Britta Velten
| Snapshot Date: 2025-12-15 13:40 -0500 (Mon, 15 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: 95474d7 |
| git_last_commit_date: 2025-10-29 10:49:21 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-16 11:35 -0500 (Tue, 16 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4875 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4583 |
| 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 915/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.27.0 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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. |
| Package: graper |
| Version: 1.27.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.27.0.tar.gz |
| StartedAt: 2025-12-15 20:06:40 -0500 (Mon, 15 Dec 2025) |
| EndedAt: 2025-12-15 20:07:14 -0500 (Mon, 15 Dec 2025) |
| EllapsedTime: 33.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* 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 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.27.0’
* 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: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.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 ... 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.27.0’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.1.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-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)
graper.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
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=-854.456
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-592.721
ELB improved by 261.735
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-529.573
ELB improved by 63.1483
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-478.612
ELB improved by 50.9611
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.387
ELB improved by 27.225
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.232
ELB improved by 11.1549
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.584
ELB improved by 5.64818
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.659
ELB improved by 3.92517
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.219
ELB improved by 3.43935
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.71
ELB improved by 3.50949
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.878
ELB improved by 3.83151
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.755
ELB improved by 4.12311
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.724
ELB improved by 4.03093
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.349
ELB improved by 3.37492
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.924
ELB improved by 2.42493
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.306
ELB improved by 1.6187
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.183
ELB improved by 1.12238
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.322
ELB improved by 0.861303
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.594
ELB improved by 0.727877
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.938
ELB improved by 0.656352
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.323
ELB improved by 0.615065
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.733
ELB improved by 0.58996
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.158
ELB improved by 0.575091
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.59
ELB improved by 0.568171
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.021
ELB improved by 0.568703
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.443
ELB improved by 0.577695
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.844
ELB improved by 0.598943
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.202
ELB improved by 0.642372
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.475
ELB improved by 0.726494
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.617
ELB improved by 0.858597
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.617
ELB improved by 0.99965
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.461
ELB improved by 1.15619
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.165
ELB improved by 1.29556
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.883
ELB improved by 1.28201
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.488
ELB improved by 1.39542
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.83
ELB improved by 1.65759
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.548
ELB improved by 1.28253
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.762
ELB improved by 0.785458
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.218
ELB improved by 0.54428
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.715
ELB improved by 0.503315
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.038
ELB improved by 0.677089
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.057
ELB improved by 0.980249
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.181
ELB improved by 0.876207
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.588
ELB improved by 0.592763
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.115
ELB improved by 0.473143
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.661
ELB improved by 0.454649
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.21
ELB improved by 0.450979
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.806
ELB improved by 0.403664
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.502
ELB improved by 0.304188
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.304
ELB improved by 0.197751
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.183
ELB improved by 0.120956
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.106
ELB improved by 0.0766699
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.053
ELB improved by 0.0529841
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.014
ELB improved by 0.0398107
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.982
ELB improved by 0.0317645
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.955
ELB improved by 0.0263367
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.933
ELB improved by 0.0223659
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.914
ELB improved by 0.0192859
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.897
ELB improved by 0.0168006
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.882
ELB improved by 0.0147423
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.869
ELB improved by 0.0130088
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.858
ELB improved by 0.0115326
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.847
ELB improved by 0.0102661
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.838
ELB improved by 0.00917389
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-855.373
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-557.137
ELB improved by 298.236
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-497.667
ELB improved by 59.4704
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.096
ELB improved by 31.5705
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.022
ELB improved by 12.0747
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.158
ELB improved by 5.86372
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.829
ELB improved by 4.32911
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.967
ELB improved by 3.86202
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.25
ELB improved by 3.71638
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.616
ELB improved by 3.63423
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.147
ELB improved by 3.46959
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.021
ELB improved by 3.12603
