Britta Velten
| Snapshot Date: 2026-02-23 13:45 -0500 (Mon, 23 Feb 2026) |
| 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 Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-24 11:57 -0500 (Tue, 24 Feb 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" | 4891 |
| 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 | | ||||||||
| 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: 1.26.0 |
| 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: 2026-02-24 00:07:15 -0500 (Tue, 24 Feb 2026) |
| EndedAt: 2026-02-24 00:08:46 -0500 (Tue, 24 Feb 2026) |
| 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=-822.712
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-567.268
ELB improved by 255.444
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-506.333
ELB improved by 60.935
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.234
ELB improved by 47.0986
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.501
ELB improved by 23.7329
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.41
ELB improved by 10.0913
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.711
ELB improved by 4.69928
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.004
ELB improved by 2.70642
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.126
ELB improved by 1.87835
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.634
ELB improved by 1.49207
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.302
ELB improved by 1.33158
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.001
ELB improved by 1.3015
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.648
ELB improved by 1.353
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.191
ELB improved by 1.45629
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.606
ELB improved by 1.58513
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.899
ELB improved by 1.70707
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.117
ELB improved by 1.78167
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.346
ELB improved by 1.77171
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.681
ELB improved by 1.6645
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.198
ELB improved by 1.48336
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.924
ELB improved by 1.27362
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.846
ELB improved by 1.07802
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.924
ELB improved by 0.922447
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.11
ELB improved by 0.814035
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.362
ELB improved by 0.74731
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.65
ELB improved by 0.712643
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.948
ELB improved by 0.70171
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.239
ELB improved by 0.709173
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.507
ELB improved by 0.732247
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.737
ELB improved by 0.769597
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.917
ELB improved by 0.820359
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.033
ELB improved by 0.883607
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.075
ELB improved by 0.957922
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.035
ELB improved by 1.04006
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.913
ELB improved by 1.1223
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.722
ELB improved by 1.1907
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.494
ELB improved by 1.22851
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.271
ELB improved by 1.22239
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.119
ELB improved by 1.15204
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.14
ELB improved by 0.979146
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.411
ELB improved by 0.729328
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.905
ELB improved by 0.505412
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.551
ELB improved by 0.354649
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.281
ELB improved by 0.26932
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.042
ELB improved by 0.239515
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.76
ELB improved by 0.2815
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.28
ELB improved by 0.48009
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.279
ELB improved by 1.00166
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.502
ELB improved by 1.7765
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.336
ELB improved by 2.16567
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.021
ELB improved by 1.31552
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.363
ELB improved by 0.658182
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.859
ELB improved by 0.503844
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.339
ELB improved by 0.52034
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.818
ELB improved by 0.520346
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.39
ELB improved by 0.427998
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.113
ELB improved by 0.277
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.963
ELB improved by 0.15038
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.885
ELB improved by 0.0774731
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.843
ELB improved by 0.0418956
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.818
ELB improved by 0.0253629
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.801
ELB improved by 0.0175505
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.787
ELB improved by 0.0135872
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.776
ELB improved by 0.0113343
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.766
ELB improved by 0.00987973
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-870.563
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-566.985
ELB improved by 303.578
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-507.139
ELB improved by 59.8461
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.391
ELB improved by 34.7475
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.869
ELB improved by 12.5227
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.979
ELB improved by 4.89028
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.11
ELB improved by 2.86874
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.926
ELB improved by 2.18399
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.026
ELB improved by 1.90023
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.277
ELB improved by 1.74848
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.642
ELB improved by 1.6351
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.109
ELB improved by 1.5329
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.674
ELB improved by 1.43559
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.333
ELB improved by 1.34092
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.088
ELB improved by 1.24508
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.945
ELB improved by 1.14281
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.914
ELB improved by 1.03087
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.003
ELB improved by 0.911311
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.209
ELB improved by 0.793387
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.514
ELB improved by 0.695613
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.872
ELB improved by 0.641821
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.223
