Britta Velten
| Snapshot Date: 2025-12-29 13:45 -0500 (Mon, 29 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: RELEASE_3_22 |
| git_last_commit: 76fc31b |
| git_last_commit_date: 2025-10-29 10:49:21 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-01-01 11:58 -0500 (Thu, 01 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4883 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 922/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.26.0 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: graper |
| Version: 1.26.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings graper_1.26.0.tar.gz |
| StartedAt: 2025-12-30 00:10:06 -0500 (Tue, 30 Dec 2025) |
| EndedAt: 2025-12-30 00:11:38 -0500 (Tue, 30 Dec 2025) |
| EllapsedTime: 91.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings graper_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.26.0’
* 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) 13.3.0’
* checking installed package size ... INFO
installed size is 6.1Mb
sub-directories of 1Mb or more:
libs 6.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) predict.graper.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:23-24: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.26.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-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++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-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++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -llapack -L/home/biocbuild/bbs-3.22-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.22-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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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=-869.272
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-575.607
ELB improved by 293.665
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-513.061
ELB improved by 62.5453
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.601
ELB improved by 40.4605
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.046
ELB improved by 17.5551
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.821
ELB improved by 7.22459
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.829
ELB improved by 3.99196
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.781
ELB improved by 3.04855
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.933
ELB improved by 2.84778
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.015
ELB improved by 2.91809
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.939
ELB improved by 3.0761
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.756
ELB improved by 3.18232
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.658
ELB improved by 3.09835
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.917
ELB improved by 2.74122
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.745
ELB improved by 2.17163
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.172
ELB improved by 1.57258
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.068
ELB improved by 1.1045
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.249
ELB improved by 0.819272
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.56
ELB improved by 0.688269
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.929
ELB improved by 0.631343
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.364
ELB improved by 0.565408
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.853
ELB improved by 0.510994
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.347
ELB improved by 0.506082
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.845
ELB improved by 0.501859
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.402
ELB improved by 0.442864
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.039
ELB improved by 0.362383
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.737
ELB improved by 0.302267
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.467
ELB improved by 0.270402
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.208
ELB improved by 0.2591
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.949
ELB improved by 0.258838
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.685
ELB improved by 0.263456
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.416
ELB improved by 0.269813
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.14
ELB improved by 0.275693
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.862
ELB improved by 0.277594
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.591
ELB improved by 0.270891
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.337
ELB improved by 0.254495
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.103
ELB improved by 0.233551
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.889
ELB improved by 0.214069
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.691
ELB improved by 0.198202
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.506
ELB improved by 0.185456
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.331
ELB improved by 0.174912
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.165
ELB improved by 0.165955
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.007
ELB improved by 0.15824
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.855
ELB improved by 0.151561
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.709
ELB improved by 0.145767
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.568
ELB improved by 0.140725
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.432
ELB improved by 0.136302
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.3
ELB improved by 0.132346
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.171
ELB improved by 0.128671
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.046
ELB improved by 0.125045
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.925
ELB improved by 0.12118
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.808
ELB improved by 0.11676
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.697
ELB improved by 0.111501
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.591
ELB improved by 0.105239
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.493
ELB improved by 0.0979954
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.403
ELB improved by 0.0899709
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.322
ELB improved by 0.0814855
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.249
ELB improved by 0.0728921
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.185
ELB improved by 0.0645145
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.128
ELB improved by 0.0566141
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.079
ELB improved by 0.0493751
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.036
ELB improved by 0.0429016
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.998
ELB improved by 0.0372244
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.966
ELB improved by 0.0323175
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.938
ELB improved by 0.0281189
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.913
ELB improved by 0.0245486
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.892
ELB improved by 0.0215223
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.873
ELB improved by 0.0189598
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.856
ELB improved by 0.0167888
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.841
ELB improved by 0.0149465
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.828
ELB improved by 0.0133793
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.816
ELB improved by 0.0120422
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.805
ELB improved by 0.0108972
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.795
ELB improved by 0.00991303
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-884.481
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-586.768
ELB improved by 297.713
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-524.724
ELB improved by 62.0443
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-486.191
ELB improved by 38.5328
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.224
ELB improved by 16.9674
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.641
ELB improved by 7.5823
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.213
ELB improved by 5.42792
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.768
ELB improved by 5.44529
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.42
ELB improved by 6.34784
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.721
ELB improved by 7.69914
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.137
ELB improved by 8.58392
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.283
ELB improved by 7.85392
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.479
ELB improved by 5.80389
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.56
ELB improved by 3.91951
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.579
ELB improved by 2.98145
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.835
ELB improved by 2.74382
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.542
ELB improved by 2.29301
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.952
ELB improved by 1.59007
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.929
ELB improved by 1.02287
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.253
ELB improved by 0.67536
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.772
ELB improved by 0.481852
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.403
