Britta Velten
| Snapshot Date: 2026-04-03 13:40 -0400 (Fri, 03 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 2026-04-04 11:35 -0400 (Sat, 04 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.6.0 alpha (2026-03-30 r89742) | 4900 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-03-28 r89739) | 4634 |
| 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 935/2381 | 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 | | ||||||||
| See other builds for graper in R Universe. | ||||||||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: graper |
| Version: 1.27.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings graper_1.27.0.tar.gz |
| StartedAt: 2026-04-04 00:08:51 -0400 (Sat, 04 Apr 2026) |
| EndedAt: 2026-04-04 00:10:20 -0400 (Sat, 04 Apr 2026) |
| EllapsedTime: 89.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings graper_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck’
* using R version 4.6.0 alpha (2026-03-30 r89742)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-04 04:08:51 UTC
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.27.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) predict.graper.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:23-24: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.27.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c fit_graper.cpp -o fit_graper.o g++ -std=gnu++20 -shared -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -llapack -L/home/biocbuild/bbs-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-graper/00new/graper/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (graper)
graper.Rcheck/tests/testthat.Rout
R version 4.6.0 alpha (2026-03-30 r89742)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(graper)
>
> test_check("graper")
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-864.413
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-583.627
ELB improved by 280.786
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-525.309
ELB improved by 58.3182
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-485.418
ELB improved by 39.8907
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.835
ELB improved by 18.5829
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.748
ELB improved by 8.08736
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.152
ELB improved by 4.59628
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.596
ELB improved by 3.55586
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.336
ELB improved by 3.26001
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.228
ELB improved by 3.10737
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.396
ELB improved by 2.83235
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.034
ELB improved by 2.36214
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.229
ELB improved by 1.80452
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.91
ELB improved by 1.31915
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.933
ELB improved by 0.976793
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.171
ELB improved by 0.762176
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.539
ELB improved by 0.632467
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.986
ELB improved by 0.552761
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.484
ELB improved by 0.502522
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.013
ELB improved by 0.470956
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.56
ELB improved by 0.452353
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.117
ELB improved by 0.443498
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.674
ELB improved by 0.44231
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.228
ELB improved by 0.446748
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.774
ELB improved by 0.453513
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.317
ELB improved by 0.457517
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.862
ELB improved by 0.454502
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.417
ELB improved by 0.445526
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.98
ELB improved by 0.437013
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.543
ELB improved by 0.436838
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.089
ELB improved by 0.453734
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.587
ELB improved by 0.502045
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.977
ELB improved by 0.609537
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.167
ELB improved by 0.810425
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.099
ELB improved by 1.06805
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.843
ELB improved by 1.25617
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.475
ELB improved by 1.36775
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.021
ELB improved by 1.45392
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.515
ELB improved by 1.50642
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.013
ELB improved by 1.5016
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.579
ELB improved by 1.43458
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.291
ELB improved by 1.28724
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.269
ELB improved by 1.02218
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.554
ELB improved by 0.715392
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.075
ELB improved by 0.478293
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.749
ELB improved by 0.326372
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.514
ELB improved by 0.234755
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.334
ELB improved by 0.180185
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.187
ELB improved by 0.147412
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.059
ELB improved by 0.127279
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.946
ELB improved by 0.113836
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.843
ELB improved by 0.102648
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.752
ELB improved by 0.0908535
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.674
ELB improved by 0.0780367
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.608
ELB improved by 0.0658024
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.552
ELB improved by 0.0558578
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.504
ELB improved by 0.0488077
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.459
ELB improved by 0.044403
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.417
ELB improved by 0.0421371
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.376
ELB improved by 0.0415009
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.334
ELB improved by 0.041937
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.291
ELB improved by 0.0427049
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.248
ELB improved by 0.0428828
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.206
ELB improved by 0.0416745
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.167
ELB improved by 0.0388805
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.132
ELB improved by 0.035042
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.101
ELB improved by 0.0310392
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.074
ELB improved by 0.0275849
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.049
ELB improved by 0.0250688
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.025
ELB improved by 0.0237194
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.001
ELB improved by 0.0238465
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.975
ELB improved by 0.0260747
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.944
ELB improved by 0.0316093
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.901
ELB improved by 0.0425517
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.839
ELB improved by 0.0619603
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.747
ELB improved by 0.0923765
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.616
ELB improved by 0.130147
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.46
ELB improved by 0.156669
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.313
ELB improved by 0.146875
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.208
ELB improved by 0.104714
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.147
ELB improved by 0.0607315
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.115
ELB improved by 0.032012
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.098
ELB improved by 0.0171028
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.088
ELB improved by 0.0101136
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.081
