Britta Velten
| Snapshot Date: 2026-02-03 13:40 -0500 (Tue, 03 Feb 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 Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-04 11:32 -0500 (Wed, 04 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4852 |
| 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 922/2347 | 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 | | ||||||||
| See other builds for graper in R Universe. | ||||||||||||||
|
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: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings graper_1.27.0.tar.gz |
| StartedAt: 2026-02-04 00:10:16 -0500 (Wed, 04 Feb 2026) |
| EndedAt: 2026-02-04 00:11:47 -0500 (Wed, 04 Feb 2026) |
| EllapsedTime: 91.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings graper_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.27.0’
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) predict.graper.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:23-24: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.27.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c fit_graper.cpp -o fit_graper.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -llapack -L/home/biocbuild/bbs-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-graper/00new/graper/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (graper)
graper.Rcheck/tests/testthat.Rout
R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(graper)
>
> test_check("graper")
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-844.301
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-601.277
ELB improved by 243.024
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-541.065
ELB improved by 60.2123
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-492.016
ELB improved by 49.0494
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.07
ELB improved by 27.9453
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.057
ELB improved by 12.0135
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.749
ELB improved by 6.3078
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.87
ELB improved by 4.87909
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.108
ELB improved by 4.76228
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.106
ELB improved by 5.00209
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.019
ELB improved by 5.08609
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.39
ELB improved by 4.62956
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.762
ELB improved by 3.62839
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.222
ELB improved by 2.53929
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.481
ELB improved by 1.74094
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.24
ELB improved by 1.24169
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.31
ELB improved by 0.929871
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.562
ELB improved by 0.747275
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.92
ELB improved by 0.642318
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.364
ELB improved by 0.556216
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.895
ELB improved by 0.468802
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.499
ELB improved by 0.395855
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.153
ELB improved by 0.346701
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.834
ELB improved by 0.318166
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.53
ELB improved by 0.304192
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.231
ELB improved by 0.299343
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.932
ELB improved by 0.298547
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.635
ELB improved by 0.297378
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.34
ELB improved by 0.294609
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.047
ELB improved by 0.293308
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.75
ELB improved by 0.297277
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.442
ELB improved by 0.307768
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.118
ELB improved by 0.323997
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.773
ELB improved by 0.34475
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.404
ELB improved by 0.369003
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.008
ELB improved by 0.395778
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.585
ELB improved by 0.423772
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.134
ELB improved by 0.451046
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.659
ELB improved by 0.474859
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.167
ELB improved by 0.49177
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.669
ELB improved by 0.498124
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.178
ELB improved by 0.490895
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.709
ELB improved by 0.468694
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.277
ELB improved by 0.432517
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.891
ELB improved by 0.385765
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.558
ELB improved by 0.333402
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.277
ELB improved by 0.280573
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.046
ELB improved by 0.23136
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.857
ELB improved by 0.188186
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.706
ELB improved by 0.151904
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.583
ELB improved by 0.122278
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.485
ELB improved by 0.0985108
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.405
ELB improved by 0.0796236
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.34
ELB improved by 0.0646735
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.288
ELB improved by 0.052844
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.244
ELB improved by 0.0434665
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.208
ELB improved by 0.0360088
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.178
ELB improved by 0.0300539
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.153
ELB improved by 0.0252777
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.131
ELB improved by 0.0214284
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.113
ELB improved by 0.0183107
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.097
ELB improved by 0.0157729
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.084
ELB improved by 0.0136967
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.072
ELB improved by 0.0119895
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.061
ELB improved by 0.0105789
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.052
ELB improved by 0.00940758
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-858.255
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-556.904
ELB improved by 301.351
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-498.887
ELB improved by 58.0166
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.631
ELB improved by 34.256
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.537
ELB improved by 14.0938
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.962
ELB improved by 6.57557
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.328
ELB improved by 4.6331
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.939
ELB improved by 4.3899
