’ ...
** this is package ‘graper’ version ‘1.24.2’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -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   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -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   -c fit_graper.cpp -o fit_graper.o
clang++ -arch arm64 -std=gnu++17 -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-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-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 version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 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=-912.76
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-584.579
ELB improved by 328.181

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-527.528
ELB improved by 57.0502

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-495.074
ELB improved by 32.4546

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-480.525
ELB improved by 14.5492

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-474.006
ELB improved by 6.51858

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.605
ELB improved by 4.40155

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.645
ELB improved by 3.95955

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.688
ELB improved by 3.9566

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.738
ELB improved by 3.94997

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.084
ELB improved by 3.65485

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.056
ELB improved by 3.02802

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.784
ELB improved by 2.27111

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.166
ELB improved by 1.61853

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.012
ELB improved by 1.15366

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.172
ELB improved by 0.839768

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.544
ELB improved by 0.628036

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.059
ELB improved by 0.485296

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.672
ELB improved by 0.386996

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.355
ELB improved by 0.31678

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.09
ELB improved by 0.264892

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.865
ELB improved by 0.22539

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.671
ELB improved by 0.194476

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.501
ELB improved by 0.169685

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.351
ELB improved by 0.14941

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.219
ELB improved by 0.13258

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.1
ELB improved by 0.118448

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.994
ELB improved by 0.106468

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.898
ELB improved by 0.0962304

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.81
ELB improved by 0.0874184

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.731
ELB improved by 0.0797828

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.657
ELB improved by 0.0731257

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.59
ELB improved by 0.0672887

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.528
ELB improved by 0.0621437

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.47
ELB improved by 0.0575867

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.417
ELB improved by 0.053532

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.367
ELB improved by 0.0499091

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.32
ELB improved by 0.046659

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.277
ELB improved by 0.0437326

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.236
ELB improved by 0.0410881

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.197
ELB improved by 0.0386904

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.16
ELB improved by 0.0365092

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.126
ELB improved by 0.0345189

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.093
ELB improved by 0.0326971

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.062
ELB improved by 0.0310247

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.033
ELB improved by 0.0294849

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.005
ELB improved by 0.0280634

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.978
ELB improved by 0.0267473

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.952
ELB improved by 0.0255257

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.928
ELB improved by 0.0243887

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.905
ELB improved by 0.0233279

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.882
ELB improved by 0.0223358

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.861
ELB improved by 0.0214058

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.84
ELB improved by 0.020532

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.821
ELB improved by 0.0197094

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.802
ELB improved by 0.0189333

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.783
ELB improved by 0.0181998

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.766
ELB improved by 0.0175055

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.749
ELB improved by 0.0168471

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.733
ELB improved by 0.0162219

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.717
ELB improved by 0.0156276

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.702
ELB improved by 0.0150619

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.688
ELB improved by 0.0145231

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.674
ELB improved by 0.0140094

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.66
ELB improved by 0.0135193

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.647
ELB improved by 0.0130515

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.634
ELB improved by 0.0126049

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.622
ELB improved by 0.0121783

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.61
ELB improved by 0.0117708

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.599
ELB improved by 0.0113816

iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.588
ELB improved by 0.0110099

iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.577
ELB improved by 0.0106549

iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.567
ELB improved by 0.010316

iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.557
ELB improved by 0.00999261

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-856.706
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-579.743
ELB improved by 276.963

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-516.969
ELB improved by 62.7749

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.59
ELB improved by 43.3784

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.107
ELB improved by 19.4832

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.268
ELB improved by 7.83888

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.012
ELB improved by 4.25596

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.856
ELB improved by 3.15632

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.076
ELB improved by 2.77952

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.381
ELB improved by 2.69508

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.617
ELB improved by 2.7643

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.706
ELB improved by 2.91091

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.663
ELB improved by 3.04346

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.616
ELB improved by 3.04609

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.778
ELB improved by 2.83871

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.335
ELB improved by 2.44233

