Britta Velten
| Snapshot Date: 2026-02-13 13:40 -0500 (Fri, 13 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 2026-02-14 11:32 -0500 (Sat, 14 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" | 4864 |
| 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 926/2352 | 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: 2026-02-14 00:28:32 -0500 (Sat, 14 Feb 2026) |
| EndedAt: 2026-02-14 00:30:04 -0500 (Sat, 14 Feb 2026) |
| EllapsedTime: 92.1 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=-873.837
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-576.437
ELB improved by 297.399
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-516.739
ELB improved by 59.6981
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-479.795
ELB improved by 36.9441
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.173
ELB improved by 16.6224
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.479
ELB improved by 7.69361
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.677
ELB improved by 4.80179
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.867
ELB improved by 3.81078
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.418
ELB improved by 3.44854
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.043
ELB improved by 3.3751
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.583
ELB improved by 3.46006
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.958
ELB improved by 3.6248
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.188
ELB improved by 3.77016
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.441
ELB improved by 3.74689
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.013
ELB improved by 3.42805
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.164
ELB improved by 2.84937
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.977
ELB improved by 2.18656
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.382
ELB improved by 1.59551
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.243
ELB improved by 1.13886
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.428
ELB improved by 0.814524
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.831
ELB improved by 0.597
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.375
ELB improved by 0.456077
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.011
ELB improved by 0.36451
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.708
ELB improved by 0.302698
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.449
ELB improved by 0.258768
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.223
ELB improved by 0.226072
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.022
ELB improved by 0.200888
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.841
ELB improved by 0.181033
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.676
ELB improved by 0.165135
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.524
ELB improved by 0.152274
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.382
ELB improved by 0.141804
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.249
ELB improved by 0.133257
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.122
ELB improved by 0.126291
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.002
ELB improved by 0.120662
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.886
ELB improved by 0.116202
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.773
ELB improved by 0.112816
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.662
ELB improved by 0.110473
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.553
ELB improved by 0.109213
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.444
ELB improved by 0.10915
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.333
ELB improved by 0.110483
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.22
ELB improved by 0.113521
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.101
ELB improved by 0.118697
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.975
ELB improved by 0.126567
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.837
ELB improved by 0.137708
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.685
ELB improved by 0.152415
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.514
ELB improved by 0.170267
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.324
ELB improved by 0.190132
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.113
ELB improved by 0.211325
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.878
ELB improved by 0.234891
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.615
ELB improved by 0.262674
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.321
ELB improved by 0.294587
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.993
ELB improved by 0.327544
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.635
ELB improved by 0.358242
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.248
ELB improved by 0.386934
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.831
ELB improved by 0.41721
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.378
ELB improved by 0.452899
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.882
ELB improved by 0.496252
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.334
ELB improved by 0.547447
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.731
ELB improved by 0.603538
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.074
ELB improved by 0.656499
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.382
ELB improved by 0.692354
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.687
ELB improved by 0.695082
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.031
ELB improved by 0.655678
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.452
ELB improved by 0.5789
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.972
ELB improved by 0.480586
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.593
ELB improved by 0.378787
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.306
ELB improved by 0.286766
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.095
ELB improved by 0.211063
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.942
ELB improved by 0.152851
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.832
ELB improved by 0.110151
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.752
ELB improved by 0.0797448
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.694
ELB improved by 0.058415
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.65
ELB improved by 0.0435099
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.617
ELB improved by 0.0330551
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.592
ELB improved by 0.0256589
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.571
ELB improved by 0.0203658
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.555
ELB improved by 0.0165266
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.541
ELB improved by 0.0137008
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.529
ELB improved by 0.0115883
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.519
ELB improved by 0.00998309
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-833.155
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-586.722
ELB improved by 246.433
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-528.09
ELB improved by 58.6324
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-483.541
ELB improved by 44.5487
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.644
ELB improved by 22.8975
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.181
ELB improved by 10.4624
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.94
ELB improved by 6.24111
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.828
ELB improved by 5.11218
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.814
ELB improved by 5.01368
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.686
ELB improved by 5.12793
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.811
ELB improved by 4.87521
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.861
