Britta Velten
| Snapshot Date: 2026-04-24 13:40 -0400 (Fri, 24 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: 95474d7 |
| git_last_commit_date: 2025-10-29 10:49:21 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-25 11:36 -0400 (Sat, 25 Apr 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" | 4978 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4722 |
| 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 942/2415 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.27.0 (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: 1.27.0 |
| 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: 2026-04-24 20:08:47 -0400 (Fri, 24 Apr 2026) |
| EndedAt: 2026-04-24 20:09:19 -0400 (Fri, 24 Apr 2026) |
| EllapsedTime: 32.4 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 version 4.6.0 alpha (2026-04-08 r89818)
* 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: 2026-04-25 00:08:47 UTC
* 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 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 ‘1.27.0’ ** 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 alpha (2026-04-08 r89818)
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=-865.128
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-578.922
ELB improved by 286.206
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-517.937
ELB improved by 60.9843
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-474.906
ELB improved by 43.0312
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.892
ELB improved by 20.0144
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.797
ELB improved by 7.09531
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.024
ELB improved by 3.77222
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.137
ELB improved by 2.88741
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.58
ELB improved by 2.55662
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.162
ELB improved by 2.41829
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.815
ELB improved by 2.34679
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.519
ELB improved by 2.29648
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.268
ELB improved by 2.25072
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.07
ELB improved by 2.19793
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.954
ELB improved by 2.11622
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.98
ELB improved by 1.97354
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.228
ELB improved by 1.75244
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.758
ELB improved by 1.46975
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.59
ELB improved by 1.16849
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.694
ELB improved by 0.895986
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.012
ELB improved by 0.682091
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.481
ELB improved by 0.530574
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.054
ELB improved by 0.426621
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.704
ELB improved by 0.350262
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.417
ELB improved by 0.287191
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.184
ELB improved by 0.232616
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.997
ELB improved by 0.187292
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.845
ELB improved by 0.151931
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.72
ELB improved by 0.125396
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.614
ELB improved by 0.10561
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.523
ELB improved by 0.0906004
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.445
ELB improved by 0.0788931
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.375
ELB improved by 0.0694978
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.313
ELB improved by 0.0617719
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.258
ELB improved by 0.0552958
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.208
ELB improved by 0.0497865
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.163
ELB improved by 0.0450457
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.122
ELB improved by 0.0409282
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.085
ELB improved by 0.037324
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.051
ELB improved by 0.0341478
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.019
ELB improved by 0.0313323
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.991
ELB improved by 0.0288231
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.964
ELB improved by 0.0265764
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.939
ELB improved by 0.0245562
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.917
ELB improved by 0.0227328
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.896
ELB improved by 0.0210815
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.876
ELB improved by 0.0195815
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.858
ELB improved by 0.0182154
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.841
ELB improved by 0.0169682
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.825
ELB improved by 0.0158272
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.81
ELB improved by 0.0147814
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.796
ELB improved by 0.0138212
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.784
ELB improved by 0.0129382
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.771
ELB improved by 0.012125
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.76
ELB improved by 0.0113753
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.749
ELB improved by 0.0106831
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.739
ELB improved by 0.0100433
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.73
ELB improved by 0.00945141
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-897.842
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-578.713
ELB improved by 319.129
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-514.398
ELB improved by 64.3149
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-477.163
ELB improved by 37.2354
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.681
ELB improved by 13.4824
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.983
ELB improved by 5.69789
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.786
ELB improved by 4.19719
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.849
ELB improved by 3.93646
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.837
ELB improved by 4.01204
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.641
ELB improved by 4.19626
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.29
ELB improved by 4.35098
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.957
ELB improved by 4.33252
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.931
ELB improved by 4.02614
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.473
ELB improved by 3.45857
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.653
ELB improved by 2.81955
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.393
ELB improved by 2.26027
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.62
ELB improved by 1.77225
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.276
ELB improved by 1.34497
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.243
ELB improved by 1.03212
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.426
ELB improved by 0.817756
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.786
ELB improved by 0.640106
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.292
ELB improved by 0.493443
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.917
ELB improved by 0.375329
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.636
ELB improved by 0.280312
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.423
ELB improved by 0.213495
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.251
ELB improved by 0.172368
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.103
ELB improved by 0.147622
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.971
ELB improved by 0.131831