ELB improved by 0.368973
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.106
ELB improved by 0.296928
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.858
ELB improved by 0.247182
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.647
ELB improved by 0.210945
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.464
ELB improved by 0.183668
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.301
ELB improved by 0.162751
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.154
ELB improved by 0.146585
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.02
ELB improved by 0.13412
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.896
ELB improved by 0.124646
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.778
ELB improved by 0.117666
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.665
ELB improved by 0.112823
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.555
ELB improved by 0.109848
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.447
ELB improved by 0.108534
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.338
ELB improved by 0.108723
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.228
ELB improved by 0.110297
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.115
ELB improved by 0.113168
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.997
ELB improved by 0.11728
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.875
ELB improved by 0.122602
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.746
ELB improved by 0.129126
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.609
ELB improved by 0.136862
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.463
ELB improved by 0.145831
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.307
ELB improved by 0.156064
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.139
ELB improved by 0.167594
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.959
ELB improved by 0.180451
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.764
ELB improved by 0.194658
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.554
ELB improved by 0.21023
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.327
ELB improved by 0.227175
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.081
ELB improved by 0.245488
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.816
ELB improved by 0.265129
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.53
ELB improved by 0.285934
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.223
ELB improved by 0.307425
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.894
ELB improved by 0.328537
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.547
ELB improved by 0.347436
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.185
ELB improved by 0.36186
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.815
ELB improved by 0.370246
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.442
ELB improved by 0.373226
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.067
ELB improved by 0.374396
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.688
ELB improved by 0.379053
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.299
ELB improved by 0.38929
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.903
ELB improved by 0.395912
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.522
ELB improved by 0.381059
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.18
ELB improved by 0.341983
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.883
ELB improved by 0.296399
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.625
ELB improved by 0.258384
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.397
ELB improved by 0.227933
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.199
ELB improved by 0.197998
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.034
ELB improved by 0.165086
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.901
ELB improved by 0.132912
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.795
ELB improved by 0.106504
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.707
ELB improved by 0.0875643
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.632
ELB improved by 0.0753548
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.563
ELB improved by 0.0687178
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.496
ELB improved by 0.0671014
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.425
ELB improved by 0.0710357
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.342
ELB improved by 0.0827441
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.235
ELB improved by 0.107316
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.081
ELB improved by 0.153782
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.852
ELB improved by 0.229106
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.544
ELB improved by 0.307493
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.228
ELB improved by 0.315937
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.987
ELB improved by 0.241375
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.833
ELB improved by 0.153725
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.741
ELB improved by 0.0925435
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.684
ELB improved by 0.0569838
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.647
ELB improved by 0.0373122
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.62
ELB improved by 0.0262662
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.6
ELB improved by 0.0197707
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.585
ELB improved by 0.0157202
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.572
ELB improved by 0.013036
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.561
ELB improved by 0.0111524
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.551
ELB improved by 0.00976222
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-901.486
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-583.916
ELB improved by 317.57
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-523.087
ELB improved by 60.8289
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-483.54
ELB improved by 39.5469
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.298
ELB improved by 17.2418
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.76
ELB improved by 6.53882
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.148
ELB improved by 3.61117
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.455
ELB improved by 2.69326
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.153
ELB improved by 2.30228
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.028
ELB improved by 2.1247
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.995
ELB improved by 2.0336
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.023
ELB improved by 1.97128
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.112
ELB improved by 1.91095
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.278
ELB improved by 1.83407
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.557
ELB improved by 1.72148
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.999
ELB improved by 1.55745
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.656
ELB improved by 1.34377
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.549
ELB improved by 1.1068
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.666
ELB improved by 0.882744
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.97
ELB improved by 0.695662
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.419
ELB improved by 0.551145
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.975
ELB improved by 0.444383
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.607
ELB improved by 0.368309
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.29
ELB improved by 0.316404
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.007
ELB improved by 0.283037
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.743
ELB improved by 0.263665
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.488
ELB improved by 0.254993
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.234
ELB improved by 0.254841
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.972
ELB improved by 0.261759
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.697
ELB improved by 0.274586
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.405
ELB improved by 0.292219
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.091
ELB improved by 0.31378
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.752
ELB improved by 0.339021
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.384
ELB improved by 0.368396
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.981
ELB improved by 0.402597
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.539
ELB improved by 0.442108
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.052
ELB improved by 0.487289
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.513
ELB improved by 0.538881
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.915
ELB improved by 0.598456
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.246
ELB improved by 0.668483
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.494
ELB improved by 0.751795
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.644
ELB improved by 0.850196
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.682
ELB improved by 0.961799
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.604
ELB improved by 1.07835
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.417
ELB improved by 1.18689
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.141