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.364
ELB improved by 1.97126

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.805
ELB improved by 1.55898

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.534
ELB improved by 1.27123

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.439
ELB improved by 1.09487

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.438
ELB improved by 1.00085

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.469
ELB improved by 0.969005

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.49
ELB improved by 0.978758

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.476
ELB improved by 1.01407

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.408
ELB improved by 1.06867

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.264
ELB improved by 1.14356

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.026
ELB improved by 1.23828

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.685
ELB improved by 1.3412

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.248
ELB improved by 1.43637

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.732
ELB improved by 1.51674

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.156
ELB improved by 1.57515

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.56
ELB improved by 1.59599

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.002
ELB improved by 1.55882

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.555
ELB improved by 1.44681

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.289
ELB improved by 1.26618

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.237
ELB improved by 1.05167

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.399
ELB improved by 0.83778

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.755
ELB improved by 0.644156

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.262
ELB improved by 0.49266

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.867
ELB improved by 0.395707

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.523
ELB improved by 0.343487

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.21
ELB improved by 0.313467

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.936
ELB improved by 0.274094

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.725
ELB improved by 0.210684

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.577
ELB improved by 0.147518

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.472
ELB improved by 0.105283

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.391
ELB improved by 0.0813045

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.324
ELB improved by 0.0670081

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.267
ELB improved by 0.0567373

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.219
ELB improved by 0.0479215

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.179
ELB improved by 0.0398442

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.147
ELB improved by 0.0326151

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.12
ELB improved by 0.0264812

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.099
ELB improved by 0.0215274

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.081
ELB improved by 0.0176635

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.066
ELB improved by 0.0147091

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.054
ELB improved by 0.0124667

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.043
ELB improved by 0.0107593

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.034
ELB improved by 0.00944387

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-864.38
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-599.685
ELB improved by 264.695

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-540.681
ELB improved by 59.0039

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-491.585
ELB improved by 49.0967

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464
ELB improved by 27.5843

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.826
ELB improved by 11.1747

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.977
ELB improved by 4.84819

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.939
ELB improved by 3.03844

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.509
ELB improved by 2.43036

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.332
ELB improved by 2.17632

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.264
ELB improved by 2.06802

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.243
ELB improved by 2.02091

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.25
ELB improved by 1.99375

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.292
ELB improved by 1.95743

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.408
ELB improved by 1.88405

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.655
ELB improved by 1.75322

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.09
ELB improved by 1.56526

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.746
ELB improved by 1.34358

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.625
ELB improved by 1.12149

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.695
ELB improved by 0.929747

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.906
ELB improved by 0.788812

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.204
ELB improved by 0.702055

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.549
ELB improved by 0.654927

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.926
ELB improved by 0.622879

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.335
ELB improved by 0.590822

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.771
ELB improved by 0.564696

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.216
ELB improved by 0.554861

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.654
ELB improved by 0.561758

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.074
ELB improved by 0.579945

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.47
ELB improved by 0.604424

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.837
ELB improved by 0.632618

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.173
ELB improved by 0.664334

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.471
ELB improved by 0.701508

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.723
ELB improved by 0.747638

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.917
ELB improved by 0.806156

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.039
ELB improved by 0.878316

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.077
ELB improved by 0.962075

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.026
ELB improved by 1.05108

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.893
ELB improved by 1.13263

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.707
ELB improved by 1.18647

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.52
ELB improved by 1.18663

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.41
ELB improved by 1.10987

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.457
ELB improved by 0.953169

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.71
ELB improved by 0.746886

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.169
ELB improved by 0.541255

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.795
ELB improved by 0.374112

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.539
ELB improved by 0.255641

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.362
ELB improved by 0.177662

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.234
ELB improved by 0.127523

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.139
ELB improved by 0.0949686

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.066
ELB improved by 0.0732619

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.007
ELB improved by 0.0583106

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.96
ELB improved by 0.0476666

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.92
ELB improved by 0.0398461

