Britta Velten
| Snapshot Date: 2026-02-19 13:40 -0500 (Thu, 19 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 2026-02-20 11:32 -0500 (Fri, 20 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" | 4869 |
| 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: 2026-02-20 00:17:47 -0500 (Fri, 20 Feb 2026) |
| EndedAt: 2026-02-20 00:19:18 -0500 (Fri, 20 Feb 2026) |
| EllapsedTime: 91.2 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=-850.184
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-594.612
ELB improved by 255.572
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-533.34
ELB improved by 61.2726
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-487.56
ELB improved by 45.7795
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.775
ELB improved by 23.7853
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.72
ELB improved by 10.0549
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.894
ELB improved by 4.82627
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.55
ELB improved by 3.34346
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.666
ELB improved by 2.88398
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.95
ELB improved by 2.71625
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.322
ELB improved by 2.62749
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.791
ELB improved by 2.53182
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.411
ELB improved by 2.37963
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.261
ELB improved by 2.15022
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.391
ELB improved by 1.87013
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.799
ELB improved by 1.59173
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.459
ELB improved by 1.34042
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.346
ELB improved by 1.11267
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.433
ELB improved by 0.91278
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.676
ELB improved by 0.75679
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.024
ELB improved by 0.652328
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.432
ELB improved by 0.59232
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.866
ELB improved by 0.565341
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.303
ELB improved by 0.563729
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.716
ELB improved by 0.586099
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.081
ELB improved by 0.635846
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.37
ELB improved by 0.710608
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.585
ELB improved by 0.784894
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.756
ELB improved by 0.828759
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.906
ELB improved by 0.850585
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.025
ELB improved by 0.880985
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.086
ELB improved by 0.939112
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.06
ELB improved by 1.02603
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.927
ELB improved by 1.13283
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.685
ELB improved by 1.24215
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.361
ELB improved by 1.32368
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.011
ELB improved by 1.34997
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.668
ELB improved by 1.3434
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.314
ELB improved by 1.35314
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.041
ELB improved by 1.27366
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.028
ELB improved by 1.01236
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.311
ELB improved by 0.717331
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.818
ELB improved by 0.493525
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.451
ELB improved by 0.366542
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.12
ELB improved by 0.330794
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.78
ELB improved by 0.340315
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.483
ELB improved by 0.29724
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.28
ELB improved by 0.202879
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.145
ELB improved by 0.135042
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.039
ELB improved by 0.105286
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.942
ELB improved by 0.0978521
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.839
ELB improved by 0.102935
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.724
ELB improved by 0.114234
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.603
ELB improved by 0.121229
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.492
ELB improved by 0.111095
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.408
ELB improved by 0.0846192
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.351
ELB improved by 0.0568726
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.313
ELB improved by 0.037713
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.286
ELB improved by 0.0268343
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.265
ELB improved by 0.0209014
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.248
ELB improved by 0.0174527
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.233
ELB improved by 0.0152036
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.219
ELB improved by 0.0135585
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.207
ELB improved by 0.0122483
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.196
ELB improved by 0.0111491
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.185
ELB improved by 0.0101997
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.176
ELB improved by 0.00936677
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-860.994
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-562.919
ELB improved by 298.075
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-506.25
ELB improved by 56.669
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-474.434
ELB improved by 31.8169
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.172
ELB improved by 13.2617
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.61
ELB improved by 6.56228
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.976
ELB improved by 4.63354
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.929
ELB improved by 4.04712
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.127
ELB improved by 3.80154
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.593
ELB improved by 3.53453
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.464
ELB improved by 3.12922
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.854
ELB improved by 2.60927
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.779
ELB improved by 2.07498
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.163
ELB improved by 1.61663
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.889
ELB improved by 1.27387
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.846
ELB improved by 1.04248
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.951
ELB improved by 0.895041
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.154
ELB improved by 0.796982
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.434
ELB improved by 0.719844
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.783
ELB improved by 0.651444
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.192
ELB improved by 0.590983
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.653
ELB improved by 0.538653
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.16
ELB improved by 0.493438
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.705
ELB improved by 0.454572
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.284
ELB improved by 0.421743
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.889
ELB improved by 0.394375
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.518
ELB improved by 0.371246
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.167
ELB improved by 0.351318
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.831
ELB improved by 0.335367
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.504
ELB improved by 0.326915
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.172
ELB improved by 0.332332
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.811
ELB improved by 0.3606
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.394
ELB improved by 0.417268
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.909
ELB improved by 0.485025
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.38
ELB improved by 0.529411
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.83
ELB improved by 0.550199
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.277
ELB improved by 0.552656
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.766
ELB improved by 0.511149
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.327
