Britta Velten
| Snapshot Date: 2026-01-22 13:45 -0500 (Thu, 22 Jan 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 2026-01-26 11:58 -0500 (Mon, 26 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" | 4886 |
| 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 | | ||||||||
|
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: 2026-01-23 00:17:47 -0500 (Fri, 23 Jan 2026) |
| EndedAt: 2026-01-23 00:19:18 -0500 (Fri, 23 Jan 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=-862.418
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-542.528
ELB improved by 319.89
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-483.526
ELB improved by 59.0024
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.019
ELB improved by 33.5071
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.691
ELB improved by 14.328
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.68
ELB improved by 7.01093
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.124
ELB improved by 4.55579
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.548
ELB improved by 3.57548
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.349
ELB improved by 3.19911
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.264
ELB improved by 3.08497
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.183
ELB improved by 3.08142
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.068
ELB improved by 3.11463
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.948
ELB improved by 3.1198
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.918
ELB improved by 3.03043
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.107
ELB improved by 2.81077
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.648
ELB improved by 2.45936
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.649
ELB improved by 1.9985
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.104
ELB improved by 1.54496
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.867
ELB improved by 1.23734
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.791
ELB improved by 1.07587
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.841
ELB improved by 0.94988
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.029
ELB improved by 0.812742
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.32
ELB improved by 0.708707
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.668
ELB improved by 0.651404
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.041
ELB improved by 0.627395
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.416
ELB improved by 0.624679
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.779
ELB improved by 0.637635
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.114
ELB improved by 0.665212
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.405
ELB improved by 0.708917
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.633
ELB improved by 0.771515
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.777
ELB improved by 0.856299
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.81
ELB improved by 0.966658
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.705
ELB improved by 1.10564
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.429
ELB improved by 1.27542
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.952
ELB improved by 1.47685
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.252
ELB improved by 1.70037
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.408
ELB improved by 1.84399
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.756
ELB improved by 1.65239
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.561
ELB improved by 1.19478
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.777
ELB improved by 0.784083
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.275
ELB improved by 0.501554
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.951
ELB improved by 0.324515
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.733
ELB improved by 0.217084
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.582
ELB improved by 0.15128
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.472
ELB improved by 0.109772
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.39
ELB improved by 0.0826221
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.326
ELB improved by 0.0641973
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.274
ELB improved by 0.0512438
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.233
ELB improved by 0.0418305
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.198
ELB improved by 0.0347785
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.168
ELB improved by 0.0293491
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.143
ELB improved by 0.0250684
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.122
ELB improved by 0.0216259
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.103
ELB improved by 0.018813
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.086
ELB improved by 0.0164864
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.072
ELB improved by 0.0145445
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.059
ELB improved by 0.0129126
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.047
ELB improved by 0.0115344
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.037
ELB improved by 0.0103658
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.028
ELB improved by 0.00937129
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-866.502
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-574.995
ELB improved by 291.508
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-513.628
ELB improved by 61.3668
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-475.186
ELB improved by 38.442
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.48
ELB improved by 16.7055
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.578
ELB improved by 7.90272
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.224
ELB improved by 5.35361
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.287
ELB improved by 4.9366
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.931
ELB improved by 5.35656
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.873
ELB improved by 6.05805
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.463
ELB improved by 6.40945
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.868
ELB improved by 5.59518
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.014
ELB improved by 3.85371
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.71
ELB improved by 2.30425
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.307
ELB improved by 1.4032
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.356
ELB improved by 0.951424
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.642
ELB improved by 0.713499
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.07
ELB improved by 0.571949
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.589
ELB improved by 0.480614
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.17
ELB improved by 0.419582
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.793
ELB improved by 0.376811
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.449
ELB improved by 0.344412
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.131
ELB improved by 0.317709
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.837
ELB improved by 0.29417
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.564
ELB improved by 0.272521
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.312
ELB improved by 0.252181
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.079
ELB improved by 0.232946
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.864
ELB improved by 0.214789
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.667
ELB improved by 0.197758
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.485
ELB improved by 0.181907
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.317
ELB improved by 0.167271
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.164
ELB improved by 0.153859
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.022
ELB improved by 0.141652
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.891
ELB improved by 0.130609
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.771
ELB improved by 0.120683
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.659
ELB improved by 0.111819
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.555
ELB improved by 0.10397
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.458