ELB improved by 3.9505
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.167
ELB improved by 2.69368
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.49
ELB improved by 1.67666
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.423
ELB improved by 1.06698
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.685
ELB improved by 0.738964
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.125
ELB improved by 0.559533
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.67
ELB improved by 0.455406
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.278
ELB improved by 0.391281
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.928
ELB improved by 0.349882
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.606
ELB improved by 0.322363
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.302
ELB improved by 0.303912
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.01
ELB improved by 0.291626
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.727
ELB improved by 0.283462
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.449
ELB improved by 0.277794
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.176
ELB improved by 0.273392
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.906
ELB improved by 0.269597
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.64
ELB improved by 0.266407
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.376
ELB improved by 0.26432
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.111
ELB improved by 0.264144
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.844
ELB improved by 0.267035
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.569
ELB improved by 0.274905
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.278
ELB improved by 0.291331
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.955
ELB improved by 0.323288
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.571
ELB improved by 0.383771
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.081
ELB improved by 0.489613
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.452
ELB improved by 0.629924
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.722
ELB improved by 0.729847
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.961
ELB improved by 0.760179
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.186
ELB improved by 0.775877
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.386
ELB improved by 0.799334
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.564
ELB improved by 0.822243
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.732
ELB improved by 0.832081
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.914
ELB improved by 0.817659
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.142
ELB improved by 0.772583
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.443
ELB improved by 0.69858
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.839
ELB improved by 0.603909
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.341
ELB improved by 0.498468
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.948
ELB improved by 0.392739
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.65
ELB improved by 0.298136
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.427
ELB improved by 0.222491
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.261
ELB improved by 0.166571
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.134
ELB improved by 0.126531
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.036
ELB improved by 0.0977996
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.96
ELB improved by 0.0768294
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.898
ELB improved by 0.0612292
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.849
ELB improved by 0.049429
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.809
ELB improved by 0.0403793
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.775
ELB improved by 0.0333573
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.747
ELB improved by 0.0278519
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.724
ELB improved by 0.0234944
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.704
ELB improved by 0.0200145
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.687
ELB improved by 0.0172117
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.672
ELB improved by 0.0149356
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.659
ELB improved by 0.0130724
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.647
ELB improved by 0.0115352
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.637
ELB improved by 0.0102573
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.628
ELB improved by 0.00918709
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-888.881
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-577.406
ELB improved by 311.475
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-521.324
ELB improved by 56.082
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-488.86
ELB improved by 32.4634
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-475.549
ELB improved by 13.3108
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.376
ELB improved by 6.17345
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.068
ELB improved by 4.30771
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.174
ELB improved by 3.89395
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.352
ELB improved by 3.82195
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.689
ELB improved by 3.66381
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.438
ELB improved by 3.25096
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.817
ELB improved by 2.62041
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.862
ELB improved by 1.95489
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.446
ELB improved by 1.41622
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.399
ELB improved by 1.04666
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.593
ELB improved by 0.806496
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.955
ELB improved by 0.638125
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.455
ELB improved by 0.499488
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.074
ELB improved by 0.38124
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.782
ELB improved by 0.292086
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.55
ELB improved by 0.231963
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.358
ELB improved by 0.191941
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.194
ELB improved by 0.163864
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.051
ELB improved by 0.142926
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.925
ELB improved by 0.126531
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.812
ELB improved by 0.113219
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.71
ELB improved by 0.102108
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.617
ELB improved by 0.0926382
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.532
ELB improved by 0.0844379
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.455
ELB improved by 0.0772499
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.384
ELB improved by 0.0708904
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.319
ELB improved by 0.0652235
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.259
ELB improved by 0.0601452
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.203
ELB improved by 0.055574
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.152
ELB improved by 0.0514441
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.104
ELB improved by 0.0477014
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.06
ELB improved by 0.0443008
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.019
ELB improved by 0.0412039
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.98
ELB improved by 0.0383779
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.945
ELB improved by 0.0357943
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.911
