Britta Velten
| Snapshot Date: 2026-02-08 13:40 -0500 (Sun, 08 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 2026-02-09 11:32 -0500 (Mon, 09 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" | 4858 |
| 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: 2026-02-09 00:20:28 -0500 (Mon, 09 Feb 2026) |
| EndedAt: 2026-02-09 00:21:59 -0500 (Mon, 09 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=-869.769
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-569.606
ELB improved by 300.164
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-512.006
ELB improved by 57.6003
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-478.108
ELB improved by 33.898
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.897
ELB improved by 15.211
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.062
ELB improved by 6.83472
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.995
ELB improved by 4.06646
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.696
ELB improved by 3.29927
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.497
ELB improved by 3.19937
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.086
ELB improved by 3.41104
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.335
ELB improved by 3.75024
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.342
ELB improved by 3.99361
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.494
ELB improved by 3.84829
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.304
ELB improved by 3.18965
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.025
ELB improved by 2.27885
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.53
ELB improved by 1.49512
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.548
ELB improved by 0.982298
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.862
ELB improved by 0.685232
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.347
ELB improved by 0.515613
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.932
ELB improved by 0.414875
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.58
ELB improved by 0.351851
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.269
ELB improved by 0.310868
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.985
ELB improved by 0.284082
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.717
ELB improved by 0.267622
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.458
ELB improved by 0.259789
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.197
ELB improved by 0.2602
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.928
ELB improved by 0.269324
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.64
ELB improved by 0.288201
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.321
ELB improved by 0.318607
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.957
ELB improved by 0.364276
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.525
ELB improved by 0.432235
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.998
ELB improved by 0.527107
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.368
ELB improved by 0.629366
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.672
ELB improved by 0.696742
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.947
ELB improved by 0.724146
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.212
ELB improved by 0.735864
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.469
ELB improved by 0.742271
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.725
ELB improved by 0.744319
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.984
ELB improved by 0.740556
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.256
ELB improved by 0.72857
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.549
ELB improved by 0.70666
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.874
ELB improved by 0.675018
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.239
ELB improved by 0.63541
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.649
ELB improved by 0.590146
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.107
ELB improved by 0.541518
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.615
ELB improved by 0.491901
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.171
ELB improved by 0.444068
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.77
ELB improved by 0.401159
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.404
ELB improved by 0.365961
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.065
ELB improved by 0.339439
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.746
ELB improved by 0.318899
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.448
ELB improved by 0.29763
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.179
ELB improved by 0.268747
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.948
ELB improved by 0.231231
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.758
ELB improved by 0.190396
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.605
ELB improved by 0.152295
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.485
ELB improved by 0.119942
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.392
ELB improved by 0.0937322
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.319
ELB improved by 0.0730104
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.262
ELB improved by 0.0569309
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.217
ELB improved by 0.0446857
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.182
ELB improved by 0.0355181
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.153
ELB improved by 0.0287341
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.129
ELB improved by 0.0237357
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.109
ELB improved by 0.0200418
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.092
ELB improved by 0.0172887
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.077
ELB improved by 0.0152136
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.063
ELB improved by 0.0136321
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.051
ELB improved by 0.0124177
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.039
ELB improved by 0.0114849
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.028
ELB improved by 0.0107773
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.018
ELB improved by 0.0102588
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.008
ELB improved by 0.00990826
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-867.217
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-567.979
ELB improved by 299.238
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-508.536
ELB improved by 59.4428
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.28
ELB improved by 35.2563
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.731
ELB improved by 16.549
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.278
ELB improved by 8.45284
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.233
ELB improved by 6.04544
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.503
ELB improved by 5.7301
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.622
ELB improved by 5.88088
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.704
ELB improved by 5.91825
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.206
ELB improved by 5.49742
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.614
ELB improved by 4.59242
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.133
ELB improved by 3.48122
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.659
ELB improved by 2.47357
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.912
ELB improved by 1.74739
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.626
ELB improved by 1.28571
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.645
ELB improved by 0.980662