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.156
ELB improved by 4.78294
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.762
ELB improved by 5.3938
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.947
ELB improved by 5.81447
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.278
ELB improved by 5.66899
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.181
ELB improved by 5.09778
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.596
ELB improved by 4.58461
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.661
ELB improved by 3.93546
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.769
ELB improved by 2.89191
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.883
ELB improved by 1.88544
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.635
ELB improved by 1.24855
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.733
ELB improved by 0.90184
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.017
ELB improved by 0.716079
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.403
ELB improved by 0.613537
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.848
ELB improved by 0.555215
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.326
ELB improved by 0.522011
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.822
ELB improved by 0.50418
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.325
ELB improved by 0.49652
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.829
ELB improved by 0.496263
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.327
ELB improved by 0.50213
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.813
ELB improved by 0.513845
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.281
ELB improved by 0.531832
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.724
ELB improved by 0.556943
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.134
ELB improved by 0.590233
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.501
ELB improved by 0.632949
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.814
ELB improved by 0.687399
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.053
ELB improved by 0.760619
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.178
ELB improved by 0.87521
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.099
ELB improved by 1.07835
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.777
ELB improved by 1.32209
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.454
ELB improved by 1.32326
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.361
ELB improved by 1.09325
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.527
ELB improved by 0.834329
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.915
ELB improved by 0.61151
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.477
ELB improved by 0.437637
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.166
ELB improved by 0.310919
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.944
ELB improved by 0.222456
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.782
ELB improved by 0.161729
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.662
ELB improved by 0.119929
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.572
ELB improved by 0.0907742
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.501
ELB improved by 0.0700852
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.446
ELB improved by 0.0551396
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.402
ELB improved by 0.0441552
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.366
ELB improved by 0.0359489
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.337
ELB improved by 0.0297219
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.312
ELB improved by 0.024926
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.29
ELB improved by 0.0211791
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.272
ELB improved by 0.0182114
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.256
ELB improved by 0.0158298
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.242
ELB improved by 0.0138945
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.23
ELB improved by 0.0123031
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.219
ELB improved by 0.0109798
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.209
ELB improved by 0.0098679
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-867.615
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-552.129
ELB improved by 315.486
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-492.686
ELB improved by 59.4429
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.105
ELB improved by 28.5813
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.2
ELB improved by 10.9045
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.035
ELB improved by 5.16502
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.451
ELB improved by 3.58441
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.303
ELB improved by 3.14798
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.28
ELB improved by 3.02292
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.28
ELB improved by 2.99945
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.276
ELB improved by 3.00398
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.296
ELB improved by 2.98015
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.438
ELB improved by 2.85775
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.864
ELB improved by 2.5744
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.731
ELB improved by 2.13291
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.108
ELB improved by 1.62289
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.949
ELB improved by 1.15937
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.14
ELB improved by 0.808637
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.567
ELB improved by 0.57331
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.143
ELB improved by 0.42358
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.815
ELB improved by 0.327907
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.551
ELB improved by 0.264238
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.332
ELB improved by 0.219462
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.145
ELB improved by 0.186232
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.985
ELB improved by 0.160456
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.845
ELB improved by 0.139792
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.722
ELB improved by 0.122834
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.614
ELB improved by 0.108687
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.517
ELB improved by 0.09674
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.43
ELB improved by 0.0865523
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.353
ELB improved by 0.077793
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.282
ELB improved by 0.0702063
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.219
ELB improved by 0.0635916
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.161
ELB improved by 0.0577897
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.108
ELB improved by 0.0526729
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.06
ELB improved by 0.0481383
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.016
ELB improved by 0.0441021
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.976
ELB improved by 0.0404952
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.938
ELB improved by 0.0372606
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.904
ELB improved by 0.0343505
