Britta Velten
| Snapshot Date: 2025-08-31 13:45 -0400 (Sun, 31 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: 82b0592 |
| git_last_commit_date: 2025-06-24 03:15:40 -0400 (Tue, 24 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-01 12:07 -0400 (Mon, 01 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
| 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 907/2320 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.25.2 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: graper |
| Version: 1.25.2 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings graper_1.25.2.tar.gz |
| StartedAt: 2025-08-29 07:51:19 -0000 (Fri, 29 Aug 2025) |
| EndedAt: 2025-08-29 07:52:25 -0000 (Fri, 29 Aug 2025) |
| EllapsedTime: 66.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings graper_1.25.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.25.2’
* 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: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking installed package size ... INFO
installed size is 6.0Mb
sub-directories of 1Mb or more:
libs 5.8Mb
* 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 ... NOTE
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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.25.2’ ** using staged installation ** libs using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c fit_graper.cpp -o fit_graper.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -lopenblas -lgfortran -lm -L/home/biocbuild/R/R-4.5.0/lib -lR installing to /home/biocbuild/R/R-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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=-861.481
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-588.117
ELB improved by 273.364
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-528.935
ELB improved by 59.1817
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-485.141
ELB improved by 43.7934
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.954
ELB improved by 21.1877
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.765
ELB improved by 8.18892
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.541
ELB improved by 4.22386
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.409
ELB improved by 3.13156
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.651
ELB improved by 2.75829
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.004
ELB improved by 2.64662
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.376
ELB improved by 2.62881
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.73
ELB improved by 2.64542
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.075
ELB improved by 2.65523
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.473
ELB improved by 2.60232
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.045
ELB improved by 2.42724
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.936
ELB improved by 2.10895
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.235
ELB improved by 1.70116
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.93
ELB improved by 1.30496
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.936
ELB improved by 0.994638
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.151
ELB improved by 0.784872
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.496
ELB improved by 0.654519
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.919
ELB improved by 0.576877
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.387
ELB improved by 0.532138
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.879
ELB improved by 0.507888
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.383
ELB improved by 0.496444
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.89
ELB improved by 0.492652
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.398
ELB improved by 0.492681
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.904
ELB improved by 0.493537
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.411
ELB improved by 0.492946
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.922
ELB improved by 0.489455
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.439
ELB improved by 0.482623
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.966
ELB improved by 0.473058
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.504
ELB improved by 0.462052
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.053
ELB improved by 0.450755
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.614
ELB improved by 0.439242
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.188
ELB improved by 0.426284
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.777
ELB improved by 0.410456
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.386
ELB improved by 0.391615
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.015
ELB improved by 0.371019
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.664
ELB improved by 0.350259
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.334
ELB improved by 0.330468
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.022
ELB improved by 0.312219
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.726
ELB improved by 0.295663
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.445
ELB improved by 0.280634
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.179
ELB improved by 0.266716
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.925
ELB improved by 0.253324
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.685
ELB improved by 0.239838
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.46
ELB improved by 0.225788
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.249
ELB improved by 0.211013
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.053
ELB improved by 0.195741
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.872
ELB improved by 0.180515
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.706
ELB improved by 0.166027
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.553
ELB improved by 0.1529
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.412
ELB improved by 0.141556
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.28
ELB improved by 0.132195
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.155
ELB improved by 0.124886
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.035
ELB improved by 0.119672
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.919
ELB improved by 0.116579
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.803
ELB improved by 0.115523
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.687
ELB improved by 0.116163
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.569
ELB improved by 0.117876
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.449
ELB improved by 0.119977
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.327
ELB improved by 0.122157
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.202
ELB improved by 0.124909
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.072
ELB improved by 0.129766
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.933
ELB improved by 0.139413
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.775
ELB improved by 0.157626
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.587
ELB improved by 0.188339
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.356
ELB improved by 0.231169
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.084
ELB improved by 0.27162
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.802
ELB improved by 0.282078
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.549
ELB improved by 0.252917
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.347
ELB improved by 0.202318
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.2
ELB improved by 0.146737
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.102
ELB improved by 0.0978207
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.039
ELB improved by 0.0635189
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.996
ELB improved by 0.0423426
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.967
ELB improved by 0.0293535
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.946
ELB improved by 0.0210791
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.93
ELB improved by 0.0156221
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.918
ELB improved by 0.0119317
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.909
ELB improved by 0.00938827
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-874.497