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.85
ELB improved by 0.120924
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.737
ELB improved by 0.112845
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.631
ELB improved by 0.106524
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.529
ELB improved by 0.101362
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.432
ELB improved by 0.0969952
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.339
ELB improved by 0.0931851
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.25
ELB improved by 0.0897657
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.163
ELB improved by 0.0866155
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.079
ELB improved by 0.0836442
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.998
ELB improved by 0.0807839
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.921
ELB improved by 0.0779852
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.845
ELB improved by 0.0752138
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.773
ELB improved by 0.0724485
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.703
ELB improved by 0.0696795
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.636
ELB improved by 0.0669067
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.572
ELB improved by 0.064138
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.511
ELB improved by 0.0613877
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.452
ELB improved by 0.0586752
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.396
ELB improved by 0.0560235
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.343
ELB improved by 0.0534585
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.292
ELB improved by 0.0510084
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.243
ELB improved by 0.0487038
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.196
ELB improved by 0.0465783
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.152
ELB improved by 0.0446699
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.109
ELB improved by 0.0430225
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.067
ELB improved by 0.0416884
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.026
ELB improved by 0.04073
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.986
ELB improved by 0.0402198
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.946
ELB improved by 0.0402352
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.905
ELB improved by 0.0408423
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.863
ELB improved by 0.0420594
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.819
ELB improved by 0.0437907
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.773
ELB improved by 0.0457373
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.726
ELB improved by 0.0473387
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.678
ELB improved by 0.0478631
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.631
ELB improved by 0.0467385
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.587
ELB improved by 0.0439528
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.547
ELB improved by 0.0401133
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.511
ELB improved by 0.0360433
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.479
ELB improved by 0.032327
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.45
ELB improved by 0.0291763
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.423
ELB improved by 0.0265581
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.399
ELB improved by 0.0243557
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.376
ELB improved by 0.0224581
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.356
ELB improved by 0.0207858
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.336
ELB improved by 0.019288
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.318
ELB improved by 0.0179332
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.302
ELB improved by 0.0167009
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.286
ELB improved by 0.0155767
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.272
ELB improved by 0.0145492
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.258
ELB improved by 0.0136092
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.245
ELB improved by 0.0127483
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.233
ELB improved by 0.0119592
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.222
ELB improved by 0.0112351
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.211
ELB improved by 0.0105701
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.201
ELB improved by 0.00995857
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-886.833
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-580.28
ELB improved by 306.553
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-522.615
ELB improved by 57.6649
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-485.584
ELB improved by 37.0306
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.91
ELB improved by 17.6741
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.277
ELB improved by 7.63333
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.896
ELB improved by 4.38124
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.669
ELB improved by 3.22664
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.788
ELB improved by 2.88114
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.887
ELB improved by 2.90052
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.79
ELB improved by 3.09718
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.426
ELB improved by 3.36399
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.859
ELB improved by 3.56731
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.346
ELB improved by 3.5133
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.267
ELB improved by 3.07851
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.869
ELB improved by 2.39847
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.126
ELB improved by 1.74296
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.874
ELB improved by 1.25176
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.962
ELB improved by 0.912059
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.281
ELB improved by 0.681046
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.75
ELB improved by 0.531218
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.311
ELB improved by 0.438667
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.927
ELB improved by 0.383704
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.575
ELB improved by 0.352485
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.242
ELB improved by 0.333007
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.929
ELB improved by 0.312955
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.643
ELB improved by 0.285547
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.389
ELB improved by 0.254436
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.162
ELB improved by 0.226752
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.957
ELB improved by 0.205106
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.77
ELB improved by 0.186768
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.604
ELB improved by 0.166631
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.462
ELB improved by 0.142021
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.346
ELB improved by 0.115777
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.253
ELB improved by 0.0930141
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.177
ELB improved by 0.0761321
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.112
ELB improved by 0.0643902
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.056
ELB improved by 0.0560718
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.006
ELB improved by 0.0498111
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.962
ELB improved by 0.0447971
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.921
ELB improved by 0.0405967
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.884
ELB improved by 0.0369795
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.85
ELB improved by 0.0338146
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.819