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.872
ELB improved by 0.0317246
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.843
ELB improved by 0.0293489
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.816
ELB improved by 0.0271941
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.79
ELB improved by 0.0252353
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.767
ELB improved by 0.0234508
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.745
ELB improved by 0.021822
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.725
ELB improved by 0.0203324
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.706
ELB improved by 0.0189678
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.688
ELB improved by 0.0177158
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.672
ELB improved by 0.0165651
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.656
ELB improved by 0.0155061
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.642
ELB improved by 0.0145302
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.628
ELB improved by 0.0136297
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.615
ELB improved by 0.0127976
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.603
ELB improved by 0.012028
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.592
ELB improved by 0.0113152
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.581
ELB improved by 0.0106545
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.571
ELB improved by 0.0100414
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.562
ELB improved by 0.00947188
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-830.843
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-558.291
ELB improved by 272.552
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-497.708
ELB improved by 60.5832
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.616
ELB improved by 35.0921
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.123
ELB improved by 12.4928
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.702
ELB improved by 4.42064
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.352
ELB improved by 2.34986
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.676
ELB improved by 1.67621
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.272
ELB improved by 1.40431
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.017
ELB improved by 1.25508
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.867
ELB improved by 1.14967
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.803
ELB improved by 1.06444
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.81
ELB improved by 0.992401
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.879
ELB improved by 0.931321
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.999
ELB improved by 0.879939
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.162
ELB improved by 0.836932
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.361
ELB improved by 0.800868
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.591
ELB improved by 0.770631
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.844
ELB improved by 0.74606
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.116
ELB improved by 0.728487
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.395
ELB improved by 0.720901
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.668
ELB improved by 0.727539
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.915
ELB improved by 0.752982
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.114
ELB improved by 0.801024
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.24
ELB improved by 0.873651
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.269
ELB improved by 0.970503
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.18
ELB improved by 1.08891
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.957
ELB improved by 1.22347
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.594
ELB improved by 1.36345
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.106
ELB improved by 1.48789
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.542
ELB improved by 1.56389
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.984
ELB improved by 1.5575
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.526
ELB improved by 1.45826
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.232
ELB improved by 1.29443
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.118
ELB improved by 1.11332
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.17
ELB improved by 0.948302
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.359
ELB improved by 0.810523
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.666
ELB improved by 0.693157
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.093
ELB improved by 0.573037
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.655
ELB improved by 0.438342
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.343
ELB improved by 0.311508
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.128
ELB improved by 0.215089
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.978
ELB improved by 0.150355
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.869
ELB improved by 0.108755
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.787
ELB improved by 0.0819939
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.723
ELB improved by 0.0644084
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.67
ELB improved by 0.0524945
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.626
ELB improved by 0.0441464
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.588
ELB improved by 0.0381042
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.554
ELB improved by 0.0336044
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.524
ELB improved by 0.030172
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.497
ELB improved by 0.0274997
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.471
ELB improved by 0.0253785
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.448
ELB improved by 0.0236576
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.426
ELB improved by 0.0222205
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.405
ELB improved by 0.0209722
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.385
ELB improved by 0.0198328
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.366
ELB improved by 0.0187369
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.348
ELB improved by 0.0176364
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.332
ELB improved by 0.0165047
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.316
ELB improved by 0.0153378
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.302
ELB improved by 0.0141515
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.289
ELB improved by 0.0129745
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.278
ELB improved by 0.0118396
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.267
ELB improved by 0.010775
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.257
ELB improved by 0.00980026
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.424 0.294 2.705
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.050 | 0.025 | 0.075 | |
| getPIPs | 0.049 | 0.014 | 0.063 | |
| graper | 0.086 | 0.013 | 0.099 | |
| makeExampleData | 0.008 | 0.003 | 0.010 | |
| makeExampleDataWithUnequalGroups | 0.012 | 0.001 | 0.013 | |
| plotELBO | 0.320 | 0.025 | 0.344 | |
| plotGroupPenalties | 1.099 | 0.055 | 1.154 | |
| plotPosterior | 0.641 | 0.023 | 0.665 | |
| predict.graper | 2.069 | 0.056 | 2.125 | |
| print.graper | 0.045 | 0.015 | 0.061 | |