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-596.923
ELB improved by 277.574
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-536.391
ELB improved by 60.5322
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-489.924
ELB improved by 46.467
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.849
ELB improved by 24.0751
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.371
ELB improved by 9.47765
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.985
ELB improved by 4.38604
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.022
ELB improved by 2.96351
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.484
ELB improved by 2.53752
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.028
ELB improved by 2.45578
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.536
ELB improved by 2.49237
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.998
ELB improved by 2.5379
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.48
ELB improved by 2.5176
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.104
ELB improved by 2.37666
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.005
ELB improved by 2.09882
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.275
ELB improved by 1.7301
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.913
ELB improved by 1.36163
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.85
ELB improved by 1.06322
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427
ELB improved by 0.84981
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.293
ELB improved by 0.707064
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.675
ELB improved by 0.618025
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.107
ELB improved by 0.568467
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.56
ELB improved by 0.546865
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.014
ELB improved by 0.54542
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.453
ELB improved by 0.56093
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.859
ELB improved by 0.594506
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.212
ELB improved by 0.647128
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.503
ELB improved by 0.708485
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.749
ELB improved by 0.754111
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.978
ELB improved by 0.771023
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.208
ELB improved by 0.769842
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.446
ELB improved by 0.762125
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.695
ELB improved by 0.750906
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.96
ELB improved by 0.735388
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.246
ELB improved by 0.714234
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.559
ELB improved by 0.686899
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.904
ELB improved by 0.654373
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.285
ELB improved by 0.619624
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.697
ELB improved by 0.587796
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.131
ELB improved by 0.56624
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.567
ELB improved by 0.564103
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.977
ELB improved by 0.589889
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.332
ELB improved by 0.645263
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.614
ELB improved by 0.717668
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.846
ELB improved by 0.767441
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.107
ELB improved by 0.739813
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.462
ELB improved by 0.644698
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.937
ELB improved by 0.525033
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.534
ELB improved by 0.403353
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.238
ELB improved by 0.295434
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.028
ELB improved by 0.210198
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.879
ELB improved by 0.149106
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.77
ELB improved by 0.108679
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.687
ELB improved by 0.0833505
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.619
ELB improved by 0.0679373
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.56
ELB improved by 0.0585841
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.508
ELB improved by 0.0526159
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.459
ELB improved by 0.0481655
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.415
ELB improved by 0.0439923
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.376
ELB improved by 0.0394859
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.341
ELB improved by 0.0346331
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.312
ELB improved by 0.0297853
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.286
ELB improved by 0.0253342
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.265
ELB improved by 0.0215067
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.246
ELB improved by 0.0183458
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.231
ELB improved by 0.015786
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.217
ELB improved by 0.013726
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.205
ELB improved by 0.0120682
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.194
ELB improved by 0.0107301
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.184
ELB improved by 0.00964452
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-845.357
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-584.627
ELB improved by 260.73
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-523.057
ELB improved by 61.5704
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.448
ELB improved by 49.609
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.857
ELB improved by 26.5911
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.185
ELB improved by 9.67155
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.006
ELB improved by 4.17857
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.327
ELB improved by 2.67982
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.293
ELB improved by 2.03401
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.564
ELB improved by 1.72882
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.992
ELB improved by 1.57215
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.514
ELB improved by 1.47788
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.105
ELB improved by 1.40882
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.756
ELB improved by 1.34911
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.464
ELB improved by 1.29205
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.23
ELB improved by 1.23417
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.057
ELB improved by 1.17261
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.953
ELB improved by 1.1044
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.926
ELB improved by 1.02673
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.988
ELB improved by 0.937897
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.149
ELB improved by 0.838484
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.417
ELB improved by 0.732164
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.792
ELB improved by 0.625389
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.266
ELB improved by 0.525803
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.826
ELB improved by 0.440114
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.453
ELB improved by 0.372505
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.129
ELB improved by 0.32423
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.835
ELB improved by 0.294281
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.555
ELB improved by 0.280478
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.274
ELB improved by 0.280417
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.982
ELB improved by 0.292071
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.668
ELB improved by 0.314099
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.322
ELB improved by 0.345866
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.935
