Britta Velten
| Snapshot Date: 2026-04-02 13:40 -0400 (Thu, 02 Apr 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 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-03 11:38 -0400 (Fri, 03 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.6.0 alpha (2026-03-30 r89742) | 4894 |
| 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 935/2381 | 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: 2026-04-03 00:06:10 -0400 (Fri, 03 Apr 2026) |
| EndedAt: 2026-04-03 00:07:40 -0400 (Fri, 03 Apr 2026) |
| EllapsedTime: 90.3 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 version 4.6.0 alpha (2026-03-30 r89742)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-03 04:06:10 UTC
* 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 13.3.0-6ubuntu2~24.04.1) 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 13.3.0-6ubuntu2~24.04.1) 13.3.0’ g++ -std=gnu++20 -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++20 -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++20 -shared -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 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 version 4.6.0 alpha (2026-03-30 r89742)
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=-855.313
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-591.314
ELB improved by 263.999
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-530.063
ELB improved by 61.2515
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-481.86
ELB improved by 48.2023
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.029
ELB improved by 26.8317
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.597
ELB improved by 11.4319
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.812
ELB improved by 5.78426
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.785
ELB improved by 4.02706
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.259
ELB improved by 3.52605
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.847
ELB improved by 3.41186
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.444
ELB improved by 3.40346
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.062
ELB improved by 3.38185
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.819
ELB improved by 3.24317
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.914
ELB improved by 2.90499
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.533
ELB improved by 2.38125
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.739
ELB improved by 1.79346
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.461
ELB improved by 1.27832
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.559
ELB improved by 0.902318
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.901
ELB improved by 0.658074
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.393
ELB improved by 0.50769
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.977
ELB improved by 0.415819
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.618
ELB improved by 0.359246
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.293
ELB improved by 0.324794
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.988
ELB improved by 0.305335
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.691
ELB improved by 0.297025
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.393
ELB improved by 0.297777
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.086
ELB improved by 0.306482
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.764
ELB improved by 0.322591
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.418
ELB improved by 0.345876
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.042
ELB improved by 0.376269
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.628
ELB improved by 0.413753
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.17
ELB improved by 0.458261
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.66
ELB improved by 0.509564
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.093
ELB improved by 0.567067
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.464
ELB improved by 0.62943
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.77
ELB improved by 0.693948
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.014
ELB improved by 0.755689
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.207
ELB improved by 0.806608
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.372
ELB improved by 0.835349
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.543
ELB improved by 0.829306
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.762
ELB improved by 0.780954
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.066
ELB improved by 0.696161
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.47
ELB improved by 0.595413
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.965
ELB improved by 0.505372
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.512
ELB improved by 0.452781
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.042
ELB improved by 0.46961
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.449
ELB improved by 0.593023
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.644
ELB improved by 0.805805
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.649
ELB improved by 0.994807
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.632
ELB improved by 1.01641
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.89
ELB improved by 0.741978
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.454
ELB improved by 0.435959
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.197
ELB improved by 0.257302
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.034
ELB improved by 0.162969
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.923
ELB improved by 0.111399
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.841
ELB improved by 0.0814857
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.778
ELB improved by 0.0629669
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.727
ELB improved by 0.050754
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.685
ELB improved by 0.0422216
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.649
ELB improved by 0.0359519
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.618
ELB improved by 0.0311451
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.591
ELB improved by 0.0273308
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.567
ELB improved by 0.0242213
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.545
ELB improved by 0.0216334
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.526
ELB improved by 0.0194459
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.508
ELB improved by 0.0175752
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.492
ELB improved by 0.0159614
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.477
ELB improved by 0.0145598
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.464
ELB improved by 0.0133366
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.452
ELB improved by 0.0122647
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.441
ELB improved by 0.0113226
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.43
ELB improved by 0.0104925
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.42
ELB improved by 0.00975972
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-870.705
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-559.326
ELB improved by 311.379
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-501.576
ELB improved by 57.7508
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.584
ELB improved by 30.991
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.63
ELB improved by 12.9544
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.484
ELB improved by 6.1459
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.8
ELB improved by 4.68398
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.182
ELB improved by 4.61862
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.119
ELB improved by 5.06264
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.332
ELB improved by 5.78656
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.845
ELB improved by 6.48742
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.259
ELB improved by 6.58638
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.679
ELB improved by 5.57963