ELB improved by 0.0971017
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.367
ELB improved by 0.0911981
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.28
ELB improved by 0.0862757
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.198
ELB improved by 0.082396
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.118
ELB improved by 0.0796879
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.04
ELB improved by 0.0783788
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.961
ELB improved by 0.0788364
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.879
ELB improved by 0.0816067
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.792
ELB improved by 0.0874058
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.695
ELB improved by 0.0969701
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.584
ELB improved by 0.110704
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.456
ELB improved by 0.128393
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.306
ELB improved by 0.149407
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.135
ELB improved by 0.171607
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.949
ELB improved by 0.185732
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.771
ELB improved by 0.177771
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.619
ELB improved by 0.152537
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.489
ELB improved by 0.130077
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.371
ELB improved by 0.117263
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.26
ELB improved by 0.111242
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.15
ELB improved by 0.109992
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.036
ELB improved by 0.113921
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.91
ELB improved by 0.126225
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.754
ELB improved by 0.156206
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.524
ELB improved by 0.22991
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.12
ELB improved by 0.404438
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.449
ELB improved by 0.670539
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.67
ELB improved by 0.779273
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.942
ELB improved by 0.727327
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.269
ELB improved by 0.673812
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.63
ELB improved by 0.638839
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.02
ELB improved by 0.609534
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.445
ELB improved by 0.575279
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.917
ELB improved by 0.527845
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.454
ELB improved by 0.463036
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.069
ELB improved by 0.384996
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.763
ELB improved by 0.306521
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.521
ELB improved by 0.241446
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.325
ELB improved by 0.196339
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.155
ELB improved by 0.169535
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392
ELB improved by 0.154994
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.855
ELB improved by 0.145526
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.721
ELB improved by 0.134065
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.605
ELB improved by 0.115386
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.516
ELB improved by 0.0896425
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.453
ELB improved by 0.0627795
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.412
ELB improved by 0.04097
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.386
ELB improved by 0.0262077
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.368
ELB improved by 0.0172084
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.357
ELB improved by 0.0119279
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.348
ELB improved by 0.00880318
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-861.394
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-583.45
ELB improved by 277.944
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-518.671
ELB improved by 64.7794
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-474.455
ELB improved by 44.2161
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.294
ELB improved by 20.1607
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.418
ELB improved by 8.87605
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.172
ELB improved by 5.24564
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.82
ELB improved by 4.35216
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.71
ELB improved by 4.11054
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.749
ELB improved by 3.96067
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.047
ELB improved by 3.70158
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.804
ELB improved by 3.24291
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.185
ELB improved by 2.61892
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.22
ELB improved by 1.96524
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.809
ELB improved by 1.41144
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.804
ELB improved by 1.00508
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.074
ELB improved by 0.72942
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.526
ELB improved by 0.548756
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.095
ELB improved by 0.430918
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.742
ELB improved by 0.352441
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.444
ELB improved by 0.298127
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.185
ELB improved by 0.258887
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.956
ELB improved by 0.229487
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.749
ELB improved by 0.206922
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.559
ELB improved by 0.189462
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.383
ELB improved by 0.176139
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.217
ELB improved by 0.166493
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.056
ELB improved by 0.160438
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.898
ELB improved by 0.158131
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.738
ELB improved by 0.159703
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.574
ELB improved by 0.164652
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.403
ELB improved by 0.170995
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.228
ELB improved by 0.175153
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.054
ELB improved by 0.17395
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.886
ELB improved by 0.16737
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.728
ELB improved by 0.158291
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.578
ELB improved by 0.149572
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.436
ELB improved by 0.142376
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.299
ELB improved by 0.136533
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.168
ELB improved by 0.13133
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.042
ELB improved by 0.125962
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.922
ELB improved by 0.119771
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.81
ELB improved by 0.112455
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.706
ELB improved by 0.104176
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.61
ELB improved by 0.095446
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.523
ELB improved by 0.0868427
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.445
ELB improved by 0.0787841
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.373
ELB improved by 0.0714663
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.308
ELB improved by 0.0649219
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.249
ELB improved by 0.0590995
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.195
ELB improved by 0.0539184
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.146
ELB improved by 0.0492957
