Britta Velten
| Snapshot Date: 2026-02-18 13:40 -0500 (Wed, 18 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 2026-02-19 11:32 -0500 (Thu, 19 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" | 4868 |
| 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 926/2354 | 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: 2026-02-19 00:35:14 -0500 (Thu, 19 Feb 2026) |
| EndedAt: 2026-02-19 00:36:48 -0500 (Thu, 19 Feb 2026) |
| EllapsedTime: 94.1 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=-893.788
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-602.827
ELB improved by 290.961
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-541.839
ELB improved by 60.9883
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-498.251
ELB improved by 43.5872
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-478.69
ELB improved by 19.5614
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.466
ELB improved by 8.22397
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.546
ELB improved by 4.92025
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.642
ELB improved by 3.90408
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.083
ELB improved by 3.55891
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.721
ELB improved by 3.36209
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.643
ELB improved by 3.07802
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.044
ELB improved by 2.5987
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.076
ELB improved by 1.96847
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.715
ELB improved by 1.36011
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.808
ELB improved by 0.907169
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.187
ELB improved by 0.621597
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.733
ELB improved by 0.453305
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.38
ELB improved by 0.353194
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.09
ELB improved by 0.29045
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.841
ELB improved by 0.248492
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.623
ELB improved by 0.218733
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.426
ELB improved by 0.196641
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.246
ELB improved by 0.179712
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.08
ELB improved by 0.166482
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.924
ELB improved by 0.156041
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.776
ELB improved by 0.147788
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.635
ELB improved by 0.141305
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.498
ELB improved by 0.136284
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.366
ELB improved by 0.132489
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.236
ELB improved by 0.129731
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.108
ELB improved by 0.127854
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.981
ELB improved by 0.126721
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.855
ELB improved by 0.126211
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.729
ELB improved by 0.126213
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.602
ELB improved by 0.126624
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.475
ELB improved by 0.127349
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.347
ELB improved by 0.128304
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.217
ELB improved by 0.129414
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.087
ELB improved by 0.130615
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.955
ELB improved by 0.131859
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.822
ELB improved by 0.133106
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.687
ELB improved by 0.134329
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.552
ELB improved by 0.135504
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.415
ELB improved by 0.136612
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.278
ELB improved by 0.137628
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.139
ELB improved by 0.138523
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439
ELB improved by 0.139255
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.86
ELB improved by 0.139771
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.72
ELB improved by 0.140007
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.58
ELB improved by 0.139887
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.441
ELB improved by 0.139334
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.303
ELB improved by 0.138269
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.166
ELB improved by 0.136625
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.032
ELB improved by 0.134348
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.9
ELB improved by 0.131409
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.772
ELB improved by 0.127805
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.649
ELB improved by 0.123564
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.53
ELB improved by 0.118743
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.417
ELB improved by 0.113429
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.309
ELB improved by 0.107729
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.207
ELB improved by 0.101766
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.112
ELB improved by 0.0956702
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.022
ELB improved by 0.0895722
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.938
ELB improved by 0.0835983
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.861
ELB improved by 0.0778655
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.788
ELB improved by 0.0724802
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.721
ELB improved by 0.0675388
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.657
ELB improved by 0.0631303
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.598
ELB improved by 0.0593392
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.542
ELB improved by 0.0562496
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.488
ELB improved by 0.0539467
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.435
ELB improved by 0.0525149
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.383
ELB improved by 0.0520285
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.331
ELB improved by 0.0525337
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.277
ELB improved by 0.0540264
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.22
ELB improved by 0.0564442
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.161
ELB improved by 0.059711
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.097
ELB improved by 0.063877
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.027
ELB improved by 0.0693621
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.95
ELB improved by 0.0772509
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.861
ELB improved by 0.0895212
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.752
ELB improved by 0.108927
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.614
ELB improved by 0.13762
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.441
ELB improved by 0.17291
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.239
ELB improved by 0.202422
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.028
ELB improved by 0.210273
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.836
ELB improved by 0.192741
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.677
ELB improved by 0.158407
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.559
ELB improved by 0.11869
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.475
ELB improved by 0.0833875
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.418
ELB improved by 0.0573489
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.378
ELB improved by 0.040316
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.348
ELB improved by 0.0297572
