Britta Velten
| Snapshot Date: 2026-05-03 13:40 -0400 (Sun, 03 May 2026) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: RELEASE_3_23 |
| git_last_commit: 7354ec6 |
| git_last_commit_date: 2026-04-28 08:49:19 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-04 11:36 -0400 (Mon, 04 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4989 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There" | 4719 |
| 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 944/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.28.0 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 1.28.0 |
| 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_1.28.0.tar.gz |
| StartedAt: 2026-05-03 19:56:25 -0400 (Sun, 03 May 2026) |
| EndedAt: 2026-05-03 19:56:55 -0400 (Sun, 03 May 2026) |
| EllapsedTime: 30.4 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_1.28.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck’
* using R version 4.6.0 Patched (2026-04-24 r89963)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-03 23:56:25 UTC
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.28.0’
* 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 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.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/Resources/library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.28.0’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’ using SDK: ‘MacOSX26.2.sdk’ clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -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/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 version 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(graper)
>
> test_check("graper")
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-850.9
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-550.127
ELB improved by 300.774
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-488.084
ELB improved by 62.0424
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.498
ELB improved by 33.5858
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.788
ELB improved by 13.7098
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.996
ELB improved by 6.79219
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.16
ELB improved by 4.83595
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.837
ELB improved by 4.32334
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.57
ELB improved by 4.26738
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.268
ELB improved by 4.30174
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.044
ELB improved by 4.22347
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.164
ELB improved by 3.88086
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.939
ELB improved by 3.22494
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.54
ELB improved by 2.39872
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.9
ELB improved by 1.63951
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.819
ELB improved by 1.08105
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.104
ELB improved by 0.715585
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.618
ELB improved by 0.485594
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.275
ELB improved by 0.34305
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.021
ELB improved by 0.254587
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.823
ELB improved by 0.197805
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.663
ELB improved by 0.1593
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.532
ELB improved by 0.131736
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.421
ELB improved by 0.111128
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.325
ELB improved by 0.0951962
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.243
ELB improved by 0.0825497
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.171
ELB improved by 0.072296
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.107
ELB improved by 0.063838
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.05
ELB improved by 0.0567628
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.999
ELB improved by 0.050776
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.953
ELB improved by 0.045662
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.912
ELB improved by 0.0412586
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.875
ELB improved by 0.0374411
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.841
ELB improved by 0.0341119
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.809
ELB improved by 0.0311931
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.781
ELB improved by 0.028622
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.754
ELB improved by 0.0263475
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.73
ELB improved by 0.0243273
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.708
ELB improved by 0.0225266
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.687
ELB improved by 0.020916
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.667
ELB improved by 0.0194709
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.649
ELB improved by 0.0181705
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.632
ELB improved by 0.016997
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.616
ELB improved by 0.0159352
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.601
ELB improved by 0.0149722
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.587
ELB improved by 0.0140966
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.574
ELB improved by 0.0132988
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.561
ELB improved by 0.0125702
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.549
ELB improved by 0.0119034
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.538
ELB improved by 0.0112919
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.527
ELB improved by 0.01073
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.517
ELB improved by 0.0102128
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.507
ELB improved by 0.00973567
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-852.785
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-570.838
ELB improved by 281.947
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-509.842
ELB improved by 60.9957
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-474.787
ELB improved by 35.0548
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.083
ELB improved by 16.7044
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.482
ELB improved by 8.60089
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.47
ELB improved by 6.0122
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.102
ELB improved by 5.36817
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.548
ELB improved by 5.55357
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.785
ELB improved by 5.76341
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.419
ELB improved by 5.3659
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.085
ELB improved by 4.3337
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.925
ELB improved by 3.15985
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.737
ELB improved by 2.18803
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.249
ELB improved by 1.48804
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.21
ELB improved by 1.03946
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.44
ELB improved by 0.770071
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.832
ELB improved by 0.607677
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.327
ELB improved by 0.505097
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.892
ELB improved by 0.434975
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.511
ELB improved by 0.381169
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.176
ELB improved by 0.334495