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.101
ELB improved by 0.0451564
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.059
ELB improved by 0.0414367
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.021
ELB improved by 0.0380833
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.986
ELB improved by 0.0350523
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.954
ELB improved by 0.032307
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.924
ELB improved by 0.0298169
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.897
ELB improved by 0.0275562
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.871
ELB improved by 0.0255023
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.847
ELB improved by 0.0236358
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.826
ELB improved by 0.0219394
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.805
ELB improved by 0.0203977
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.786
ELB improved by 0.0189968
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.768
ELB improved by 0.0177244
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.752
ELB improved by 0.0165693
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.736
ELB improved by 0.0155212
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.722
ELB improved by 0.014571
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.708
ELB improved by 0.0137102
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.695
ELB improved by 0.0129311
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.683
ELB improved by 0.0122264
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.671
ELB improved by 0.0115893
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.66
ELB improved by 0.0110133
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.65
ELB improved by 0.0104919
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.64
ELB improved by 0.0100189
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.63
ELB improved by 0.00958769
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-844.15
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-558.287
ELB improved by 285.862
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-497.621
ELB improved by 60.6663
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.933
ELB improved by 36.6879
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.906
ELB improved by 14.0266
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.638
ELB improved by 6.26792
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.689
ELB improved by 4.94943
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.709
ELB improved by 4.98008
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.469
ELB improved by 5.23996
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.354
ELB improved by 5.11533
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.076
ELB improved by 4.27718
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.067
ELB improved by 3.00959
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.165
ELB improved by 1.90172
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.95
ELB improved by 1.21501
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.093
ELB improved by 0.857262
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.42
ELB improved by 0.672461
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.855
ELB improved by 0.565821
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.354
ELB improved by 0.500427
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.888
ELB improved by 0.466377
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.429
ELB improved by 0.458456
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.959
ELB improved by 0.470713
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.462
ELB improved by 0.496808
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.932
ELB improved by 0.529721
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.37
ELB improved by 0.562309
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.781
ELB improved by 0.588723
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.176
ELB improved by 0.605029
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.567
ELB improved by 0.60916
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.966
ELB improved by 0.600925
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.384
ELB improved by 0.581797
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.83
ELB improved by 0.554273
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.309
ELB improved by 0.521153
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.824
ELB improved by 0.485024
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.376
ELB improved by 0.447998
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.964
ELB improved by 0.411657
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.587
ELB improved by 0.377098
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.242
ELB improved by 0.345007
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.926
ELB improved by 0.315739
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.637
ELB improved by 0.289389
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.371
ELB improved by 0.265878
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.126
ELB improved by 0.245094
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.899
ELB improved by 0.227127
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.686
ELB improved by 0.212756
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.481
ELB improved by 0.204544
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.272
ELB improved by 0.209477
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.028
ELB improved by 0.243571
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.702
ELB improved by 0.326774
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.263
ELB improved by 0.438887
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.722
ELB improved by 0.541192
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.114
ELB improved by 0.607767
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.593
ELB improved by 0.52076
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.216
ELB improved by 0.377363
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.937
ELB improved by 0.278978
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.722
ELB improved by 0.214872
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.551
ELB improved by 0.170862
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.409
ELB improved by 0.141656
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.286
ELB improved by 0.123438
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.174
ELB improved by 0.112239
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.068
ELB improved by 0.10516
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.966
ELB improved by 0.102371
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.858
ELB improved by 0.107956
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.731
ELB improved by 0.126653
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.579
ELB improved by 0.152316
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.423
ELB improved by 0.156222
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.302
ELB improved by 0.120507
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.229
ELB improved by 0.0734736
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.187
ELB improved by 0.0415372
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.162
ELB improved by 0.0252298
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.145
ELB improved by 0.0175986
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.131
ELB improved by 0.0138668
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.119
ELB improved by 0.0117829
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.109
ELB improved by 0.0104185
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.099
ELB improved by 0.00940305
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.450 0.181 2.618
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.053 | 0.000 | 0.054 | |
| getPIPs | 0.050 | 0.002 | 0.052 | |
| graper | 0.082 | 0.003 | 0.085 | |
| makeExampleData | 0.008 | 0.001 | 0.010 | |
| makeExampleDataWithUnequalGroups | 0.009 | 0.002 | 0.012 | |
| plotELBO | 0.323 | 0.019 | 0.342 | |
| plotGroupPenalties | 1.093 | 0.037 | 1.131 | |
| plotPosterior | 0.648 | 0.007 | 0.656 | |
| predict.graper | 2.052 | 0.014 | 2.065 | |
| print.graper | 0.047 | 0.005 | 0.052 | |