ELB improved by 0.00691066
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-856.128
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-563.677
ELB improved by 292.452
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-503.881
ELB improved by 59.7952
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.906
ELB improved by 37.9754
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.569
ELB improved by 16.3368
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.909
ELB improved by 6.65998
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.135
ELB improved by 3.77442
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.434
ELB improved by 2.70075
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.183
ELB improved by 2.25104
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.092
ELB improved by 2.09109
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.029
ELB improved by 2.06259
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.942
ELB improved by 2.08758
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.824
ELB improved by 2.11788
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.715
ELB improved by 2.10874
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.7
ELB improved by 2.01469
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.892
ELB improved by 1.80887
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.382
ELB improved by 1.50985
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.201
ELB improved by 1.1809
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.31
ELB improved by 0.890619
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.636
ELB improved by 0.67402
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.108
ELB improved by 0.528453
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.675
ELB improved by 0.43283
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.309
ELB improved by 0.366094
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.993
ELB improved by 0.315984
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.715
ELB improved by 0.278333
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.463
ELB improved by 0.251945
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.227
ELB improved by 0.235345
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.001
ELB improved by 0.226556
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.777
ELB improved by 0.223776
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.551
ELB improved by 0.22569
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.32
ELB improved by 0.231429
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.079
ELB improved by 0.240387
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.827
ELB improved by 0.252056
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.561
ELB improved by 0.265895
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.28
ELB improved by 0.281283
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.983
ELB improved by 0.297571
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.668
ELB improved by 0.31426
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.337
ELB improved by 0.331201
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.988
ELB improved by 0.3487
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.621
ELB improved by 0.367395
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.233
ELB improved by 0.387955
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.822
ELB improved by 0.410703
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.387
ELB improved by 0.435248
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.927
ELB improved by 0.460176
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.444
ELB improved by 0.482858
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.945
ELB improved by 0.499538
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.439
ELB improved by 0.505886
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.941
ELB improved by 0.498053
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.467
ELB improved by 0.473951
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.032
ELB improved by 0.434203
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.65
ELB improved by 0.38229
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.326
ELB improved by 0.32375
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.062
ELB improved by 0.264706
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.851
ELB improved by 0.210303
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.688
ELB improved by 0.163702
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.562
ELB improved by 0.125966
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.465
ELB improved by 0.0966217
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.391
ELB improved by 0.0744015
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.333
ELB improved by 0.0578309
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.287
ELB improved by 0.0455546
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.251
ELB improved by 0.0364615
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.221
ELB improved by 0.0296958
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.197
ELB improved by 0.0246216
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.176
ELB improved by 0.0207756
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.158
ELB improved by 0.0178235
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.142
ELB improved by 0.0155252
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.129
ELB improved by 0.0137084
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.116
ELB improved by 0.0122491
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.105
ELB improved by 0.0110581
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.095
ELB improved by 0.0100707
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.086
ELB improved by 0.00923973
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-891.113
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-565.374
ELB improved by 325.739
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-505.006
ELB improved by 60.3677
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.025
ELB improved by 31.9813
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.65
ELB improved by 12.3752
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.947
ELB improved by 5.70259
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.902
ELB improved by 4.04548
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.225
ELB improved by 3.67653
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.562
ELB improved by 3.66304
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.782
ELB improved by 3.77999
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.846
ELB improved by 3.93668
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.768
ELB improved by 4.07742
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.626
ELB improved by 4.14257
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.568
ELB improved by 4.05724
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.813
ELB improved by 3.75524
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.575
ELB improved by 3.23839
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.971
ELB improved by 2.60341
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.996
ELB improved by 1.97518
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.559
ELB improved by 1.43681
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.536
ELB improved by 1.02316
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.804
ELB improved by 0.731963
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.267
ELB improved by 0.537616
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.857
ELB improved by 0.409676
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.533
ELB improved by 0.323852
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.269
ELB improved by 0.264051
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.048
ELB improved by 0.220535
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.861
ELB improved by 0.187596
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.699
ELB improved by 0.161852
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.558
ELB improved by 0.141227
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.433
ELB improved by 0.12438
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.323
ELB improved by 0.110401
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.224
ELB improved by 0.0986478
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.136
ELB improved by 0.0886496
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.056
ELB improved by 0.0800549
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.983
ELB improved by 0.0725954
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.917