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.874
ELB improved by 0.771159
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.243
ELB improved by 0.630573
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.716
ELB improved by 0.527192
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.277
ELB improved by 0.439656
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.908
ELB improved by 0.36841
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.59
ELB improved by 0.318016
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.305
ELB improved by 0.285464
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.041
ELB improved by 0.263907
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.794
ELB improved by 0.246418
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.567
ELB improved by 0.227125
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.364
ELB improved by 0.202889
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.189
ELB improved by 0.17514
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.041
ELB improved by 0.148352
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.915
ELB improved by 0.125981
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.806
ELB improved by 0.10873
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.711
ELB improved by 0.0956445
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.625
ELB improved by 0.0854685
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.548
ELB improved by 0.0772111
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.478
ELB improved by 0.0702153
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.414
ELB improved by 0.0640854
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.355
ELB improved by 0.0586101
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.301
ELB improved by 0.0537013
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.252
ELB improved by 0.049343
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.206
ELB improved by 0.0455491
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.164
ELB improved by 0.042335
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.124
ELB improved by 0.0397069
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.087
ELB improved by 0.0376629
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.05
ELB improved by 0.0361999
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.015
ELB improved by 0.0353189
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.98
ELB improved by 0.0350237
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.945
ELB improved by 0.0353094
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.909
ELB improved by 0.036137
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.871
ELB improved by 0.0373913
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.832
ELB improved by 0.0388305
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.792
ELB improved by 0.0400542
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.752
ELB improved by 0.0405491
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.712
ELB improved by 0.0398542
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.674
ELB improved by 0.0377941
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.64
ELB improved by 0.0346003
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.609
ELB improved by 0.0307881
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.582
ELB improved by 0.0268868
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.559
ELB improved by 0.0232528
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.539
ELB improved by 0.0200515
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.521
ELB improved by 0.0173263
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.506
ELB improved by 0.0150607
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.493
ELB improved by 0.0132097
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.481
ELB improved by 0.0117137
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.471
ELB improved by 0.0105079
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.461
ELB improved by 0.00953032
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-915.355
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-576.047
ELB improved by 339.308
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-513.525
ELB improved by 62.5223
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-477.013
ELB improved by 36.5115
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.6
ELB improved by 14.4132
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.97
ELB improved by 6.63043
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.906
ELB improved by 4.06362
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.87
ELB improved by 3.03582
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.21
ELB improved by 2.6601
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.589
ELB improved by 2.62152
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.785
ELB improved by 2.80409
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.609
ELB improved by 3.17549
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.914
ELB improved by 3.69486
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.716
ELB improved by 4.1985
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.361
ELB improved by 4.35472
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.447
ELB improved by 3.91428
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.406
ELB improved by 3.04115
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.266
ELB improved by 2.13949
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.814
ELB improved by 1.45224
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.808
ELB improved by 1.00615
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.06
ELB improved by 0.747296
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.442
ELB improved by 0.618003
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.861
ELB improved by 0.581144
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.241
ELB improved by 0.619985
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.532
ELB improved by 0.709071
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.75
ELB improved by 0.782265
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.951
ELB improved by 0.799014
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.157
ELB improved by 0.793702
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.355
ELB improved by 0.802269
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.509
ELB improved by 0.846179
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.552
ELB improved by 0.956276
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.397
ELB improved by 1.1551
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.021
ELB improved by 1.37618
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.418
ELB improved by 1.60327
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.67
ELB improved by 1.74824
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.084
ELB improved by 1.58563
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.741
ELB improved by 1.34326
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.591
ELB improved by 1.14989
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.559
ELB improved by 1.03163
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.606
ELB improved by 0.952774
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.86
ELB improved by 0.746255
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.391
ELB improved by 0.468812
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.106
ELB improved by 0.285893
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.918
ELB improved by 0.187217
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.787
ELB improved by 0.131376
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.69