ELB improved by 0.0334283
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.88
ELB improved by 0.0312583
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.851
ELB improved by 0.0292652
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.823
ELB improved by 0.027432
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.797
ELB improved by 0.0257439
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.773
ELB improved by 0.0241875
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.75
ELB improved by 0.0227509
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.729
ELB improved by 0.0214235
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.709
ELB improved by 0.0201958
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.69
ELB improved by 0.0190593
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.672
ELB improved by 0.0180061
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.655
ELB improved by 0.0170294
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.639
ELB improved by 0.0161229
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.623
ELB improved by 0.0152809
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.609
ELB improved by 0.0144983
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.595
ELB improved by 0.0137704
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.582
ELB improved by 0.013093
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.57
ELB improved by 0.0124621
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.558
ELB improved by 0.0118742
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.546
ELB improved by 0.0113262
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.535
ELB improved by 0.0108151
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.525
ELB improved by 0.0103381
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.515
ELB improved by 0.00989278
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-873.055
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-585.723
ELB improved by 287.332
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-527.098
ELB improved by 58.625
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-484.574
ELB improved by 42.5247
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.747
ELB improved by 22.8271
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.735
ELB improved by 10.0113
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.127
ELB improved by 4.60861
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.165
ELB improved by 2.96185
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.754
ELB improved by 2.41034
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.503
ELB improved by 2.25177
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.217
ELB improved by 2.28607
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.777
ELB improved by 2.43974
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.096
ELB improved by 2.68044
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.126
ELB improved by 2.97051
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.915
ELB improved by 3.21096
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.681
ELB improved by 3.2344
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.728
ELB improved by 2.95285
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.247
ELB improved by 2.48066
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.237
ELB improved by 2.00995
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.64
ELB improved by 1.59753
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.416
ELB improved by 1.22392
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.475
ELB improved by 0.94027
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.715
ELB improved by 0.760728
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.065
ELB improved by 0.649868
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.489
ELB improved by 0.575322
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.967
ELB improved by 0.522901
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.476
ELB improved by 0.490133
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408
ELB improved by 0.476432
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.52
ELB improved by 0.480219
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.021
ELB improved by 0.499148
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.493
ELB improved by 0.527496
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.94
ELB improved by 0.552935
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.376
ELB improved by 0.564157
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.812
ELB improved by 0.564075
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.247
ELB improved by 0.564589
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.672
ELB improved by 0.575571
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.066
ELB improved by 0.605921
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.395
ELB improved by 0.670409
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.597
ELB improved by 0.798079
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.574
ELB improved by 1.02319
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.292
ELB improved by 1.28184
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.901
ELB improved by 1.39153
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.551
ELB improved by 1.35007
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.318
ELB improved by 1.23292
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.254
ELB improved by 1.06345
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.392
ELB improved by 0.86207
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.733
ELB improved by 0.659539
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.247
ELB improved by 0.485474
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.893
ELB improved by 0.354673
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.626
ELB improved by 0.26654
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.412
ELB improved by 0.213886
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.223
ELB improved by 0.189614
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.037
ELB improved by 0.186038
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.85
ELB improved by 0.186879
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.681
ELB improved by 0.168777
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.551
ELB improved by 0.129424
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.461
ELB improved by 0.0900263
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.399
ELB improved by 0.0625612
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.354
ELB improved by 0.0453579
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.319
ELB improved by 0.0343082
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.292
ELB improved by 0.026829
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.271
ELB improved by 0.0215819
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.253
ELB improved by 0.017821
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.238
ELB improved by 0.0150739
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.225
ELB improved by 0.0130224
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.213
ELB improved by 0.0114523
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.203
ELB improved by 0.010221
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.194
ELB improved by 0.0092342
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.306 0.210 2.503
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.048 | 0.018 | 0.067 | |
| getPIPs | 0.054 | 0.010 | 0.062 | |
| graper | 0.083 | 0.015 | 0.099 | |
| makeExampleData | 0.011 | 0.000 | 0.010 | |
| makeExampleDataWithUnequalGroups | 0.011 | 0.001 | 0.013 | |
| plotELBO | 0.314 | 0.036 | 0.349 | |
| plotGroupPenalties | 1.090 | 0.051 | 1.142 | |
| plotPosterior | 0.633 | 0.024 | 0.657 | |
| predict.graper | 2.052 | 0.080 | 2.132 | |
| print.graper | 0.048 | 0.014 | 0.062 | |