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.708
ELB improved by 3.97063
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.085
ELB improved by 2.62302
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.327
ELB improved by 1.75807
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.104
ELB improved by 1.2235
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.213
ELB improved by 0.890533
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.523
ELB improved by 0.690649
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.949
ELB improved by 0.573316
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.445
ELB improved by 0.503758
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.983
ELB improved by 0.462024
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.546
ELB improved by 0.437371
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.123
ELB improved by 0.422748
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.712
ELB improved by 0.41083
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.318
ELB improved by 0.394099
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.949
ELB improved by 0.369832
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.607
ELB improved by 0.341862
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.292
ELB improved by 0.314921
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.001
ELB improved by 0.290769
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.732
ELB improved by 0.269269
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.482
ELB improved by 0.249969
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.249
ELB improved by 0.232566
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.032
ELB improved by 0.216871
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.83
ELB improved by 0.202727
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.64
ELB improved by 0.189973
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.461
ELB improved by 0.178443
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.293
ELB improved by 0.167972
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.135
ELB improved by 0.158395
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.985
ELB improved by 0.14956
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.844
ELB improved by 0.141325
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.71
ELB improved by 0.133563
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.584
ELB improved by 0.12616
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.465
ELB improved by 0.119021
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.353
ELB improved by 0.112066
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.248
ELB improved by 0.105235
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.149
ELB improved by 0.0984914
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.058
ELB improved by 0.0918163
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.972
ELB improved by 0.0852141
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.894
ELB improved by 0.0787086
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.821
ELB improved by 0.0723395
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.755
ELB improved by 0.0661576
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.695
ELB improved by 0.0602186
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.64
ELB improved by 0.0545764
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.591
ELB improved by 0.0492777
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.547
ELB improved by 0.0443578
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.507
ELB improved by 0.0398382
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.471
ELB improved by 0.0357267
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.439
ELB improved by 0.0320185
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.41
ELB improved by 0.0286982
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.385
ELB improved by 0.0257432
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.362
ELB improved by 0.0231256
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.341
ELB improved by 0.0208149
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.322
ELB improved by 0.0187798
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.305
ELB improved by 0.0169897
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.29
ELB improved by 0.0154152
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.276
ELB improved by 0.0140292
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.263
ELB improved by 0.0128068
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.251
ELB improved by 0.0117257
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.24
ELB improved by 0.010766
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.23
ELB improved by 0.0099104
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-856.929
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-562.602
ELB improved by 294.328
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-504.999
ELB improved by 57.6028
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.027
ELB improved by 31.9713
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.411
ELB improved by 12.6161
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.871
ELB improved by 5.5408
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.019
ELB improved by 3.85184
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.352
ELB improved by 3.66671
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.377
ELB improved by 3.97521
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.951
ELB improved by 4.42605
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.272
ELB improved by 4.67883
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.884
ELB improved by 4.38802
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.32
ELB improved by 3.56355
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.675
ELB improved by 2.64497
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.691
ELB improved by 1.98488
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.088
ELB improved by 1.60267
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.714
ELB improved by 1.37341
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.482
ELB improved by 1.23291
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.318
ELB improved by 1.16355
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.172
ELB improved by 1.14608
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.997
ELB improved by 1.17476
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.726
ELB improved by 1.27071
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.249
ELB improved by 1.47765
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.487
ELB improved by 1.76147
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.575
ELB improved by 1.91257
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.659
ELB improved by 1.91613
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.782
ELB improved by 1.87715
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.98
ELB improved by 1.80182
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.271
ELB improved by 1.70824
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.567
ELB improved by 1.70462
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.726
ELB improved by 1.8404
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.173
ELB improved by 1.55311
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.252
ELB improved by 0.921436
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.736
ELB improved by 0.516219
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.418
ELB improved by 0.317974
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.202
ELB improved by 0.215707
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.044
ELB improved by 0.157737
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.921
ELB improved by 0.12345
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.816
ELB improved by 0.104462
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.719
ELB improved by 0.0974955
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.618
ELB improved by 0.10108
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.506
ELB improved by 0.112154