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.325
ELB improved by 0.023193
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.306
ELB improved by 0.0189468
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.29
ELB improved by 0.0160477
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.276
ELB improved by 0.0139627
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.263
ELB improved by 0.0123971
iteration 99
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.252
ELB improved by 0.011181
iteration 100
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.242
ELB improved by 0.0102111
iteration 101
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.232
ELB improved by 0.00942135
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-830.251
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-575.824
ELB improved by 254.427
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-513.965
ELB improved by 61.8593
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.308
ELB improved by 47.6575
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.771
ELB improved by 24.5368
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.951
ELB improved by 8.81962
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.888
ELB improved by 4.06326
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.354
ELB improved by 2.53386
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.459
ELB improved by 1.89533
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.881
ELB improved by 1.57742
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.483
ELB improved by 1.39865
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.193
ELB improved by 1.28939
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.972
ELB improved by 1.22137
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.787
ELB improved by 1.18454
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.611
ELB improved by 1.17592
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.417
ELB improved by 1.19397
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.182
ELB improved by 1.23493
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.893
ELB improved by 1.28926
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.554
ELB improved by 1.33885
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.195
ELB improved by 1.35943
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.864
ELB improved by 1.33105
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.615
ELB improved by 1.24922
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.49
ELB improved by 1.12428
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.518
ELB improved by 0.972427
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.706
ELB improved by 0.811682
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.047
ELB improved by 0.659492
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.52
ELB improved by 0.527028
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.102
ELB improved by 0.417463
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.773
ELB improved by 0.329435
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.513
ELB improved by 0.260201
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.306
ELB improved by 0.206768
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.14
ELB improved by 0.166141
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.004
ELB improved by 0.135507
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.892
ELB improved by 0.112415
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.797
ELB improved by 0.0948823
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.716
ELB improved by 0.081392
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.645
ELB improved by 0.0708295
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.582
ELB improved by 0.0623966
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.527
ELB improved by 0.0555293
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.477
ELB improved by 0.0498307
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.432
ELB improved by 0.0450205
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.391
ELB improved by 0.0408995
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.354
ELB improved by 0.0373239
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.32
ELB improved by 0.0341886
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.288
ELB improved by 0.031415
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.259
ELB improved by 0.0289437
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.232
ELB improved by 0.0267286
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.208
ELB improved by 0.0247333
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.185
ELB improved by 0.0229285
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.164
ELB improved by 0.0212904
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.144
ELB improved by 0.0197991
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.125
ELB improved by 0.0184381
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.108
ELB improved by 0.017193
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.092
ELB improved by 0.0160519
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.077
ELB improved by 0.0150041
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.063
ELB improved by 0.0140406
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.05
ELB improved by 0.0131531
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.038
ELB improved by 0.0123346
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.026
ELB improved by 0.0115788
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.015
ELB improved by 0.01088
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.005
ELB improved by 0.0102332
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.995
ELB improved by 0.00963397
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-884.908
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-588.834
ELB improved by 296.073
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-526.607
ELB improved by 62.2271
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-483.145
ELB improved by 43.462
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.323
ELB improved by 20.8222
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.294
ELB improved by 10.0289
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.077
ELB improved by 8.21685
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.337
ELB improved by 8.73979
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.428
ELB improved by 9.9095
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.132
ELB improved by 10.2958
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.167
ELB improved by 8.96504
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.566
ELB improved by 6.60104
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.168
ELB improved by 4.39788
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.286
ELB improved by 2.88166
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.315
ELB improved by 1.97123
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.839
ELB improved by 1.47625
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.6
ELB improved by 1.23851
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.507
ELB improved by 1.09362
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.622
ELB improved by 0.885367
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.967
ELB improved by 0.654434
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.468
ELB improved by 0.498767
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.059
ELB improved by 0.40916
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.712
ELB improved by 0.347368
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.424
ELB improved by 0.287494
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.198
ELB improved by 0.225872
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.025
ELB improved by 0.173871
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.887
ELB improved by 0.137437
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.774
ELB improved by 0.113384
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.677
ELB improved by 0.0967483
