Britta Velten
| Snapshot Date: 2026-02-16 13:40 -0500 (Mon, 16 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 2026-02-17 11:32 -0500 (Tue, 17 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" | 4865 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 926/2352 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.27.0 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for graper in R Universe. | ||||||||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: graper |
| Version: 1.27.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings graper_1.27.0.tar.gz |
| StartedAt: 2026-02-17 00:24:23 -0500 (Tue, 17 Feb 2026) |
| EndedAt: 2026-02-17 00:25:54 -0500 (Tue, 17 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=-849.023
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-564.124
ELB improved by 284.9
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-501.187
ELB improved by 62.9365
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.532
ELB improved by 40.6551
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.947
ELB improved by 17.5856
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.39
ELB improved by 7.55701
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.716
ELB improved by 4.67348
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.004
ELB improved by 3.71205
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.56
ELB improved by 3.44443
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.102
ELB improved by 3.45731
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.533
ELB improved by 3.56895
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.887
ELB improved by 3.64611
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.328
ELB improved by 3.55961
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.103
ELB improved by 3.22451
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.45
ELB improved by 2.65261
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.479
ELB improved by 1.97171
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.106
ELB improved by 1.373
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.153
ELB improved by 0.953203
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.462
ELB improved by 0.690083
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.933
ELB improved by 0.529267
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.503
ELB improved by 0.429801
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.136
ELB improved by 0.366996
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.809
ELB improved by 0.327009
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.507
ELB improved by 0.302362
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.219
ELB improved by 0.288409
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.937
ELB improved by 0.281731
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.657
ELB improved by 0.279797
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.376
ELB improved by 0.280809
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.093
ELB improved by 0.283487
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.806
ELB improved by 0.28688
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.516
ELB improved by 0.290235
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.223
ELB improved by 0.292945
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.928
ELB improved by 0.29453
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.634
ELB improved by 0.294653
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.34
ELB improved by 0.293138
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.05
ELB improved by 0.289995
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.765
ELB improved by 0.285429
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.485
ELB improved by 0.27983
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.211
ELB improved by 0.273772
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.943
ELB improved by 0.268021
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.68
ELB improved by 0.263604
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.418
ELB improved by 0.261985
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.152
ELB improved by 0.265371
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.875
ELB improved by 0.277061
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.574
ELB improved by 0.301037
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.236
ELB improved by 0.338279
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.857
ELB improved by 0.378628
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.455
ELB improved by 0.402622
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.05
ELB improved by 0.404817
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.653
ELB improved by 0.397046
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.265
ELB improved by 0.387677
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.888
ELB improved by 0.377611
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.522
ELB improved by 0.36532
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.173
ELB improved by 0.349333
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.844
ELB improved by 0.329385
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.536
ELB improved by 0.307458
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.248
ELB improved by 0.288233
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.97
ELB improved by 0.277947
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.689
ELB improved by 0.280496
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.399
ELB improved by 0.290151
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.11
ELB improved by 0.289373
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.843
ELB improved by 0.267253
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.606
ELB improved by 0.236698
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.388
ELB improved by 0.218293
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.164
ELB improved by 0.223198
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.915
ELB improved by 0.249848
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.643
ELB improved by 0.271909
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.394
ELB improved by 0.248898
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.208
ELB improved by 0.185867
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.084
ELB improved by 0.123958
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.001
ELB improved by 0.0828535
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.94
ELB improved by 0.0606799
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.89
ELB improved by 0.0508846
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.841
ELB improved by 0.0482209
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.792
ELB improved by 0.0488679
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.743
ELB improved by 0.0492705
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.697
ELB improved by 0.0461679
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.658
ELB improved by 0.0386006
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.629
ELB improved by 0.0289847
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.609
ELB improved by 0.020565
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.594
ELB improved by 0.0146913
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.583
ELB improved by 0.0110181
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.574
ELB improved by 0.00877281
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-867.775
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-596.891
ELB improved by 270.884
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-540.501
ELB improved by 56.3908
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-495.948
ELB improved by 44.5522
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.279
ELB improved by 22.6699
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.634
ELB improved by 8.64441
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.628
ELB improved by 4.00621
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.673
ELB improved by 2.95508
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.976
ELB improved by 2.69712
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.329
ELB improved by 2.64652
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.679
ELB improved by 2.64988
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.016
ELB improved by 2.66297
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.35