ELB improved by 0.649093
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.507
ELB improved by 0.715253
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.705
ELB improved by 0.802402
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.857
ELB improved by 0.847528
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.028
ELB improved by 0.829276
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.254
ELB improved by 0.77385
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.55
ELB improved by 0.704688
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.913
ELB improved by 0.636356
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.332
ELB improved by 0.58116
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.781
ELB improved by 0.55102
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.222
ELB improved by 0.559182
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.611
ELB improved by 0.610845
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.948
ELB improved by 0.662565
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.304
ELB improved by 0.644653
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.718
ELB improved by 0.585433
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.181
ELB improved by 0.537818
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.673
ELB improved by 0.507838
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.184
ELB improved by 0.488906
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.708
ELB improved by 0.475983
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.243
ELB improved by 0.465301
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.789
ELB improved by 0.453583
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.351
ELB improved by 0.438012
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.934
ELB improved by 0.416497
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.547
ELB improved by 0.387936
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.194
ELB improved by 0.352404
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.883
ELB improved by 0.311318
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.615
ELB improved by 0.267499
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.391
ELB improved by 0.224745
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.204
ELB improved by 0.186865
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.047
ELB improved by 0.156869
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.91
ELB improved by 0.137063
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.779
ELB improved by 0.130264
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.638
ELB improved by 0.141701
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.46
ELB improved by 0.17828
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.227
ELB improved by 0.232012
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.973
ELB improved by 0.254832
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.754
ELB improved by 0.218895
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.579
ELB improved by 0.174302
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.415
ELB improved by 0.164488
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.223
ELB improved by 0.191882
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.003
ELB improved by 0.22036
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.799
ELB improved by 0.203308
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.646
ELB improved by 0.153661
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.539
ELB improved by 0.106843
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.466
ELB improved by 0.0727576
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.417
ELB improved by 0.049484
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.383
ELB improved by 0.0341412
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.358
ELB improved by 0.0243303
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.34
ELB improved by 0.0181547
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.326
ELB improved by 0.0142413
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.314
ELB improved by 0.0116862
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.304
ELB improved by 0.00993627
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-882.364
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-573.462
ELB improved by 308.902
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-510.697
ELB improved by 62.7648
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.692
ELB improved by 37.0046
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.742
ELB improved by 14.9506
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.829
ELB improved by 6.91267
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.253
ELB improved by 4.57595
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.461
ELB improved by 3.79244
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.827
ELB improved by 3.63317
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.054
ELB improved by 3.77347
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.019
ELB improved by 4.03511
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.845
ELB improved by 4.17401
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.971
ELB improved by 3.87349
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.898
ELB improved by 3.07303
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.755
ELB improved by 2.14298
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.294
ELB improved by 1.46127
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.188
ELB improved by 1.1059
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.151
ELB improved by 1.03707
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.953
ELB improved by 1.19787
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.638
ELB improved by 1.31516
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.529
ELB improved by 1.10855
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.743
ELB improved by 0.786187
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.178
ELB improved by 0.565293
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.75
ELB improved by 0.428034
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.422
ELB improved by 0.328301
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.167
ELB improved by 0.254471
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.965
ELB improved by 0.201907
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.801
ELB improved by 0.163991
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.665
ELB improved by 0.135828
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.551
ELB improved by 0.114545
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.453
ELB improved by 0.0982057
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.367
ELB improved by 0.0853761
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.292
ELB improved by 0.0750387
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.226
ELB improved by 0.0665142
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.166
ELB improved by 0.0593573
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.113
ELB improved by 0.0532694
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.065
ELB improved by 0.0480406
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.022
ELB improved by 0.0435162
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.982
ELB improved by 0.0395778
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.946
ELB improved by 0.0361319
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.913
ELB improved by 0.0331033
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.882