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.593
ELB improved by 0.0842961
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.518
ELB improved by 0.0743751
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.452
ELB improved by 0.0661686
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.393
ELB improved by 0.059236
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.34
ELB improved by 0.053306
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.291
ELB improved by 0.0481901
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.248
ELB improved by 0.0437474
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.208
ELB improved by 0.0398678
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.171
ELB improved by 0.036463
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.138
ELB improved by 0.0334615
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.107
ELB improved by 0.0308046
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.079
ELB improved by 0.0284436
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.052
ELB improved by 0.0263382
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.028
ELB improved by 0.0244545
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.005
ELB improved by 0.022764
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.984
ELB improved by 0.0212426
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.964
ELB improved by 0.0198698
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.945
ELB improved by 0.0186279
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.928
ELB improved by 0.0175019
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.911
ELB improved by 0.0164787
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.896
ELB improved by 0.015547
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.881
ELB improved by 0.0146971
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.867
ELB improved by 0.0139204
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.854
ELB improved by 0.0132094
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.841
ELB improved by 0.0125575
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.829
ELB improved by 0.0119589
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.818
ELB improved by 0.0114086
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.807
ELB improved by 0.010902
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.797
ELB improved by 0.0104351
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.787
ELB improved by 0.0100044
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.777
ELB improved by 0.00960671
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-837.782
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-590.684
ELB improved by 247.098
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-528.901
ELB improved by 61.783
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-478.741
ELB improved by 50.1596
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.153
ELB improved by 25.588
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.2
ELB improved by 8.95351
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.018
ELB improved by 4.18191
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.043
ELB improved by 2.97535
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.415
ELB improved by 2.62719
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.742
ELB improved by 2.67366
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.799
ELB improved by 2.9431
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.472
ELB improved by 3.32633
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.806
ELB improved by 3.66624
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.07
ELB improved by 3.73602
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.686
ELB improved by 3.38399
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.968
ELB improved by 2.71848
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.941
ELB improved by 2.02665
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.428
ELB improved by 1.51296
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.219
ELB improved by 1.20912
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.158
ELB improved by 1.06052
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.152
ELB improved by 1.00586
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.153
ELB improved by 0.999818
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.14
ELB improved by 1.01289
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.111
ELB improved by 1.02823
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.073
ELB improved by 1.03824
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.033
ELB improved by 1.04058
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.998
ELB improved by 1.03418
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.982
ELB improved by 1.0165
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.999
ELB improved by 0.983083
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.069
ELB improved by 0.929434
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.215
ELB improved by 0.854075
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.455
ELB improved by 0.760627
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.797
ELB improved by 0.657427
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.243
ELB improved by 0.554685
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.782
ELB improved by 0.460883
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.401
ELB improved by 0.380636
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.086
ELB improved by 0.315054
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.822
ELB improved by 0.263728
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.596
ELB improved by 0.226618
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.391
ELB improved by 0.205071
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.189
ELB improved by 0.201588
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.974
ELB improved by 0.215095
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.747
ELB improved by 0.227
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.543
ELB improved by 0.203611
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.396
ELB improved by 0.147326
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.301
ELB improved by 0.095161
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.238
ELB improved by 0.0626975
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.193
ELB improved by 0.0449406
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.158
ELB improved by 0.0350339
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.129
ELB improved by 0.0290028
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.104
ELB improved by 0.024935
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.082
ELB improved by 0.0219363
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.063
ELB improved by 0.0195755
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.045
ELB improved by 0.0176318
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.029
ELB improved by 0.0159842
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.015
ELB improved by 0.0145611
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.001
ELB improved by 0.0133164
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.989
ELB improved by 0.0122186
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.978
ELB improved by 0.0112443
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.967
ELB improved by 0.0103759
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.958
ELB improved by 0.00959899
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.300 0.189 2.477
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.055 | 0.011 | 0.066 | |
| getPIPs | 0.054 | 0.010 | 0.064 | |
| graper | 0.080 | 0.023 | 0.102 | |
| makeExampleData | 0.007 | 0.003 | 0.011 | |
| makeExampleDataWithUnequalGroups | 0.010 | 0.003 | 0.013 | |
| plotELBO | 0.327 | 0.036 | 0.363 | |
| plotGroupPenalties | 1.063 | 0.050 | 1.113 | |
| plotPosterior | 0.619 | 0.022 | 0.640 | |
| predict.graper | 2.063 | 0.056 | 2.118 | |
| print.graper | 0.049 | 0.012 | 0.062 | |