Britta Velten
| Snapshot Date: 2026-01-09 13:40 -0500 (Fri, 09 Jan 2026) |
| 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 2026-01-10 11:35 -0500 (Sat, 10 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" | 4818 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4594 |
| 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: 2026-01-09 20:14:06 -0500 (Fri, 09 Jan 2026) |
| EndedAt: 2026-01-09 20:14:38 -0500 (Fri, 09 Jan 2026) |
| EllapsedTime: 31.4 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=-881.46
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-568.27
ELB improved by 313.19
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-507.974
ELB improved by 60.2959
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.997
ELB improved by 34.9769
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.763
ELB improved by 14.2343
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.85
ELB improved by 5.91321
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.372
ELB improved by 3.47828
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.638
ELB improved by 2.73384
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.177
ELB improved by 2.46091
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.86
ELB improved by 2.31705
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.655
ELB improved by 2.20438
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.566
ELB improved by 2.08959
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.604
ELB improved by 1.9617
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.785
ELB improved by 1.81883
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.123
ELB improved by 1.66258
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.626
ELB improved by 1.49639
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.301
ELB improved by 1.32559
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.144
ELB improved by 1.15657
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.149
ELB improved by 0.994852
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.304
ELB improved by 0.844742
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.595
ELB improved by 0.70988
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.002
ELB improved by 0.592334
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.511
ELB improved by 0.491533
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.105
ELB improved by 0.405495
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.772
ELB improved by 0.333186
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.497
ELB improved by 0.274736
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.268
ELB improved by 0.229687
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.071
ELB improved by 0.196188
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.9
ELB improved by 0.171686
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.746
ELB improved by 0.153793
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.605
ELB improved by 0.140658
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.474
ELB improved by 0.130974
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.35
ELB improved by 0.123856
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.232
ELB improved by 0.11872
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.117
ELB improved by 0.115188
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.004
ELB improved by 0.113028
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.891
ELB improved by 0.112116
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.779
ELB improved by 0.112409
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.665
ELB improved by 0.113939
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.548
ELB improved by 0.116807
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.427
ELB improved by 0.121188
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.3
ELB improved by 0.127335
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.164
ELB improved by 0.135596
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.018
ELB improved by 0.146414
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.857
ELB improved by 0.160328
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.68
ELB improved by 0.177917
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.48
ELB improved by 0.199643
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.254
ELB improved by 0.225511
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420
ELB improved by 0.254577
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.715
ELB improved by 0.284629
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.402
ELB improved by 0.312747
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.066
ELB improved by 0.33688
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.708
ELB improved by 0.357117
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.333
ELB improved by 0.375247
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.94
ELB improved by 0.393284
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.527
ELB improved by 0.412464
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.094
ELB improved by 0.433018
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.64
ELB improved by 0.454154
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.166
ELB improved by 0.473753
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.679
ELB improved by 0.487619
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.19
ELB improved by 0.489289
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.717
ELB improved by 0.472603
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.281
ELB improved by 0.436392
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.895
ELB improved by 0.385841
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.566
ELB improved by 0.328926
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.293
ELB improved by 0.272677
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.071
ELB improved by 0.221858
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.892
ELB improved by 0.17917
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.746
ELB improved by 0.145768
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.625
ELB improved by 0.121658
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.519
ELB improved by 0.106112
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.42
ELB improved by 0.0981159
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.324
ELB improved by 0.0966263
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.223
ELB improved by 0.10047
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.115
ELB improved by 0.107966
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.999
ELB improved by 0.116588
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.876
ELB improved by 0.122847
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.754
ELB improved by 0.122201
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.643
ELB improved by 0.110432
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.555
ELB improved by 0.0883888
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.491
ELB improved by 0.0637596
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.447
ELB improved by 0.0440664
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.416
ELB improved by 0.0312564
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.392
ELB improved by 0.0236494
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.373
ELB improved by 0.0191183
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.357
ELB improved by 0.0162312
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.343
ELB improved by 0.0142101
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.33
ELB improved by 0.0126663
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.319
ELB improved by 0.0114096
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.308
ELB improved by 0.0103442
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.299
ELB improved by 0.00941961
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-864.534
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-578.892
ELB improved by 285.642
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-518.937
ELB improved by 59.955
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-483.218
ELB improved by 35.7187
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.57
ELB improved by 15.648
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.843
ELB improved by 7.72732
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.063
ELB improved by 5.78018
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.994
ELB improved by 6.06905
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.87
ELB improved by 7.1238
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.74
ELB improved by 8.13024
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.769
ELB improved by 7.97075
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.429
ELB improved by 6.34004
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.049
ELB improved by 4.38039