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.886
ELB improved by 0.0339288

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.857
ELB improved by 0.0293303

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.831
ELB improved by 0.0256706

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.808
ELB improved by 0.0226975

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.788
ELB improved by 0.0202395

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.77
ELB improved by 0.0181778

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.754
ELB improved by 0.0164276

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.739
ELB improved by 0.0149273

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.725
ELB improved by 0.0136307

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.712
ELB improved by 0.0125026

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.701
ELB improved by 0.0115156

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.69
ELB improved by 0.0106476

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.68
ELB improved by 0.00988113

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-844.068
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-567.467
ELB improved by 276.602

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-509.24
ELB improved by 58.2266

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.67
ELB improved by 41.5703

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.677
ELB improved by 17.9924

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.372
ELB improved by 6.30588

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.212
ELB improved by 3.15928

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.999
ELB improved by 2.2134

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.127
ELB improved by 1.87156

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.375
ELB improved by 1.75192

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.639
ELB improved by 1.73633

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.859
ELB improved by 1.7801

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.997
ELB improved by 1.86188

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.036
ELB improved by 1.96082

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.99
ELB improved by 2.04659

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.905
ELB improved by 2.08475

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.846
ELB improved by 2.05863

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.863
ELB improved by 1.98304

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.005
ELB improved by 1.85826

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.4
ELB improved by 1.60472

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.19
ELB improved by 1.21023

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.365
ELB improved by 0.825123

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.819
ELB improved by 0.545674

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.45
ELB improved by 0.369275

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.187
ELB improved by 0.26346

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.987
ELB improved by 0.199806

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.827
ELB improved by 0.160179

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.692
ELB improved by 0.134273

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.576
ELB improved by 0.116402

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.472
ELB improved by 0.103399

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.379
ELB improved by 0.0934491

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.294
ELB improved by 0.0854851

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.215
ELB improved by 0.078859

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.141
ELB improved by 0.0731677

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.073
ELB improved by 0.0681543

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.01
ELB improved by 0.0636515

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.95
ELB improved by 0.0595482

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.894
ELB improved by 0.055769

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.842
ELB improved by 0.0522624

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.793
ELB improved by 0.0489919

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.747
ELB improved by 0.0459317

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.704
ELB improved by 0.0430629

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.664
ELB improved by 0.0403712

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.626
ELB improved by 0.0378452

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.59
ELB improved by 0.0354757

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.557
ELB improved by 0.0332545

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.526
ELB improved by 0.0311741

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.497
ELB improved by 0.0292277

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.469
ELB improved by 0.0274084

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.444
ELB improved by 0.0257095

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.42
ELB improved by 0.0241244

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.397
ELB improved by 0.0226466

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.376
ELB improved by 0.0212698

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.356
ELB improved by 0.0199876

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.337
ELB improved by 0.0187939

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.319
ELB improved by 0.0176829

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.303
ELB improved by 0.0166488

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.287
ELB improved by 0.0156865

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.272
ELB improved by 0.0147906

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.258
ELB improved by 0.0139565

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.245
ELB improved by 0.0131796

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.232
ELB improved by 0.0124558

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.221
ELB improved by 0.0117811

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.21
ELB improved by 0.0111519

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.199
ELB improved by 0.0105648

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.189
ELB improved by 0.0100167

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.179
ELB improved by 0.00950475

ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
> 
> proc.time()
   user  system elapsed 
  2.898   0.289   3.219 

Example timings

graper.Rcheck/graper-Ex.timings

nameusersystemelapsed
coef.graper0.0820.0180.101
getPIPs0.0780.0140.093
graper0.1300.0200.154
makeExampleData0.0120.0010.014
makeExampleDataWithUnequalGroups0.0150.0020.016
plotELBO0.3850.0250.413
plotGroupPenalties1.3540.0551.426
plotPosterior0.7110.0400.762
predict.graper2.9820.0813.097
print.graper0.0310.0060.037