ELB improved by 0.0304307
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.854
ELB improved by 0.0280635
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.828
ELB improved by 0.0259596
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.804
ELB improved by 0.0240837
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.782
ELB improved by 0.022406
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.761
ELB improved by 0.0209014
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.741
ELB improved by 0.0195483
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.723
ELB improved by 0.0183284
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.706
ELB improved by 0.0172256
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.69
ELB improved by 0.0162264
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.674
ELB improved by 0.0153189
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.66
ELB improved by 0.0144928
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.646
ELB improved by 0.0137391
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.633
ELB improved by 0.0130499
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.621
ELB improved by 0.0124183
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.609
ELB improved by 0.0118381
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.597
ELB improved by 0.0113041
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.587
ELB improved by 0.0108115
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.576
ELB improved by 0.0103561
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.566
ELB improved by 0.0099342
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-836.466
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-576.473
ELB improved by 259.993
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-515.873
ELB improved by 60.6005
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-474.45
ELB improved by 41.4225
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.346
ELB improved by 18.1042
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.516
ELB improved by 8.83047
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.41
ELB improved by 6.10566
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.117
ELB improved by 5.29322
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.999
ELB improved by 5.11831
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.051
ELB improved by 4.94721
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.591
ELB improved by 4.46061
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.892
ELB improved by 3.69887
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.956
ELB improved by 2.93568
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.681
ELB improved by 2.27541
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.018
ELB improved by 1.66252
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.849
ELB improved by 1.16936
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.998
ELB improved by 0.850757
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.333
ELB improved by 0.665231
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.776
ELB improved by 0.557199
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.29
ELB improved by 0.485938
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.859
ELB improved by 0.430884
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.471
ELB improved by 0.387623
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.12
ELB improved by 0.351497
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.81
ELB improved by 0.310225
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.551
ELB improved by 0.258757
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.343
ELB improved by 0.207558
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.176
ELB improved by 0.167047
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.038
ELB improved by 0.13837
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.92
ELB improved by 0.118182
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.816
ELB improved by 0.103269
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.725
ELB improved by 0.0916065
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.643
ELB improved by 0.0820639
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.569
ELB improved by 0.0740133
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.502
ELB improved by 0.0670869
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.441
ELB improved by 0.0610519
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.385
ELB improved by 0.0557491
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.334
ELB improved by 0.0510625
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.287
ELB improved by 0.0469032
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.244
ELB improved by 0.043201
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.204
ELB improved by 0.0398988
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.167
ELB improved by 0.0369499
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.133
ELB improved by 0.0343153
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.101
ELB improved by 0.0319626
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.071
ELB improved by 0.0298647
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.043
ELB improved by 0.0279987
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.016
ELB improved by 0.0263462
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.991
ELB improved by 0.0248916
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.968
ELB improved by 0.0236225
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.945
ELB improved by 0.0225288
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.924
ELB improved by 0.0216015
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.903
ELB improved by 0.020832
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.883
ELB improved by 0.02021
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.863
ELB improved by 0.0197211
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.844
ELB improved by 0.0193432
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.825
ELB improved by 0.0190434
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.806
ELB improved by 0.0187753
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.787
ELB improved by 0.0184791
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.769
ELB improved by 0.0180879
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.752
ELB improved by 0.0175396
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.735
ELB improved by 0.0167933
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.719
ELB improved by 0.0158441
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.704
ELB improved by 0.0147271
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.691
ELB improved by 0.0135083
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.679
ELB improved by 0.012266
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.667
ELB improved by 0.0110704
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.657
ELB improved by 0.00997139
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.365 0.190 2.540
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.053 | 0.011 | 0.065 | |
| getPIPs | 0.049 | 0.003 | 0.052 | |
| graper | 0.080 | 0.005 | 0.085 | |
| makeExampleData | 0.010 | 0.000 | 0.011 | |
| makeExampleDataWithUnequalGroups | 0.011 | 0.000 | 0.013 | |
| plotELBO | 0.357 | 0.010 | 0.369 | |
| plotGroupPenalties | 1.093 | 0.043 | 1.137 | |
| plotPosterior | 0.639 | 0.012 | 0.652 | |
| predict.graper | 2.048 | 0.017 | 2.066 | |
| print.graper | 0.046 | 0.006 | 0.052 | |