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.013
ELB improved by 3.03597
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.9
ELB improved by 2.11268
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.52
ELB improved by 1.38047
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.598
ELB improved by 0.921466
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.926
ELB improved by 0.671851
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.39
ELB improved by 0.536345
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.933
ELB improved by 0.457198
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.533
ELB improved by 0.399192
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.191
ELB improved by 0.342729
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.904
ELB improved by 0.286792
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.665
ELB improved by 0.239017
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.463
ELB improved by 0.202285
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.288
ELB improved by 0.174537
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.135
ELB improved by 0.153047
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.999
ELB improved by 0.135937
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.877
ELB improved by 0.122044
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.766
ELB improved by 0.110617
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.665
ELB improved by 0.101129
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.572
ELB improved by 0.0931941
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.486
ELB improved by 0.0865203
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.405
ELB improved by 0.0808808
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.329
ELB improved by 0.0760987
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.257
ELB improved by 0.0720346
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.188
ELB improved by 0.0685784
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.122
ELB improved by 0.0656433
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.059
ELB improved by 0.0631621
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.998
ELB improved by 0.0610843
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.939
ELB improved by 0.0593749
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.881
ELB improved by 0.0580145
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.824
ELB improved by 0.0570003
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.767
ELB improved by 0.0563492
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.711
ELB improved by 0.0561031
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.655
ELB improved by 0.0563372
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.598
ELB improved by 0.0571706
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.539
ELB improved by 0.0587802
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.478
ELB improved by 0.0614078
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.412
ELB improved by 0.0653433
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.341
ELB improved by 0.0708416
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.263
ELB improved by 0.0779226
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.177
ELB improved by 0.086083
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.083
ELB improved by 0.0941898
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.982
ELB improved by 0.100965
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.876
ELB improved by 0.105894
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.767
ELB improved by 0.109558
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.654
ELB improved by 0.113019
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.537
ELB improved by 0.117128
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.414
ELB improved by 0.12236
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.285
ELB improved by 0.128982
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.148
ELB improved by 0.137206
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.001
ELB improved by 0.147273
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.841
ELB improved by 0.159474
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.667
ELB improved by 0.174154
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.475
ELB improved by 0.191732
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.263
ELB improved by 0.212734
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.025
ELB improved by 0.237896
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.756
ELB improved by 0.268364
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.451
ELB improved by 0.305953
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.098
ELB improved by 0.352966
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.688
ELB improved by 0.409763
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.219
ELB improved by 0.468307
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.71
ELB improved by 0.50911
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.194
ELB improved by 0.5159
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.698
ELB improved by 0.496017
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.225
ELB improved by 0.47324
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.769
ELB improved by 0.456397
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.328
ELB improved by 0.440572
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.882
ELB improved by 0.446721
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.385
ELB improved by 0.496658
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.869
ELB improved by 0.515376
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.439
ELB improved by 0.430528
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.077
ELB improved by 0.361627
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.666
ELB improved by 0.411037
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.119
ELB improved by 0.546894
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.569
ELB improved by 0.549997
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.197
ELB improved by 0.372247
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.977
ELB improved by 0.220044
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.836
ELB improved by 0.141368
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.737
ELB improved by 0.0988912
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.667
ELB improved by 0.0695019
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.619
ELB improved by 0.0479261
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.586
ELB improved by 0.0336712
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.561
ELB improved by 0.0250582
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.541
ELB improved by 0.0198713
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.524
ELB improved by 0.0165118
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.51
ELB improved by 0.0140864
iteration 99
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.498
ELB improved by 0.0121467
iteration 100
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.488
ELB improved by 0.0104852
iteration 101
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.479
ELB improved by 0.00901971
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-863.961
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-579.602
ELB improved by 284.359
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-516.505
ELB improved by 63.0968
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.383
ELB improved by 47.1219
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.777
ELB improved by 25.6058
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.889
ELB improved by 11.8883
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.027
ELB improved by 5.86247
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.555
ELB improved by 3.4715
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.184
ELB improved by 2.37105
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.373
ELB improved by 1.81143
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.876
ELB improved by 1.49658
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.582
ELB improved by 1.2946
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.433
ELB improved by 1.14899
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.396
ELB improved by 1.03685
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.447
ELB improved by 0.948841
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.566
ELB improved by 0.880454
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.738
ELB improved by 0.828553
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.948
ELB improved by 0.790052
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.186
ELB improved by 0.761413
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.448
ELB improved by 0.738521
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.731