ELB improved by 0.096963
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.616
ELB improved by 0.07436
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.557
ELB improved by 0.0588428
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.509
ELB improved by 0.0478122
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.469
ELB improved by 0.0397262
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.436
ELB improved by 0.0336282
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.407
ELB improved by 0.0289072
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.382
ELB improved by 0.0251643
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.359
ELB improved by 0.0221345
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.34
ELB improved by 0.0196379
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.322
ELB improved by 0.0175502
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.306
ELB improved by 0.0157836
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.292
ELB improved by 0.0142742
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.279
ELB improved by 0.0129746
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.267
ELB improved by 0.0118487
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.256
ELB improved by 0.0108682
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.246
ELB improved by 0.0100106
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.237
ELB improved by 0.00925778
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-860.796
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-602.795
ELB improved by 258.001
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-543.936
ELB improved by 58.8589
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-497.669
ELB improved by 46.2673
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.307
ELB improved by 24.3617
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.433
ELB improved by 10.8743
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.974
ELB improved by 6.4592
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.343
ELB improved by 5.63134
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.72
ELB improved by 5.62305
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.273
ELB improved by 5.44646
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.506
ELB improved by 4.76675
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.777
ELB improved by 3.72943
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.057
ELB improved by 2.72047
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.096
ELB improved by 1.96017
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.693
ELB improved by 1.40364
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.698
ELB improved by 0.995068
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.973
ELB improved by 0.724538
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.414
ELB improved by 0.559568
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.95
ELB improved by 0.463074
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.541
ELB improved by 0.409169
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.159
ELB improved by 0.382668
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.783
ELB improved by 0.375503
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.4
ELB improved by 0.38308
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420
ELB improved by 0.400331
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.581
ELB improved by 0.418805
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.151
ELB improved by 0.429739
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.72
ELB improved by 0.431182
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.293
ELB improved by 0.427046
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.872
ELB improved by 0.420536
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.46
ELB improved by 0.412545
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.057
ELB improved by 0.403237
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.664
ELB improved by 0.392915
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.282
ELB improved by 0.382088
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.91
ELB improved by 0.37138
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.549
ELB improved by 0.36154
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.195
ELB improved by 0.353656
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.845
ELB improved by 0.349729
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.491
ELB improved by 0.354078
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.115
ELB improved by 0.37654
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.678
ELB improved by 0.436844
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.128
ELB improved by 0.550078
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.476
ELB improved by 0.651642
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.836
ELB improved by 0.640181
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.269
ELB improved by 0.566534
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.774
ELB improved by 0.495442
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.34
ELB improved by 0.433736
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.963
ELB improved by 0.377674
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.637
ELB improved by 0.325956
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.358
ELB improved by 0.278114
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.125
ELB improved by 0.233297
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.934
ELB improved by 0.191033
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.782
ELB improved by 0.152247
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.663
ELB improved by 0.118844
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.571
ELB improved by 0.0921752
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.499
ELB improved by 0.0721838
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.441
ELB improved by 0.0577376
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.394
ELB improved by 0.0473875
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.354
ELB improved by 0.0398722
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.319
ELB improved by 0.034274
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.289
ELB improved by 0.0299791
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.263
ELB improved by 0.0265811
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.239
ELB improved by 0.0237989
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.218
ELB improved by 0.0214279
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.198
ELB improved by 0.0193208
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.181
ELB improved by 0.017384
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.165
ELB improved by 0.0155735
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.151
ELB improved by 0.0138836
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.139
ELB improved by 0.0123299
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.128
ELB improved by 0.0109318
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.119
ELB improved by 0.00970147
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.249 0.207 2.444
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.053 | 0.021 | 0.074 | |
| getPIPs | 0.050 | 0.013 | 0.063 | |
| graper | 0.077 | 0.023 | 0.100 | |
| makeExampleData | 0.009 | 0.002 | 0.011 | |
| makeExampleDataWithUnequalGroups | 0.011 | 0.002 | 0.013 | |
| plotELBO | 0.312 | 0.026 | 0.338 | |
| plotGroupPenalties | 1.059 | 0.058 | 1.116 | |
| plotPosterior | 0.618 | 0.019 | 0.638 | |
| predict.graper | 2.059 | 0.065 | 2.124 | |
| print.graper | 0.048 | 0.013 | 0.061 | |