ELB improved by 0.438501
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.953
ELB improved by 0.374432
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.623
ELB improved by 0.329735
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.324
ELB improved by 0.29901
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.047
ELB improved by 0.276753
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.787
ELB improved by 0.260108
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.539
ELB improved by 0.24799
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.299
ELB improved by 0.240078
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.063
ELB improved by 0.236307
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.827
ELB improved by 0.236349
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.588
ELB improved by 0.23809
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.353
ELB improved by 0.235568
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.132
ELB improved by 0.221152
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.938
ELB improved by 0.193861
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.777
ELB improved by 0.161224
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.646
ELB improved by 0.130833
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.54
ELB improved by 0.10576
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.454
ELB improved by 0.0861123
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.383
ELB improved by 0.0709981
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.324
ELB improved by 0.0593899
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.273
ELB improved by 0.0504092
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.23
ELB improved by 0.0433852
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.192
ELB improved by 0.0378342
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.158
ELB improved by 0.0334193
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.129
ELB improved by 0.0299149
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.101
ELB improved by 0.0271789
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.076
ELB improved by 0.0251361
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.052
ELB improved by 0.0237691
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.029
ELB improved by 0.0231154
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.006
ELB improved by 0.0232674
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.982
ELB improved by 0.0243598
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.955
ELB improved by 0.0265151
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.926
ELB improved by 0.0296943
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.892
ELB improved by 0.0334191
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.856
ELB improved by 0.0365175
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.818
ELB improved by 0.0373766
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.783
ELB improved by 0.0350201
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.753
ELB improved by 0.0300802
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.729
ELB improved by 0.0243011
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.71
ELB improved by 0.0191641
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.694
ELB improved by 0.0152418
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.682
ELB improved by 0.0124592
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.671
ELB improved by 0.0105271
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.662
ELB improved by 0.0091743
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-892.929
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-567.293
ELB improved by 325.635
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-511.781
ELB improved by 55.5123
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-482.204
ELB improved by 29.5765
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.451
ELB improved by 12.7534
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.669
ELB improved by 6.78167
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.002
ELB improved by 4.66782
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.983
ELB improved by 4.01881
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.047
ELB improved by 3.93586
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.042
ELB improved by 4.00529
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.043
ELB improved by 3.99824
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.313
ELB improved by 3.73023
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.178
ELB improved by 3.13514
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.808
ELB improved by 2.36974
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.134
ELB improved by 1.67397
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.98
ELB improved by 1.15452
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.18
ELB improved by 0.799534
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.607
ELB improved by 0.572957
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.173
ELB improved by 0.434561
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.822
ELB improved by 0.350605
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.519
ELB improved by 0.303551
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.227
ELB improved by 0.29125
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.905
ELB improved by 0.321798
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.513
ELB improved by 0.392966
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.062
ELB improved by 0.450509
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.638
ELB improved by 0.423588
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.31
ELB improved by 0.328352
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.082
ELB improved by 0.227693
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.927
ELB improved by 0.155411
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.814
ELB improved by 0.112487
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.726
ELB improved by 0.0885091
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.651
ELB improved by 0.0746657
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.585
ELB improved by 0.0659738
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.525
ELB improved by 0.0599828
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.47
ELB improved by 0.0555218
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.418
ELB improved by 0.0520132
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.369
ELB improved by 0.0491518
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.322
ELB improved by 0.0467617
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.277
ELB improved by 0.0447314
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.234
ELB improved by 0.042984
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.193
ELB improved by 0.0414623
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.153
ELB improved by 0.0401218
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.114
ELB improved by 0.0389259
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.076
ELB improved by 0.0378444
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.039
ELB improved by 0.0368514
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.003
ELB improved by 0.0359249
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.968
ELB improved by 0.0350459
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.934
ELB improved by 0.0341983
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.9
ELB improved by 0.0333684
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.868
ELB improved by 0.0325449
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.836
ELB improved by 0.0317188
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.805
ELB improved by 0.0308829
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.775
ELB improved by 0.0300324
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.746
ELB improved by 0.029164
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.718
ELB improved by 0.0282765
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.69
ELB improved by 0.0273698
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.664
ELB improved by 0.0264457
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.638
ELB improved by 0.0255069
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.614
ELB improved by 0.0245571
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.59
ELB improved by 0.0236006
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.568
ELB improved by 0.0226424
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.546
ELB improved by 0.0216876
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.525
ELB improved by 0.0207412
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.505
ELB improved by 0.0198083
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.487
ELB improved by 0.0188934
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.469
ELB improved by 0.0180006