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.885
ELB improved by 0.291615
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.631
ELB improved by 0.253496
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.409
ELB improved by 0.222077
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.211
ELB improved by 0.197746
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.032
ELB improved by 0.179351
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.867
ELB improved by 0.165324
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.712
ELB improved by 0.154402
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.566
ELB improved by 0.145769
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.427
ELB improved by 0.138983
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.294
ELB improved by 0.133887
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.163
ELB improved by 0.13059
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.033
ELB improved by 0.129533
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.902
ELB improved by 0.131654
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.763
ELB improved by 0.13868
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.61
ELB improved by 0.153389
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.431
ELB improved by 0.178919
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.216
ELB improved by 0.214641
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.967
ELB improved by 0.249032
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.702
ELB improved by 0.265088
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.44
ELB improved by 0.261748
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.189
ELB improved by 0.251284
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.948
ELB improved by 0.241238
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.715
ELB improved by 0.233228
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.487
ELB improved by 0.227384
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.263
ELB improved by 0.223822
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.041
ELB improved by 0.222744
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.816
ELB improved by 0.224397
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.587
ELB improved by 0.22909
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.35
ELB improved by 0.237264
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.1
ELB improved by 0.249624
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.833
ELB improved by 0.267338
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.541
ELB improved by 0.292394
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.212
ELB improved by 0.328251
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.831
ELB improved by 0.380953
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.371
ELB improved by 0.460207
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.797
ELB improved by 0.573737
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.104
ELB improved by 0.693032
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.376
ELB improved by 0.728014
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.724
ELB improved by 0.651917
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.19
ELB improved by 0.534823
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.769
ELB improved by 0.421026
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.445
ELB improved by 0.323327
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.2
ELB improved by 0.244752
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.016
ELB improved by 0.184106
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.878
ELB improved by 0.138232
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.774
ELB improved by 0.10368
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.697
ELB improved by 0.077614
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.639
ELB improved by 0.0579942
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.595
ELB improved by 0.0433643
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.563
ELB improved by 0.0325987
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.538
ELB improved by 0.0247734
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.519
ELB improved by 0.0191304
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.504
ELB improved by 0.0150706
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.492
ELB improved by 0.0121398
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.482
ELB improved by 0.0100055
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.473
ELB improved by 0.00843068
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-863.32
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-574.97
ELB improved by 288.35
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-514.645
ELB improved by 60.3254
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-474.342
ELB improved by 40.3026
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.518
ELB improved by 17.824
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.748
ELB improved by 7.76996
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.864
ELB improved by 4.88424
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.704
ELB improved by 4.15949
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.567
ELB improved by 4.13714
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.125
ELB improved by 4.44225
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.322
ELB improved by 4.80348
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.503
ELB improved by 4.8185
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.361
ELB improved by 4.14225
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.4
ELB improved by 2.96067
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.533
ELB improved by 1.86708
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.36
ELB improved by 1.17331
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.557
ELB improved by 0.803213
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.947
ELB improved by 0.609557
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.441
ELB improved by 0.505827
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.991
ELB improved by 0.450569
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.568
ELB improved by 0.422565
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.158
ELB improved by 0.410157
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.751
ELB improved by 0.406823
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.342
ELB improved by 0.408917
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.928
ELB improved by 0.414489
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.505
ELB improved by 0.4227
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.071
ELB improved by 0.43352
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.624
ELB improved by 0.447523
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.158
ELB improved by 0.465675
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.669
ELB improved by 0.489051
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.151
ELB improved by 0.518452
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.597
ELB improved by 0.553852
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.003
ELB improved by 0.593706
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.369
ELB improved by 0.63423
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.7
ELB improved by 0.669059
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.01
ELB improved by 0.689967
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.321
ELB improved by 0.689198
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.658
ELB improved by 0.662914
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.044
ELB improved by 0.613575