ELB improved by 2.66689
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.729
ELB improved by 2.62076
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.285
ELB improved by 2.44388
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.2
ELB improved by 2.08513
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.576
ELB improved by 1.62353
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.375
ELB improved by 1.2015
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.485
ELB improved by 0.890095
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.802
ELB improved by 0.682722
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.251
ELB improved by 0.551121
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.779
ELB improved by 0.471496
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.353
ELB improved by 0.425917
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.953
ELB improved by 0.400819
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.566
ELB improved by 0.38665
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.189
ELB improved by 0.377226
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.82
ELB improved by 0.368834
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.46
ELB improved by 0.359496
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.112
ELB improved by 0.348502
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.776
ELB improved by 0.336053
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.453
ELB improved by 0.322949
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.143
ELB improved by 0.310276
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.843
ELB improved by 0.299169
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.553
ELB improved by 0.290667
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.267
ELB improved by 0.285709
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.982
ELB improved by 0.285228
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.691
ELB improved by 0.290357
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.389
ELB improved by 0.302723
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.064
ELB improved by 0.32487
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.703
ELB improved by 0.36077
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.287
ELB improved by 0.416103
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.79
ELB improved by 0.496998
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.187
ELB improved by 0.603126
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.481
ELB improved by 0.705834
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.747
ELB improved by 0.733765
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.086
ELB improved by 0.661008
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.535
ELB improved by 0.551007
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.086
ELB improved by 0.449154
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.723
ELB improved by 0.363103
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.432
ELB improved by 0.291206
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.2
ELB improved by 0.231777
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.016
ELB improved by 0.183769
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.87
ELB improved by 0.14611
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.753
ELB improved by 0.117289
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.657
ELB improved by 0.0954986
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.578
ELB improved by 0.0789706
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.512
ELB improved by 0.0662146
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.456
ELB improved by 0.056098
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.408
ELB improved by 0.0478314
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.367
ELB improved by 0.0409097
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.332
ELB improved by 0.035036
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.302
ELB improved by 0.0300421
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.276
ELB improved by 0.0258225
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.254
ELB improved by 0.0222905
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.235
ELB improved by 0.0193597
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.218
ELB improved by 0.0169413
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.203
ELB improved by 0.0149496
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.19
ELB improved by 0.0133067
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.178
ELB improved by 0.0119455
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.167
ELB improved by 0.0108106
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.157
ELB improved by 0.00985703
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-889.808
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-578.354
ELB improved by 311.454
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-514.568
ELB improved by 63.7866
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-474.404
ELB improved by 40.1637
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.804
ELB improved by 17.6002
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.662
ELB improved by 7.14179
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.362
ELB improved by 4.29997
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.081
ELB improved by 3.28063
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.131
ELB improved by 2.95069
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.176
ELB improved by 2.95435
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.041
ELB improved by 3.13538
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.615
ELB improved by 3.42596
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.888
ELB improved by 3.7272
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.057
ELB improved by 3.8308
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.554
ELB improved by 3.50246
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.794
ELB improved by 2.76099
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.854
ELB improved by 1.93986
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.53
ELB improved by 1.32321
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.584
ELB improved by 0.946185
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.854
ELB improved by 0.730333
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.248
ELB improved by 0.606373
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.714
ELB improved by 0.533147
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.226
ELB improved by 0.488066
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.766
ELB improved by 0.459891
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.322
ELB improved by 0.444293
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.882
ELB improved by 0.440403
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.435
ELB improved by 0.446675
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.979
ELB improved by 0.455757
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.524
ELB improved by 0.455182
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.085
ELB improved by 0.439494
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.669
ELB improved by 0.415135
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.28
ELB improved by 0.389725
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.913
ELB improved by 0.36629
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.568
ELB improved by 0.345163
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.242
ELB improved by 0.325858
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.935
ELB improved by 0.307688
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.645
ELB improved by 0.289947
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.373
ELB improved by 0.272023
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.119
ELB improved by 0.253476
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.885
ELB improved by 0.234102
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.671
ELB improved by 0.213948
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.478
ELB improved by 0.193287
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.305
ELB improved by 0.172556
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.153
ELB improved by 0.152276
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.02
ELB improved by 0.132956
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.905
