Britta Velten
| Snapshot Date: 2025-12-04 13:40 -0500 (Thu, 04 Dec 2025) |
| 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 Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-05 11:35 -0500 (Fri, 05 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4576 |
| 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 914/2331 | 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 | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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. |
| Package: graper |
| Version: 1.27.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.27.0.tar.gz |
| StartedAt: 2025-12-04 20:17:19 -0500 (Thu, 04 Dec 2025) |
| EndedAt: 2025-12-04 20:17:50 -0500 (Thu, 04 Dec 2025) |
| EllapsedTime: 31.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.27.0’
* 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: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.27.0’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.1.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fit_graper.cpp -o fit_graper.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o graper.so RcppExports.o fit_graper.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/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) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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=-864.274
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-577.928
ELB improved by 286.346
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-520.935
ELB improved by 56.9931
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-480.756
ELB improved by 40.1794
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.228
ELB improved by 20.5279
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.52
ELB improved by 8.70823
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.142
ELB improved by 5.37786
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.302
ELB improved by 4.83948
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.426
ELB improved by 4.87647
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.305
ELB improved by 5.12115
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.933
ELB improved by 5.3719
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.567
ELB improved by 5.3654
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.715
ELB improved by 4.85211
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.806
ELB improved by 3.90917
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.851
ELB improved by 2.95524
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.67
ELB improved by 2.18137
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.111
ELB improved by 1.55902
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.977
ELB improved by 1.1332
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.084
ELB improved by 0.89293
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.315
ELB improved by 0.769539
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.609
ELB improved by 0.705523
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.939
ELB improved by 0.670202
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.291
ELB improved by 0.648603
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.657
ELB improved by 0.633265
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.037
ELB improved by 0.620718
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.426
ELB improved by 0.6101
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.824
ELB improved by 0.602617
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.222
ELB improved by 0.601448
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.611
ELB improved by 0.611712
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.971
ELB improved by 0.639264
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.286
ELB improved by 0.685383
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.549
ELB improved by 0.737387
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.776
ELB improved by 0.773107
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.987
ELB improved by 0.788299
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.183
ELB improved by 0.803828
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.333
ELB improved by 0.850864
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.401
ELB improved by 0.931191
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.482
ELB improved by 0.919748
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.734
ELB improved by 0.747207
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.187
ELB improved by 0.547815
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.794
ELB improved by 0.392395
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.512
ELB improved by 0.281865
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.307
ELB improved by 0.205492
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.153
ELB improved by 0.15339
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.035
ELB improved by 0.118
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.942
ELB improved by 0.0939293
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.864
ELB improved by 0.0775163
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.798
ELB improved by 0.0663772
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.739
ELB improved by 0.0590219
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.684
ELB improved by 0.0545613
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.632
ELB improved by 0.0524963
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.579
ELB improved by 0.0525601
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.524
ELB improved by 0.0545826
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.466
ELB improved by 0.0583814
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.402
ELB improved by 0.0637467
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.332
ELB improved by 0.0706557
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.252
ELB improved by 0.0797976
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.159
ELB improved by 0.093099
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.046
ELB improved by 0.112632
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.912
ELB improved by 0.13385
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.776
ELB improved by 0.136769
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.669
ELB improved by 0.106831
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.603
ELB improved by 0.0657809
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.565
ELB improved by 0.037676
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.542
ELB improved by 0.0233576
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.525
ELB improved by 0.0163831
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.513
ELB improved by 0.0126689
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.502
ELB improved by 0.0104366
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.493
ELB improved by 0.00895466
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-876.208
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-573.677
ELB improved by 302.532
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-511.635
ELB improved by 62.0421
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-474.85
ELB improved by 36.7843
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.506
ELB improved by 16.3445
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.184
ELB improved by 8.32197
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.837
ELB improved by 6.34738
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.739
ELB improved by 6.09716
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.702
ELB improved by 6.03777
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.033
ELB improved by 5.66885
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.041
ELB improved by 4.99187
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.896
ELB improved by 4.14528
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.728
ELB improved by 3.16757
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.465
ELB improved by 2.26323
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.867
ELB improved by 1.59815
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.707
ELB improved by 1.15995
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.839
ELB improved by 0.867259
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.188
ELB improved by 0.651133
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.701
ELB improved by 0.487705
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.328
ELB improved by 0.372105
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.035
ELB improved by 0.293796
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.795
ELB improved by 0.240052
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.593
ELB improved by 0.201528
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.421
ELB improved by 0.172586
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.271