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.383
ELB improved by 0.122628
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.26
ELB improved by 0.12262
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.149
ELB improved by 0.111484
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.051
ELB improved by 0.09835
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.96
ELB improved by 0.0901946
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.873
ELB improved by 0.0874386
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.785
ELB improved by 0.0877066
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.696
ELB improved by 0.0893651
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.603
ELB improved by 0.0931311
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.501
ELB improved by 0.101272
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.387
ELB improved by 0.113914
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.263
ELB improved by 0.12492
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.138
ELB improved by 0.124706
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.025
ELB improved by 0.112673
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.925
ELB improved by 0.0997397
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.83
ELB improved by 0.095651
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.726
ELB improved by 0.104192
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.601
ELB improved by 0.125106
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.451
ELB improved by 0.149072
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.298
ELB improved by 0.153787
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.169
ELB improved by 0.128792
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.074
ELB improved by 0.0945986
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.003
ELB improved by 0.0712142
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.943
ELB improved by 0.0603099
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.887
ELB improved by 0.0556546
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.836
ELB improved by 0.0513534
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.791
ELB improved by 0.0446747
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.755
ELB improved by 0.0361886
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.727
ELB improved by 0.0278302
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.706
ELB improved by 0.0209603
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.69
ELB improved by 0.0159093
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.678
ELB improved by 0.0124121
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.668
ELB improved by 0.0100476
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.659
ELB improved by 0.00844416
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-886.146
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-561.888
ELB improved by 324.258
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-499.127
ELB improved by 62.7608
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.128
ELB improved by 33.9997
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.162
ELB improved by 13.9658
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.042
ELB improved by 6.11953
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.385
ELB improved by 3.6568
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.556
ELB improved by 2.8299
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.043
ELB improved by 2.51291
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.64
ELB improved by 2.40247
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.255
ELB improved by 2.38546
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.847
ELB improved by 2.40744
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.424
ELB improved by 2.42315
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.043
ELB improved by 2.38153
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.803
ELB improved by 2.23973
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.815
ELB improved by 1.98784
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.157
ELB improved by 1.65805
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.846
ELB improved by 1.31118
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.843
ELB improved by 1.00314
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.087
ELB improved by 0.75532
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.527
ELB improved by 0.560794
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.115
ELB improved by 0.411352
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.811
ELB improved by 0.303939
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.58
ELB improved by 0.231145
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.398
ELB improved by 0.182308
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.249
ELB improved by 0.148666
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.125
ELB improved by 0.124571
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.018
ELB improved by 0.106642
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.925
ELB improved by 0.0928385
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.843
ELB improved by 0.0818895
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.77
ELB improved by 0.0729748
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.705
ELB improved by 0.0655517
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.645
ELB improved by 0.0592545
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.592
ELB improved by 0.0538313
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.542
ELB improved by 0.0491048
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.497
ELB improved by 0.0449469
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.456
ELB improved by 0.041262
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.418
ELB improved by 0.0379769
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.383
ELB improved by 0.0350341
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.351
ELB improved by 0.0323871
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.321
ELB improved by 0.0299978
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.293
ELB improved by 0.0278345
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.267
ELB improved by 0.0258706
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.243
ELB improved by 0.0240832
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.221
ELB improved by 0.0224529
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.2
ELB improved by 0.0209628
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.18
ELB improved by 0.0195983
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.162
ELB improved by 0.0183465
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.144
ELB improved by 0.0171963
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.128
ELB improved by 0.0161378
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.113
ELB improved by 0.0151624
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.099
ELB improved by 0.0142622
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.085
ELB improved by 0.0134304
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.073
ELB improved by 0.012661
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.061
ELB improved by 0.0119483
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.05
ELB improved by 0.0112876
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.039
ELB improved by 0.0106744
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.029
ELB improved by 0.0101048
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.019
ELB improved by 0.00957513
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.293 0.223 2.504
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.055 | 0.015 | 0.070 | |
| getPIPs | 0.049 | 0.013 | 0.062 | |
| graper | 0.081 | 0.018 | 0.099 | |
| makeExampleData | 0.009 | 0.001 | 0.010 | |
| makeExampleDataWithUnequalGroups | 0.009 | 0.004 | 0.013 | |
| plotELBO | 0.324 | 0.029 | 0.353 | |
| plotGroupPenalties | 1.066 | 0.063 | 1.129 | |
| plotPosterior | 0.604 | 0.025 | 0.629 | |
| predict.graper | 2.096 | 0.072 | 2.172 | |
| print.graper | 0.054 | 0.008 | 0.062 | |