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.451
ELB improved by 0.0171336
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.435
ELB improved by 0.0162954
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.42
ELB improved by 0.0154883
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.405
ELB improved by 0.0147142
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.391
ELB improved by 0.0139743
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.378
ELB improved by 0.0132691
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.365
ELB improved by 0.0125989
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.353
ELB improved by 0.0119634
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.342
ELB improved by 0.0113622
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.331
ELB improved by 0.0107942
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.321
ELB improved by 0.0102584
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.311
ELB improved by 0.00975357
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-839.872
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-537.04
ELB improved by 302.832
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-485.508
ELB improved by 51.5324
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.048
ELB improved by 26.4591
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.803
ELB improved by 10.245
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.527
ELB improved by 5.27685
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.549
ELB improved by 3.97806
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.751
ELB improved by 3.7972
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.764
ELB improved by 3.98742
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.56
ELB improved by 4.20343
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.415
ELB improved by 4.14497
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.793
ELB improved by 3.62203
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.028
ELB improved by 2.76518
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.119
ELB improved by 1.90897
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.844
ELB improved by 1.27577
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.963
ELB improved by 0.880107
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.317
ELB improved by 0.646602
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.811
ELB improved by 0.505732
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.396
ELB improved by 0.414964
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.045
ELB improved by 0.351563
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.741
ELB improved by 0.303926
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.474
ELB improved by 0.266319
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.238
ELB improved by 0.23596
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.027
ELB improved by 0.211375
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.835
ELB improved by 0.191551
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.66
ELB improved by 0.17561
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.497
ELB improved by 0.162757
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.345
ELB improved by 0.152302
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.201
ELB improved by 0.14368
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.065
ELB improved by 0.136448
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.934
ELB improved by 0.13027
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.809
ELB improved by 0.124892
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.689
ELB improved by 0.120123
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.574
ELB improved by 0.115823
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.462
ELB improved by 0.111888
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.353
ELB improved by 0.108245
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.249
ELB improved by 0.104849
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.147
ELB improved by 0.101676
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.048
ELB improved by 0.0987205
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.952
ELB improved by 0.0959987
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.859
ELB improved by 0.0935437
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.767
ELB improved by 0.0914085
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.678
ELB improved by 0.089667
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.589
ELB improved by 0.0884163
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.501
ELB improved by 0.0877779
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.413
ELB improved by 0.0878931
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.325
ELB improved by 0.0889059
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.234
ELB improved by 0.0909213
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.14
ELB improved by 0.0939322
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.042
ELB improved by 0.0977295
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.94
ELB improved by 0.101866
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.834
ELB improved by 0.105769
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.725
ELB improved by 0.109017
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.614
ELB improved by 0.111583
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.5
ELB improved by 0.113816
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.384
ELB improved by 0.116214
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.264
ELB improved by 0.119228
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.141
ELB improved by 0.123214
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.013
ELB improved by 0.128493
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.877
ELB improved by 0.135412
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.733
ELB improved by 0.144345
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.577
ELB improved by 0.155527
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.409
ELB improved by 0.168534
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.228
ELB improved by 0.181292
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.038
ELB improved by 0.189491
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.849
ELB improved by 0.188819
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.67
ELB improved by 0.179606
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.503
ELB improved by 0.166906
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.348
ELB improved by 0.154967
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.203
ELB improved by 0.14466
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.068
ELB improved by 0.135198
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.942
ELB improved by 0.125792
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.826
ELB improved by 0.116072
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.72
ELB improved by 0.106008
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.624
ELB improved by 0.0957609
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.539
ELB improved by 0.0855756
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.463
ELB improved by 0.0757083
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.397
ELB improved by 0.0663793
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.339
ELB improved by 0.0577483
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.289
ELB improved by 0.0499093
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.246
ELB improved by 0.0428985
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.209
ELB improved by 0.0367082
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.178
ELB improved by 0.031301
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.152
ELB improved by 0.0266223
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.129
ELB improved by 0.0226081
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.11
ELB improved by 0.0191908
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.093
ELB improved by 0.0163021
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.08
ELB improved by 0.0138757
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.068
ELB improved by 0.0118487
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.058
ELB improved by 0.010163
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.049
ELB improved by 0.00876591
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.435 0.231 2.654
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.052 | 0.015 | 0.067 | |
| getPIPs | 0.049 | 0.013 | 0.063 | |
| graper | 0.085 | 0.015 | 0.099 | |
| makeExampleData | 0.009 | 0.001 | 0.011 | |
| makeExampleDataWithUnequalGroups | 0.013 | 0.000 | 0.013 | |
| plotELBO | 0.333 | 0.023 | 0.356 | |
| plotGroupPenalties | 1.067 | 0.061 | 1.128 | |
| plotPosterior | 0.624 | 0.021 | 0.644 | |
| predict.graper | 2.053 | 0.070 | 2.132 | |
| print.graper | 0.050 | 0.011 | 0.062 | |