ELB improved by 0.717041
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.038
ELB improved by 0.693325
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.372
ELB improved by 0.665577
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.737
ELB improved by 0.634512
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.135
ELB improved by 0.602842
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.561
ELB improved by 0.57373
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.012
ELB improved by 0.549324
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.481
ELB improved by 0.530329
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.965
ELB improved by 0.516551
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.457
ELB improved by 0.507552
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.955
ELB improved by 0.502545
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.455
ELB improved by 0.499267
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.962
ELB improved by 0.493171
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.483
ELB improved by 0.479421
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.026
ELB improved by 0.456699
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.598
ELB improved by 0.427542
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.203
ELB improved by 0.395296
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.841
ELB improved by 0.362369
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.511
ELB improved by 0.330239
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.211
ELB improved by 0.299718
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.94
ELB improved by 0.27111
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.695
ELB improved by 0.244388
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.476
ELB improved by 0.219362
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.28
ELB improved by 0.195836
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.106
ELB improved by 0.173699
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.953
ELB improved by 0.152974
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.82
ELB improved by 0.133785
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.703
ELB improved by 0.116296
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.603
ELB improved by 0.100641
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.516
ELB improved by 0.0868708
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.441
ELB improved by 0.0749389
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.376
ELB improved by 0.0647163
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.32
ELB improved by 0.0560206
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.272
ELB improved by 0.0486482
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.229
ELB improved by 0.042399
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.192
ELB improved by 0.037092
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.159
ELB improved by 0.032571
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.131
ELB improved by 0.0287058
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.105
ELB improved by 0.0253897
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.083
ELB improved by 0.0225353
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.063
ELB improved by 0.0200714
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.045
ELB improved by 0.0179393
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.029
ELB improved by 0.0160904
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.014
ELB improved by 0.0144838
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.001
ELB improved by 0.013085
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.989
ELB improved by 0.011865
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.979
ELB improved by 0.0107988
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.969
ELB improved by 0.00986516
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-853.778
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-555.904
ELB improved by 297.875
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-487.331
ELB improved by 68.5723
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.674
ELB improved by 42.6576
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.2
ELB improved by 17.4738
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.549
ELB improved by 7.65096
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.764
ELB improved by 4.78457
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.068
ELB improved by 3.69677
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.845
ELB improved by 3.22279
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.77
ELB improved by 3.07453
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.665
ELB improved by 3.10579
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.426
ELB improved by 3.23874
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.015
ELB improved by 3.41106
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.496
ELB improved by 3.51902
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.07
ELB improved by 3.42544
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.994
ELB improved by 3.07661
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.406
ELB improved by 2.58756
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.268
ELB improved by 2.13805
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.429
ELB improved by 1.8387
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.719
ELB improved by 1.71036
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375
ELB improved by 1.71896
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.191
ELB improved by 1.80913
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.254
ELB improved by 1.93703
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.168
ELB improved by 2.08612
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.913
ELB improved by 2.25473
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-364.487
ELB improved by 2.42591
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-361.953
ELB improved by 2.53408
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-359.478
ELB improved by 2.47539
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-357.281
ELB improved by 2.19709
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-355.508
ELB improved by 1.77258
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-354.153
ELB improved by 1.35516
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-353.074
ELB improved by 1.07928
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-352.13
ELB improved by 0.943146
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-351.234
ELB improved by 0.896313
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-350.25
ELB improved by 0.983724
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-349.395
ELB improved by 0.855835
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-348.912
ELB improved by 0.482687
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-348.674
ELB improved by 0.237895
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-348.546
ELB improved by 0.127893
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-348.466
ELB improved by 0.0799081
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-348.409
ELB improved by 0.0567585
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-348.366
ELB improved by 0.0438343
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-348.33
ELB improved by 0.0355944
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-348.3
ELB improved by 0.0298108
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-348.275
ELB improved by 0.0254831
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-348.253
ELB improved by 0.0221028
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-348.233
ELB improved by 0.019382
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-348.216
ELB improved by 0.0171435
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-348.201
ELB improved by 0.0152713
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-348.187
ELB improved by 0.013686
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-348.175
ELB improved by 0.0123303
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-348.164
ELB improved by 0.0111622
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-348.153
ELB improved by 0.0101494
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-348.144
ELB improved by 0.00926666
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
1.112 0.093 1.223
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.013 | 0.006 | 0.020 | |
| getPIPs | 0.012 | 0.006 | 0.024 | |
| graper | 0.021 | 0.008 | 0.030 | |
| makeExampleData | 0.002 | 0.000 | 0.003 | |
| makeExampleDataWithUnequalGroups | 0.002 | 0.000 | 0.003 | |
| plotELBO | 0.114 | 0.008 | 0.127 | |
| plotGroupPenalties | 0.349 | 0.006 | 0.359 | |
| plotPosterior | 0.307 | 0.014 | 0.328 | |
| predict.graper | 0.213 | 0.030 | 0.249 | |
| print.graper | 0.012 | 0.006 | 0.017 | |