ELB improved by 0.15
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.139
ELB improved by 0.131876
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.022
ELB improved by 0.117039
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.917
ELB improved by 0.104709
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.823
ELB improved by 0.0943417
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.737
ELB improved by 0.085541
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.659
ELB improved by 0.0780096
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.587
ELB improved by 0.0715191
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.522
ELB improved by 0.0658911
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.461
ELB improved by 0.0609837
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.404
ELB improved by 0.0566832
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.351
ELB improved by 0.052897
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.301
ELB improved by 0.0495492
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.255
ELB improved by 0.0465772
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.211
ELB improved by 0.0439285
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.169
ELB improved by 0.0415591
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.13
ELB improved by 0.0394319
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.092
ELB improved by 0.037515
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.057
ELB improved by 0.0357815
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.022
ELB improved by 0.0342078
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.99
ELB improved by 0.0327739
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.958
ELB improved by 0.0314622
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.928
ELB improved by 0.0302572
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.899
ELB improved by 0.0291457
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.871
ELB improved by 0.0281158
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.844
ELB improved by 0.0271573
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.817
ELB improved by 0.0262609
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.792
ELB improved by 0.0254189
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.767
ELB improved by 0.024624
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.743
ELB improved by 0.0238701
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.72
ELB improved by 0.0231519
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.698
ELB improved by 0.0224647
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.676
ELB improved by 0.0218043
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.655
ELB improved by 0.0211673
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.634
ELB improved by 0.0205507
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.614
ELB improved by 0.0199519
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.595
ELB improved by 0.019369
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.576
ELB improved by 0.0188002
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.558
ELB improved by 0.0182441
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.54
ELB improved by 0.0176996
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.523
ELB improved by 0.017166
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.506
ELB improved by 0.0166427
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.49
ELB improved by 0.0161292
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.475
ELB improved by 0.0156254
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.46
ELB improved by 0.0151312
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.445
ELB improved by 0.0146465
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.431
ELB improved by 0.0141715
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.417
ELB improved by 0.0137063
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.404
ELB improved by 0.0132511
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.391
ELB improved by 0.0128061
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.379
ELB improved by 0.0123715
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.367
ELB improved by 0.0119476
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.355
ELB improved by 0.0115347
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.344
ELB improved by 0.0111328
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.333
ELB improved by 0.0107422
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.323
ELB improved by 0.010363
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.313
ELB improved by 0.00999537
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-845.025
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-576.178
ELB improved by 268.847
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-514.63
ELB improved by 61.5479
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.315
ELB improved by 43.315
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.193
ELB improved by 20.1216
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.061
ELB improved by 8.1322
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.042
ELB improved by 4.01951
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.116
ELB improved by 2.9257
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.496
ELB improved by 2.62012
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.946
ELB improved by 2.54965
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.36
ELB improved by 2.58591
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.689
ELB improved by 2.67074
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.958
ELB improved by 2.73188
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.305
ELB improved by 2.65247
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.97
ELB improved by 2.3352
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.147
ELB improved by 1.8232
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.86
ELB improved by 1.28632
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.996
ELB improved by 0.864443
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.408
ELB improved by 0.587545
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.988
ELB improved by 0.420667
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.666
ELB improved by 0.321556
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.405
ELB improved by 0.261133
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.182
ELB improved by 0.222715
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.985
ELB improved by 0.197228
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.805
ELB improved by 0.179725
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.638
ELB improved by 0.167439
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.479
ELB improved by 0.158776
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.326
ELB improved by 0.152782
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.177
ELB improved by 0.148864
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.031
ELB improved by 0.146635
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.885
ELB improved by 0.145827
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.739
ELB improved by 0.146243
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.591
ELB improved by 0.147724
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.441
ELB improved by 0.150133
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.288
ELB improved by 0.153344
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.13
ELB improved by 0.157237
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.969
ELB improved by 0.161697
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.802
ELB improved by 0.166621
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.63
ELB improved by 0.171925
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.453
ELB improved by 0.177549
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.269
ELB improved by 0.183454
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.08
ELB improved by 0.189571
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.884
ELB improved by 0.195682
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.683
ELB improved by 0.20119
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.478
ELB improved by 0.204885
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.273
ELB improved by 0.205074
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.072
ELB improved by 0.200421
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.881
ELB improved by 0.190997
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.703
ELB improved by 0.178326
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.539
ELB improved by 0.164302
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.388
ELB improved by 0.150255
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.252
ELB improved by 0.136818
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.127