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.496
ELB improved by 0.548382
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.022
ELB improved by 0.473789
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.629
ELB improved by 0.392943
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.317
ELB improved by 0.311964
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.075
ELB improved by 0.242032
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.885
ELB improved by 0.19008
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.729
ELB improved by 0.156098
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.59
ELB improved by 0.138826
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.449
ELB improved by 0.140845
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.275
ELB improved by 0.173992
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.011
ELB improved by 0.264526
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.599
ELB improved by 0.411956
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.13
ELB improved by 0.468379
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.759
ELB improved by 0.37122
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.481
ELB improved by 0.27772
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.256
ELB improved by 0.225892
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.067
ELB improved by 0.188983
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.916
ELB improved by 0.150562
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.806
ELB improved by 0.109562
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.733
ELB improved by 0.0735353
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.685
ELB improved by 0.0475705
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.654
ELB improved by 0.031155
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.633
ELB improved by 0.0214625
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.617
ELB improved by 0.0158597
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.604
ELB improved by 0.0125544
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.594
ELB improved by 0.0104901
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.585
ELB improved by 0.00909455
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-881.296
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-588.345
ELB improved by 292.952
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-528.909
ELB improved by 59.4361
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-485.81
ELB improved by 43.0982
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.569
ELB improved by 21.2411
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.58
ELB improved by 8.98924
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.493
ELB improved by 5.08739
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.481
ELB improved by 4.01122
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.8
ELB improved by 3.68142
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.206
ELB improved by 3.59398
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.709
ELB improved by 3.49693
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.472
ELB improved by 3.2374
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.698
ELB improved by 2.77372
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.511
ELB improved by 2.18689
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.889
ELB improved by 1.62204
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.711
ELB improved by 1.17819
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.844
ELB improved by 0.866481
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.187
ELB improved by 0.657024
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.667
ELB improved by 0.519808
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.239
ELB improved by 0.428764
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.876
ELB improved by 0.362704
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.567
ELB improved by 0.308752
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.305
ELB improved by 0.262351
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.082
ELB improved by 0.223365
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.89
ELB improved by 0.191856
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.723
ELB improved by 0.16673
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.577
ELB improved by 0.146412
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.447
ELB improved by 0.129566
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.332
ELB improved by 0.115293
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.229
ELB improved by 0.103023
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.136
ELB improved by 0.0923869
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.053
ELB improved by 0.0831212
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.978
ELB improved by 0.0750201
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.91
ELB improved by 0.0679147
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.849
ELB improved by 0.0616625
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.792
ELB improved by 0.0561426
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.741
ELB improved by 0.0512521
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.694
ELB improved by 0.0469041
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.651
ELB improved by 0.0430249
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.612
ELB improved by 0.0395526
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.575
ELB improved by 0.0364345
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.542
ELB improved by 0.0336263
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.511
ELB improved by 0.0310902
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.482
ELB improved by 0.028794
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.455
ELB improved by 0.0267099
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.43
ELB improved by 0.0248143
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.407
ELB improved by 0.0230865
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.386
ELB improved by 0.0215085
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.366
ELB improved by 0.0200648
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.347
ELB improved by 0.0187416
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.329
ELB improved by 0.017527
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.313
ELB improved by 0.0164103
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.298
ELB improved by 0.0153822
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.283
ELB improved by 0.0144343
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.27
ELB improved by 0.0135593
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.257
ELB improved by 0.0127505
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.245
ELB improved by 0.012002
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.233
ELB improved by 0.0113085
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.223
ELB improved by 0.0106654
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.213
ELB improved by 0.0100683
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.203
ELB improved by 0.00951343
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
1.020 0.081 1.106
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.028 | 0.006 | 0.035 | |
| getPIPs | 0.026 | 0.005 | 0.032 | |
| graper | 0.044 | 0.010 | 0.057 | |
| makeExampleData | 0.004 | 0.000 | 0.004 | |
| makeExampleDataWithUnequalGroups | 0.004 | 0.000 | 0.005 | |
| plotELBO | 0.123 | 0.007 | 0.131 | |
| plotGroupPenalties | 0.421 | 0.010 | 0.437 | |
| plotPosterior | 0.211 | 0.007 | 0.218 | |
| predict.graper | 1.009 | 0.025 | 1.035 | |
| print.graper | 0.027 | 0.004 | 0.030 | |