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.423
ELB improved by 2.59728
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.432
ELB improved by 1.99117
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.986
ELB improved by 1.44586
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.953
ELB improved by 1.03342
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.201
ELB improved by 0.752212
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.632
ELB improved by 0.568685
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.184
ELB improved by 0.447995
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.819
ELB improved by 0.364544
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.517
ELB improved by 0.302529
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.263
ELB improved by 0.253495
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.05
ELB improved by 0.213502
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.869
ELB improved by 0.180774
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.715
ELB improved by 0.154204
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.582
ELB improved by 0.132765
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.467
ELB improved by 0.115446
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.365
ELB improved by 0.101346
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.276
ELB improved by 0.0897333
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.196
ELB improved by 0.0800447
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.124
ELB improved by 0.0718605
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.059
ELB improved by 0.0648697
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415
ELB improved by 0.0588408
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.946
ELB improved by 0.0535992
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.897
ELB improved by 0.0490107
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.852
ELB improved by 0.0449706
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.811
ELB improved by 0.0413957
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.773
ELB improved by 0.0382185
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.737
ELB improved by 0.0353842
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.705
ELB improved by 0.0328471
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.674
ELB improved by 0.030569
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.646
ELB improved by 0.0285179
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.619
ELB improved by 0.0266665
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.594
ELB improved by 0.0249915
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.57
ELB improved by 0.0234727
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.548
ELB improved by 0.0220929
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.527
ELB improved by 0.0208371
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.508
ELB improved by 0.019692
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.489
ELB improved by 0.0186464
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.471
ELB improved by 0.0176901
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.455
ELB improved by 0.0168142
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.439
ELB improved by 0.0160109
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.423
ELB improved by 0.0152733
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.409
ELB improved by 0.0145952
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.395
ELB improved by 0.013971
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.381
ELB improved by 0.0133959
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.369
ELB improved by 0.0128655
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.356
ELB improved by 0.0123758
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.344
ELB improved by 0.0119232
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.333
ELB improved by 0.0115046
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.322
ELB improved by 0.0111171
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.311
ELB improved by 0.010758
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.3
ELB improved by 0.0104251
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.29
ELB improved by 0.0101161
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.28
ELB improved by 0.00982923
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-875.042
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-576.488
ELB improved by 298.554
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-514.923
ELB improved by 61.565
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-480.335
ELB improved by 34.5875
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.116
ELB improved by 14.2196
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.171
ELB improved by 6.94512
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.25
ELB improved by 4.92061
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.569
ELB improved by 4.68097
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.474
ELB improved by 5.09498
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.639
ELB improved by 5.83535
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.123
ELB improved by 6.51614
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.763
ELB improved by 6.35974
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.768
ELB improved by 4.99497
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.555
ELB improved by 3.21339
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.666
ELB improved by 1.88861
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.514
ELB improved by 1.152
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.735
ELB improved by 0.779116
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.151
ELB improved by 0.584069
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.677
ELB improved by 0.473835
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.269
ELB improved by 0.407686
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.903
ELB improved by 0.365968
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.566
ELB improved by 0.336877
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.252
ELB improved by 0.313967
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.956
ELB improved by 0.295898
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.674
ELB improved by 0.282717
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.401
ELB improved by 0.272833
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.136
ELB improved by 0.26481
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.877
ELB improved by 0.259443
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.618
ELB improved by 0.258532
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.355
ELB improved by 0.262956
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.083
ELB improved by 0.27256
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.796
ELB improved by 0.287026
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.489
ELB improved by 0.306451
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.158
ELB improved by 0.331481
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.794
ELB improved by 0.363315
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.391
ELB improved by 0.403819
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.935
ELB improved by 0.455939
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.41
ELB improved by 0.524294
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.797
ELB improved by 0.613473
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.082
ELB improved by 0.71482