ELB improved by 0.124223
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.015
ELB improved by 0.112548
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.913
ELB improved by 0.101844
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.821
ELB improved by 0.092165
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.737
ELB improved by 0.0835826
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.661
ELB improved by 0.0761986
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.591
ELB improved by 0.0701719
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.525
ELB improved by 0.0657593
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.462
ELB improved by 0.0633673
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.398
ELB improved by 0.0635739
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.331
ELB improved by 0.0669784
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.258
ELB improved by 0.0735577
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.176
ELB improved by 0.0813205
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.091
ELB improved by 0.0855321
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.009
ELB improved by 0.0815533
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.939
ELB improved by 0.0699137
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.883
ELB improved by 0.055874
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.839
ELB improved by 0.0439493
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.804
ELB improved by 0.0354393
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.774
ELB improved by 0.0297267
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.748
ELB improved by 0.0258283
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.725
ELB improved by 0.0230011
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.705
ELB improved by 0.0207955
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.686
ELB improved by 0.0189626
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.668
ELB improved by 0.0173692
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.652
ELB improved by 0.0159438
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.638
ELB improved by 0.0146475
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.624
ELB improved by 0.0134585
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.612
ELB improved by 0.0123637
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.601
ELB improved by 0.0113547
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.59
ELB improved by 0.010425
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.581
ELB improved by 0.00956963
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-894.518
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-593.826
ELB improved by 300.693
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-537.293
ELB improved by 56.5326
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-501.011
ELB improved by 36.2823
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-484.988
ELB improved by 16.0232
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-478.084
ELB improved by 6.90381
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.969
ELB improved by 4.11478
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.408
ELB improved by 3.56132
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.741
ELB improved by 3.66665
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.792
ELB improved by 3.94881
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.731
ELB improved by 4.06142
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.012
ELB improved by 3.7185
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.057
ELB improved by 2.95569
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.938
ELB improved by 2.11834
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.453
ELB improved by 1.48586
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.354
ELB improved by 1.0987
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.473
ELB improved by 0.880643
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.721
ELB improved by 0.752343
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.056
ELB improved by 0.665293
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.452
ELB improved by 0.603189
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.889
ELB improved by 0.563619
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.346
ELB improved by 0.542608
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.812
ELB improved by 0.534389
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.277
ELB improved by 0.534624
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.736
ELB improved by 0.541417
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.18
ELB improved by 0.555377
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.601
ELB improved by 0.579646
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.982
ELB improved by 0.619047
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.306
ELB improved by 0.675721
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.563
ELB improved by 0.74264
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.752
ELB improved by 0.811019
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.863
ELB improved by 0.889127
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.864
ELB improved by 0.999539
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.696
ELB improved by 1.16788
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.309
ELB improved by 1.38629
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.762
ELB improved by 1.54785
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.16
ELB improved by 1.60118
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.53
ELB improved by 1.63081
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.751
ELB improved by 1.77809
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.633
ELB improved by 2.11853
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.665
ELB improved by 1.96818
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.266
ELB improved by 1.39919
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.342
ELB improved by 0.92326
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.749
ELB improved by 0.593416
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.366
ELB improved by 0.382922
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.11
ELB improved by 0.256017
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.929
ELB improved by 0.180584
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.795
ELB improved by 0.134563
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.69
ELB improved by 0.105024
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.605
ELB improved by 0.0849383
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.534
ELB improved by 0.0705528
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.474
ELB improved by 0.0598303
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.423
ELB improved by 0.0516263
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.378
ELB improved by 0.0452729
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.337
ELB improved by 0.0403691
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.301
ELB improved by 0.0366719
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.266
ELB improved by 0.0340357
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.234
ELB improved by 0.0323692
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.203
ELB improved by 0.031586
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.171
ELB improved by 0.0315312
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.139
ELB improved by 0.0318838
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.107
ELB improved by 0.0320862
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.076
ELB improved by 0.0314328
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.046
ELB improved by 0.0294025
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.02
ELB improved by 0.0260444
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.998
ELB improved by 0.0219957
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.98
ELB improved by 0.0180548
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.965
ELB improved by 0.0147455
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.953
ELB improved by 0.0122151
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.943
ELB improved by 0.0103751
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.934
ELB improved by 0.00906092
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
1.052 0.093 1.188
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.014 | 0.008 | 0.021 | |
| getPIPs | 0.012 | 0.006 | 0.018 | |
| graper | 0.025 | 0.008 | 0.034 | |
| makeExampleData | 0.002 | 0.001 | 0.002 | |
| makeExampleDataWithUnequalGroups | 0.002 | 0.000 | 0.002 | |
| plotELBO | 0.112 | 0.007 | 0.121 | |
| plotGroupPenalties | 0.449 | 0.012 | 0.469 | |
| plotPosterior | 0.209 | 0.009 | 0.228 | |
| predict.graper | 0.220 | 0.024 | 0.245 | |
| print.graper | 0.011 | 0.004 | 0.016 | |