ELB improved by 0.0660644
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.857
ELB improved by 0.0603009
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.801
ELB improved by 0.0551787
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.751
ELB improved by 0.0505984
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.704
ELB improved by 0.0464815
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.662
ELB improved by 0.0427654
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.622
ELB improved by 0.0393996
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.586
ELB improved by 0.0363433
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.552
ELB improved by 0.0335627
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.521
ELB improved by 0.0310294
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.493
ELB improved by 0.028719
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.466
ELB improved by 0.0266105
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.441
ELB improved by 0.024685
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.418
ELB improved by 0.0229258
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.397
ELB improved by 0.0213176
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.377
ELB improved by 0.0198468
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.359
ELB improved by 0.0185007
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.341
ELB improved by 0.017268
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.325
ELB improved by 0.0161383
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.31
ELB improved by 0.0151021
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.296
ELB improved by 0.0141508
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.283
ELB improved by 0.0132767
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.27
ELB improved by 0.0124728
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.259
ELB improved by 0.0117327
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.247
ELB improved by 0.0110506
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.237
ELB improved by 0.0104214
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.227
ELB improved by 0.00984041
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-858.317
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-557.684
ELB improved by 300.633
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-497.606
ELB improved by 60.078
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.407
ELB improved by 35.199
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.586
ELB improved by 13.8209
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.719
ELB improved by 5.8671
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.127
ELB improved by 3.59227
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.276
ELB improved by 2.85108
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.639
ELB improved by 2.63656
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.008
ELB improved by 2.63143
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.301
ELB improved by 2.707
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.517
ELB improved by 2.78356
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.729
ELB improved by 2.78871
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.079
ELB improved by 2.64966
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.748
ELB improved by 2.33049
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.863
ELB improved by 1.88542
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.428
ELB improved by 1.4354
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.354
ELB improved by 1.07373
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.531
ELB improved by 0.823246
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.867
ELB improved by 0.663196
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.308
ELB improved by 0.559163
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.827
ELB improved by 0.481143
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.412
ELB improved by 0.415183
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.051
ELB improved by 0.360511
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.732
ELB improved by 0.319126
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.441
ELB improved by 0.290837
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.168
ELB improved by 0.273524
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.903
ELB improved by 0.264636
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.641
ELB improved by 0.262159
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.376
ELB improved by 0.264823
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.104
ELB improved by 0.271946
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.821
ELB improved by 0.283255
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.522
ELB improved by 0.298756
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.204
ELB improved by 0.318683
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.86
ELB improved by 0.343466
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.486
ELB improved by 0.373721
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.076
ELB improved by 0.41022
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.622
ELB improved by 0.453827
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.117
ELB improved by 0.505352
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.552
ELB improved by 0.565202
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.919
ELB improved by 0.63265
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.215
ELB improved by 0.704492
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.441
ELB improved by 0.773468
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.613
ELB improved by 0.828121
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.757
ELB improved by 0.856607
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.902
ELB improved by 0.854331
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.071
ELB improved by 0.830849
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.262
ELB improved by 0.809629
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.448
ELB improved by 0.814216
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.604
ELB improved by 0.843053
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.729
ELB improved by 0.875565
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.774
ELB improved by 0.954789
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.627
ELB improved by 1.14714
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.45
ELB improved by 1.17741
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.602
ELB improved by 0.847828
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.103
ELB improved by 0.49905
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.823
ELB improved by 0.279403
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.661
ELB improved by 0.162389
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.559
ELB improved by 0.102337
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.488
ELB improved by 0.0703876
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.436
ELB improved by 0.0521359
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.395
ELB improved by 0.0408352
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.362
ELB improved by 0.0332932
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.334
ELB improved by 0.0279294
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.31
ELB improved by 0.0239141
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.289
ELB improved by 0.0207853
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.271
ELB improved by 0.018271
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.255
ELB improved by 0.0162028
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.24
ELB improved by 0.0144715
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.227
ELB improved by 0.013003
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.216
ELB improved by 0.011745
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.205
ELB improved by 0.010659
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.195
ELB improved by 0.00971606
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.349 0.189 2.523
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.054 | 0.012 | 0.067 | |
| getPIPs | 0.051 | 0.013 | 0.064 | |
| graper | 0.079 | 0.023 | 0.102 | |
| makeExampleData | 0.010 | 0.001 | 0.011 | |
| makeExampleDataWithUnequalGroups | 0.012 | 0.001 | 0.012 | |
| plotELBO | 0.316 | 0.033 | 0.349 | |
| plotGroupPenalties | 1.037 | 0.061 | 1.097 | |
| plotPosterior | 0.588 | 0.021 | 0.609 | |
| predict.graper | 2.058 | 0.066 | 2.123 | |
| print.graper | 0.049 | 0.013 | 0.062 | |