ELB improved by 1.2761
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.8
ELB improved by 1.34095
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.415
ELB improved by 1.38536
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.991
ELB improved by 1.42381
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.529
ELB improved by 1.46174
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.083
ELB improved by 1.44638
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.781
ELB improved by 1.30138
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.735
ELB improved by 1.04646
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.965
ELB improved by 0.769744
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.427
ELB improved by 0.538457
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.055
ELB improved by 0.37155
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.796
ELB improved by 0.258927
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.612
ELB improved by 0.184249
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.478
ELB improved by 0.1344
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.377
ELB improved by 0.100619
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.3
ELB improved by 0.0773147
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.239
ELB improved by 0.060914
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.19
ELB improved by 0.0491152
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.149
ELB improved by 0.0404304
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.115
ELB improved by 0.0338925
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.086
ELB improved by 0.0288655
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.061
ELB improved by 0.0249247
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.04
ELB improved by 0.0217811
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.02
ELB improved by 0.0192345
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.003
ELB improved by 0.0171433
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.988
ELB improved by 0.0154056
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.974
ELB improved by 0.0139468
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.961
ELB improved by 0.0127113
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.95
ELB improved by 0.0116569
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.939
ELB improved by 0.0107509
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.929
ELB improved by 0.0099679
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-822.88
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-600.863
ELB improved by 222.017
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-543.803
ELB improved by 57.0607
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-490.888
ELB improved by 52.9142
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.733
ELB improved by 35.1552
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.739
ELB improved by 15.9947
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.322
ELB improved by 7.41604
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.792
ELB improved by 4.53078
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.162
ELB improved by 3.62949
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.765
ELB improved by 3.39763
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.287
ELB improved by 3.47746
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.584
ELB improved by 3.70284
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.655
ELB improved by 3.92949
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.672
ELB improved by 3.98295
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.968
ELB improved by 3.70405
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.884
ELB improved by 3.08362
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.607
ELB improved by 2.27748
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.093
ELB improved by 1.5135
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.131
ELB improved by 0.962337
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.5
ELB improved by 0.631241
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.052
ELB improved by 0.447534
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.705
ELB improved by 0.347583
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.411
ELB improved by 0.29348
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.148
ELB improved by 0.263315
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.906
ELB improved by 0.241678
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.688
ELB improved by 0.217788
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.499
ELB improved by 0.189027
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.339
ELB improved by 0.159829
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.205
ELB improved by 0.134837
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.089
ELB improved by 0.115508
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.988
ELB improved by 0.101239
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.897
ELB improved by 0.0909105
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.813
ELB improved by 0.0835672
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.735
ELB improved by 0.0785621
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.659
ELB improved by 0.0755184
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.585
ELB improved by 0.0742594
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.51
ELB improved by 0.0747532
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.433
ELB improved by 0.0770801
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.352
ELB improved by 0.0814157
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.264
ELB improved by 0.0880258
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.166
ELB improved by 0.0972712
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.057
ELB improved by 0.109627
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.931
ELB improved by 0.125718
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.785
ELB improved by 0.146366
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.612
ELB improved by 0.172637
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.406
ELB improved by 0.20588
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.158
ELB improved by 0.247745
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.858
ELB improved by 0.300198
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.493
ELB improved by 0.365521
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.046
ELB improved by 0.44628
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.501
ELB improved by 0.545107
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.837
ELB improved by 0.663902
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.036
ELB improved by 0.801682
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.086
ELB improved by 0.950242
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.997
ELB improved by 1.08862
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.814
ELB improved by 1.18277
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.614
ELB improved by 1.19971
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.485
ELB improved by 1.12995
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.491
ELB improved by 0.993873
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.664
ELB improved by 0.826689
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.003
ELB improved by 0.660749
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.486
ELB improved by 0.517002
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.082
ELB improved by 0.404226
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.76
ELB improved by 0.322473
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.492
ELB improved by 0.267428
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.259
ELB improved by 0.232917
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.048
ELB improved by 0.210811
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.858
ELB improved by 0.190754
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.693
ELB improved by 0.164188
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.563
ELB improved by 0.130725
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.466
ELB improved by 0.0968928
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.397
ELB improved by 0.0685296
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.35
ELB improved by 0.0474797
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.317
ELB improved by 0.0330324
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.293
ELB improved by 0.0236091
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.276
ELB improved by 0.0176179
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.262
ELB improved by 0.0138069
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.25
ELB improved by 0.0113248
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.241
ELB improved by 0.00964194
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.307 0.172 2.460
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.050 | 0.002 | 0.054 | |
| getPIPs | 0.051 | 0.007 | 0.058 | |
| graper | 0.081 | 0.005 | 0.086 | |
| makeExampleData | 0.007 | 0.004 | 0.011 | |
| makeExampleDataWithUnequalGroups | 0.009 | 0.004 | 0.013 | |
| plotELBO | 0.329 | 0.031 | 0.361 | |
| plotGroupPenalties | 1.069 | 0.058 | 1.127 | |
| plotPosterior | 0.634 | 0.010 | 0.645 | |
| predict.graper | 2.050 | 0.014 | 2.064 | |
| print.graper | 0.050 | 0.002 | 0.052 | |