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.297
ELB improved by 0.78523
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.514
ELB improved by 0.782467
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.794
ELB improved by 0.720619
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.165
ELB improved by 0.628521
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.642
ELB improved by 0.522994
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.224
ELB improved by 0.417763
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.9
ELB improved by 0.32394
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.653
ELB improved by 0.247168
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.465
ELB improved by 0.18786
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.322
ELB improved by 0.143497
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.211
ELB improved by 0.110753
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.125
ELB improved by 0.0866134
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.056
ELB improved by 0.0687137
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.001
ELB improved by 0.0553165
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.955
ELB improved by 0.0451778
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.918
ELB improved by 0.0374136
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.887
ELB improved by 0.0313956
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.86
ELB improved by 0.0266743
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.837
ELB improved by 0.0229258
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.817
ELB improved by 0.0199147
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.8
ELB improved by 0.0174685
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.784
ELB improved by 0.0154594
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.77
ELB improved by 0.013792
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.758
ELB improved by 0.0123943
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.747
ELB improved by 0.0112117
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.737
ELB improved by 0.0102022
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.727
ELB improved by 0.00933322
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-827.04
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-562.481
ELB improved by 264.56
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-501.497
ELB improved by 60.9836
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.644
ELB improved by 41.8531
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.234
ELB improved by 16.4101
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.775
ELB improved by 5.45835
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.95
ELB improved by 2.8251
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.899
ELB improved by 2.05138
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.153
ELB improved by 1.74607
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.54
ELB improved by 1.61291
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.957
ELB improved by 1.58264
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.315
ELB improved by 1.64228
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.518
ELB improved by 1.79682
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.469
ELB improved by 2.04921
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.094
ELB improved by 2.37491
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.403
ELB improved by 2.69068
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.553
ELB improved by 2.85079
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.829
ELB improved by 2.72331
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.507
ELB improved by 2.32207
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.68
ELB improved by 1.82752
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.263
ELB improved by 1.41716
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.125
ELB improved by 1.13752
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.17
ELB improved by 0.955019
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.336
ELB improved by 0.834239
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.576
ELB improved by 0.759426
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.845
ELB improved by 0.730985
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.081
ELB improved by 0.764697
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.193
ELB improved by 0.888041
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.123
ELB improved by 1.06977
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.977
ELB improved by 1.1454
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.875
ELB improved by 1.10252
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.836
ELB improved by 1.03901
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.882
ELB improved by 0.954165
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.045
ELB improved by 0.836236
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.352
ELB improved by 0.693285
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.807
ELB improved by 0.544732
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.397
ELB improved by 0.410138
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.096
ELB improved by 0.301035
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.877
ELB improved by 0.219428
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.716
ELB improved by 0.16131
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.595
ELB improved by 0.120822
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.502
ELB improved by 0.0926661
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.429
ELB improved by 0.0728632
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.371
ELB improved by 0.058673
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.322
ELB improved by 0.0482784
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.282
ELB improved by 0.0404875
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.247
ELB improved by 0.034516
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.217
ELB improved by 0.0298414
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.191
ELB improved by 0.0261104
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.168
ELB improved by 0.0230796
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.148
ELB improved by 0.0205783
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.129
ELB improved by 0.0184848
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.112
ELB improved by 0.0167106
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.097
ELB improved by 0.01519
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.083
ELB improved by 0.0138741
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.071
ELB improved by 0.0127253
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.059
ELB improved by 0.0117147
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.048
ELB improved by 0.0108195
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.038
ELB improved by 0.010022
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.029
ELB improved by 0.00930755
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
1.115 0.100 1.249
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.014 | 0.008 | 0.027 | |
| getPIPs | 0.012 | 0.006 | 0.018 | |
| graper | 0.02 | 0.01 | 0.03 | |
| makeExampleData | 0.002 | 0.000 | 0.002 | |
| makeExampleDataWithUnequalGroups | 0.003 | 0.001 | 0.003 | |
| plotELBO | 0.119 | 0.011 | 0.132 | |
| plotGroupPenalties | 0.359 | 0.007 | 0.380 | |
| plotPosterior | 0.326 | 0.017 | 0.361 | |
| predict.graper | 0.219 | 0.045 | 0.280 | |
| print.graper | 0.012 | 0.007 | 0.018 | |