ELB improved by 0.11503
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.806
ELB improved by 0.0988045
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.722
ELB improved by 0.0844504
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.65
ELB improved by 0.0720097
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.588
ELB improved by 0.0614227
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.536
ELB improved by 0.0525612
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.491
ELB improved by 0.045259
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.451
ELB improved by 0.039337
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.417
ELB improved by 0.0346205
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.386
ELB improved by 0.0309475
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.358
ELB improved by 0.0281692
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.331
ELB improved by 0.0261438
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.307
ELB improved by 0.0247257
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.283
ELB improved by 0.0237535
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.26
ELB improved by 0.0230449
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.238
ELB improved by 0.0224068
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.216
ELB improved by 0.0216646
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.195
ELB improved by 0.0207019
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.176
ELB improved by 0.0194878
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.158
ELB improved by 0.0180725
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.141
ELB improved by 0.0165522
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.126
ELB improved by 0.0150273
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.112
ELB improved by 0.0135746
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.1
ELB improved by 0.0122395
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.089
ELB improved by 0.0110408
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.079
ELB improved by 0.0099796
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-906.291
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-575.569
ELB improved by 330.723
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-514.965
ELB improved by 60.6038
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-481.622
ELB improved by 33.3433
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.343
ELB improved by 14.2782
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.852
ELB improved by 6.49188
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.399
ELB improved by 4.45279
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.292
ELB improved by 4.10661
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.089
ELB improved by 4.2033
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.731
ELB improved by 4.35832
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.407
ELB improved by 4.32316
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.429
ELB improved by 3.97866
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.023
ELB improved by 3.4056
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.303
ELB improved by 2.72034
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.253
ELB improved by 2.04943
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.749
ELB improved by 1.50435
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.667
ELB improved by 1.08235
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.891
ELB improved by 0.775691
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.315
ELB improved by 0.576457
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.862
ELB improved by 0.452137
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.492
ELB improved by 0.370647
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.18
ELB improved by 0.311857
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.915
ELB improved by 0.264794
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.691
ELB improved by 0.224385
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.501
ELB improved by 0.189406
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.341
ELB improved by 0.160263
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.204
ELB improved by 0.137092
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.085
ELB improved by 0.119154
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.98
ELB improved by 0.105255
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.885
ELB improved by 0.0942615
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.8
ELB improved by 0.0853284
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.722
ELB improved by 0.0778889
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.65
ELB improved by 0.0715735
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.584
ELB improved by 0.0661359
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.523
ELB improved by 0.0614036
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.466
ELB improved by 0.0572495
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.412
ELB improved by 0.053576
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.362
ELB improved by 0.0503056
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.314
ELB improved by 0.0473754
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.27
ELB improved by 0.044734
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.227
ELB improved by 0.0423382
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.187
ELB improved by 0.0401522
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.149
ELB improved by 0.0381456
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.113
ELB improved by 0.036293
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.078
ELB improved by 0.0345728
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.045
ELB improved by 0.0329667
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.014
ELB improved by 0.0314595
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.984
ELB improved by 0.0300381
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.955
ELB improved by 0.028692
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.928
ELB improved by 0.027412
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.901
ELB improved by 0.0261909
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.876
ELB improved by 0.0250227
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.853
ELB improved by 0.0239026
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.83
ELB improved by 0.0228267
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.808
ELB improved by 0.0217922
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.787
ELB improved by 0.0207966
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.767
ELB improved by 0.0198383
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.748
ELB improved by 0.0189161
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.73
ELB improved by 0.0180288
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.713
ELB improved by 0.017176
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.697
ELB improved by 0.0163569
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.681
ELB improved by 0.0155713
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.666
ELB improved by 0.0148187
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.652
ELB improved by 0.0140987
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.639
ELB improved by 0.0134109
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.626
ELB improved by 0.0127549
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.614
ELB improved by 0.01213
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.602
ELB improved by 0.0115356
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.591
ELB improved by 0.010971
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.581
ELB improved by 0.0104354
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.571
ELB improved by 0.00992798
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.343 0.202 2.532
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.050 | 0.017 | 0.067 | |
| getPIPs | 0.052 | 0.011 | 0.063 | |
| graper | 0.087 | 0.015 | 0.101 | |
| makeExampleData | 0.009 | 0.001 | 0.011 | |
| makeExampleDataWithUnequalGroups | 0.010 | 0.002 | 0.013 | |
| plotELBO | 0.336 | 0.024 | 0.361 | |
| plotGroupPenalties | 1.114 | 0.058 | 1.172 | |
| plotPosterior | 0.645 | 0.016 | 0.660 | |
| predict.graper | 2.059 | 0.072 | 2.130 | |
| print.graper | 0.048 | 0.013 | 0.062 | |