ELB improved by 0.387167
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.497
ELB improved by 0.437728
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407
ELB improved by 0.496675
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.438
ELB improved by 0.562201
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.807
ELB improved by 0.63164
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.105
ELB improved by 0.702075
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.333
ELB improved by 0.771533
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.492
ELB improved by 0.840591
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.579
ELB improved by 0.912961
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.592
ELB improved by 0.987042
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.566
ELB improved by 1.02658
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.598
ELB improved by 0.968254
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.77
ELB improved by 0.828013
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.089
ELB improved by 0.680316
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.537
ELB improved by 0.552022
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.096
ELB improved by 0.441055
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.749
ELB improved by 0.347586
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.474
ELB improved by 0.274862
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.25
ELB improved by 0.223889
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.057
ELB improved by 0.193037
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.877
ELB improved by 0.179762
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.697
ELB improved by 0.180032
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.512
ELB improved by 0.184655
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.334
ELB improved by 0.178564
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.181
ELB improved by 0.152769
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.065
ELB improved by 0.115973
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.982
ELB improved by 0.083024
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.922
ELB improved by 0.0599848
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.877
ELB improved by 0.0453614
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.841
ELB improved by 0.036063
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.811
ELB improved by 0.0298376
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.785
ELB improved by 0.0253926
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.763
ELB improved by 0.0220342
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.744
ELB improved by 0.0193871
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.727
ELB improved by 0.0172384
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.711
ELB improved by 0.0154584
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.697
ELB improved by 0.0139622
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.685
ELB improved by 0.0126902
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.673
ELB improved by 0.0115985
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.662
ELB improved by 0.0106539
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.653
ELB improved by 0.0098306
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-870.352
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-587.072
ELB improved by 283.28
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-526.136
ELB improved by 60.9361
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-483.486
ELB improved by 42.6494
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.752
ELB improved by 18.7344
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.739
ELB improved by 8.01323
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.192
ELB improved by 5.54633
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.901
ELB improved by 5.29183
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.214
ELB improved by 5.6869
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.09
ELB improved by 6.12357
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.019
ELB improved by 6.07073
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.821
ELB improved by 5.19793
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.064
ELB improved by 3.75722
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.664
ELB improved by 2.39976
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.181
ELB improved by 1.48373
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.227
ELB improved by 0.953871
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.572
ELB improved by 0.654364
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.095
ELB improved by 0.477911
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.727
ELB improved by 0.367307
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.434
ELB improved by 0.293507
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.192
ELB improved by 0.241451
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.989
ELB improved by 0.202965
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.816
ELB improved by 0.173379
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.666
ELB improved by 0.149906
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.535
ELB improved by 0.130813
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.42
ELB improved by 0.11498
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.319
ELB improved by 0.10166
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.228
ELB improved by 0.0903313
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.148
ELB improved by 0.0806178
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.075
ELB improved by 0.0722358
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.01
ELB improved by 0.0649644
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.952
ELB improved by 0.0586269
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.899
ELB improved by 0.0530794
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.851
ELB improved by 0.0482029
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.807
ELB improved by 0.0438989
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.767
ELB improved by 0.0400854
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.73
ELB improved by 0.0366937
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.696
ELB improved by 0.0336664
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.665
ELB improved by 0.0309554
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.637
ELB improved by 0.0285198
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.61
ELB improved by 0.0263253
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.586
ELB improved by 0.0243426
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.563
ELB improved by 0.0225467
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.543
ELB improved by 0.020916
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.523
ELB improved by 0.0194321
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.505
ELB improved by 0.018079
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.488
ELB improved by 0.0168427
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.473
ELB improved by 0.0157111
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.458
ELB improved by 0.0146735
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.444
ELB improved by 0.0137205
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.431
ELB improved by 0.012844
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.419
ELB improved by 0.0120367
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.408
ELB improved by 0.011292
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.397
ELB improved by 0.0106043
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.387
ELB improved by 0.00996828
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.900 0.155 3.046
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.053 | 0.000 | 0.055 | |
| getPIPs | 0.044 | 0.004 | 0.049 | |
| graper | 0.063 | 0.012 | 0.075 | |
| makeExampleData | 0.009 | 0.000 | 0.009 | |
| makeExampleDataWithUnequalGroups | 0.025 | 0.000 | 0.026 | |
| plotELBO | 0.237 | 0.008 | 0.245 | |
| plotGroupPenalties | 0.974 | 0.004 | 0.980 | |
| plotPosterior | 0.680 | 0.004 | 0.685 | |
| predict.graper | 0.985 | 0.020 | 1.008 | |
| print.graper | 0.047 | 0.000 | 0.047 | |