ELB improved by 0.0310193
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.791
ELB improved by 0.0285357
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.764
ELB improved by 0.0263195
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.74
ELB improved by 0.0243357
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.717
ELB improved by 0.0225548
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.696
ELB improved by 0.0209522
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.677
ELB improved by 0.0195071
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.659
ELB improved by 0.0182014
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.642
ELB improved by 0.0170194
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.626
ELB improved by 0.0159477
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.611
ELB improved by 0.0149744
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.597
ELB improved by 0.0140894
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.583
ELB improved by 0.0132835
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.571
ELB improved by 0.0125488
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.559
ELB improved by 0.0118783
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.548
ELB improved by 0.0112657
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.537
ELB improved by 0.0107056
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.527
ELB improved by 0.0101931
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.517
ELB improved by 0.00972379
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-937.942
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-606.138
ELB improved by 331.804
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-544.991
ELB improved by 61.1474
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-501.517
ELB improved by 43.4735
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-482.028
ELB improved by 19.4892
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-474.622
ELB improved by 7.40564
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.455
ELB improved by 4.16708
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.111
ELB improved by 3.34456
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.873
ELB improved by 3.23778
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.466
ELB improved by 3.40749
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.795
ELB improved by 3.67078
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.949
ELB improved by 3.84564
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.239
ELB improved by 3.71001
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.064
ELB improved by 3.17539
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.627
ELB improved by 2.43634
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.844
ELB improved by 1.78332
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.504
ELB improved by 1.34031
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.424
ELB improved by 1.08004
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.49
ELB improved by 0.934
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.645
ELB improved by 0.844952
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.863
ELB improved by 0.78137
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.131
ELB improved by 0.732005
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.436
ELB improved by 0.695442
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.762
ELB improved by 0.673554
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.095
ELB improved by 0.667662
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.421
ELB improved by 0.673706
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.748
ELB improved by 0.672995
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.107
ELB improved by 0.641445
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.517
ELB improved by 0.589959
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.971
ELB improved by 0.545605
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.457
ELB improved by 0.514266
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.966
ELB improved by 0.490617
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.496
ELB improved by 0.46993
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.047
ELB improved by 0.44963
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.618
ELB improved by 0.428753
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.21
ELB improved by 0.407948
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.82
ELB improved by 0.39028
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.436
ELB improved by 0.383161
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.035
ELB improved by 0.401576
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.572
ELB improved by 0.462776
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.04
ELB improved by 0.531744
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.541
ELB improved by 0.498937
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.16
ELB improved by 0.381126
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.89
ELB improved by 0.27046
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.7
ELB improved by 0.190184
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.564
ELB improved by 0.135843
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.464
ELB improved by 0.100226
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.387
ELB improved by 0.076996
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.325
ELB improved by 0.0615843
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.274
ELB improved by 0.0510658
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.23
ELB improved by 0.0436779
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.192
ELB improved by 0.0383898
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.157
ELB improved by 0.0346144
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.125
ELB improved by 0.0320377
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.095
ELB improved by 0.0305283
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.065
ELB improved by 0.0301005
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.034
ELB improved by 0.0309092
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424
ELB improved by 0.0332512
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.963
ELB improved by 0.0375091
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.919
ELB improved by 0.0438757
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.867
ELB improved by 0.051614
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.809
ELB improved by 0.0580249
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.751
ELB improved by 0.0588437
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.699
ELB improved by 0.0519324
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.658
ELB improved by 0.0403644
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.629
ELB improved by 0.0293083
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.608
ELB improved by 0.021432
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.591
ELB improved by 0.0166366
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.577
ELB improved by 0.013886
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.565
ELB improved by 0.0122896
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.553
ELB improved by 0.0113117
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.543
ELB improved by 0.0106769
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.532
ELB improved by 0.010256
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.522
ELB improved by 0.00999353
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
1.048 0.091 1.154
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.032 | 0.010 | 0.043 | |
| getPIPs | 0.026 | 0.006 | 0.033 | |
| graper | 0.044 | 0.009 | 0.053 | |
| makeExampleData | 0.004 | 0.000 | 0.004 | |
| makeExampleDataWithUnequalGroups | 0.005 | 0.000 | 0.005 | |
| plotELBO | 0.126 | 0.008 | 0.134 | |
| plotGroupPenalties | 0.436 | 0.009 | 0.446 | |
| plotPosterior | 0.245 | 0.011 | 0.263 | |
| predict.graper | 1.021 | 0.041 | 1.064 | |
| print.graper | 0.027 | 0.006 | 0.032 | |