Britta Velten
| Snapshot Date: 2026-02-27 13:45 -0500 (Fri, 27 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 2026-02-28 11:57 -0500 (Sat, 28 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: 2026-02-28 00:16:38 -0500 (Sat, 28 Feb 2026) |
| EndedAt: 2026-02-28 00:18:09 -0500 (Sat, 28 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=-838.561
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-550.961
ELB improved by 287.6
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-491.596
ELB improved by 59.365
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.768
ELB improved by 35.8281
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.865
ELB improved by 15.9036
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.581
ELB improved by 7.28418
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.595
ELB improved by 4.98566
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.851
ELB improved by 4.74382
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.484
ELB improved by 5.36715
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.92
ELB improved by 6.56427
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.167
ELB improved by 7.75295
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.448
ELB improved by 7.71849
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.433
ELB improved by 6.0148
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.598
ELB improved by 3.83518
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.324
ELB improved by 2.27385
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.891
ELB improved by 1.43296
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.877
ELB improved by 1.01396
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.086
ELB improved by 0.791243
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.427
ELB improved by 0.6591
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.855
ELB improved by 0.572417
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.344
ELB improved by 0.510894
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.879
ELB improved by 0.464345
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.452
ELB improved by 0.427034
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.057
ELB improved by 0.395565
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.689
ELB improved by 0.368051
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.345
ELB improved by 0.343642
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.023
ELB improved by 0.322157
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.719
ELB improved by 0.30383
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.43
ELB improved by 0.289169
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.151
ELB improved by 0.278971
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.877
ELB improved by 0.274451
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.599
ELB improved by 0.27737
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.31
ELB improved by 0.289559
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374
ELB improved by 0.310167
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.67
ELB improved by 0.329709
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.339
ELB improved by 0.33065
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.032
ELB improved by 0.306765
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.761
ELB improved by 0.271048
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.525
ELB improved by 0.23586
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.321
ELB improved by 0.204643
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.144
ELB improved by 0.177161
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.991
ELB improved by 0.152801
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.86
ELB improved by 0.131179
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.748
ELB improved by 0.112079
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.652
ELB improved by 0.0953549
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.571
ELB improved by 0.0808645
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.503
ELB improved by 0.0684403
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.445
ELB improved by 0.0578878
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.396
ELB improved by 0.0489952
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.355
ELB improved by 0.0415464
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.319
ELB improved by 0.0353337
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.289
ELB improved by 0.0301655
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.263
ELB improved by 0.0258714
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.241
ELB improved by 0.0223035
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.222
ELB improved by 0.0193357
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.205
ELB improved by 0.0168624
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.19
ELB improved by 0.0147958
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.177
ELB improved by 0.0130633
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.165
ELB improved by 0.0116056
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.155
ELB improved by 0.0103739
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.145
ELB improved by 0.00932873
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-849.636
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-557.641
ELB improved by 291.996
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-501.028
ELB improved by 56.6127
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.741
ELB improved by 31.2867
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.78
ELB improved by 11.9607
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.84
ELB improved by 4.94029
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.764
ELB improved by 3.07583
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.223
ELB improved by 2.54157
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.811
ELB improved by 2.41203
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.361
ELB improved by 2.45023
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.795
ELB improved by 2.56588
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.111
ELB improved by 2.68359
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.41
ELB improved by 2.70078
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.916
ELB improved by 2.49431
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.882
ELB improved by 2.03439
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.392
ELB improved by 1.49008
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.341
ELB improved by 1.05059
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.569
ELB improved by 0.772015
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.944
ELB improved by 0.624681
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.383
ELB improved by 0.561283
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.84
ELB improved by 0.543009
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.296
ELB improved by 0.543987
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.744
ELB improved by 0.551597
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.18
ELB improved by 0.564228
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.596
ELB improved by 0.584167
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.983
ELB improved by 0.613239
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.328
ELB improved by 0.654605
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.612
ELB improved by 0.716509
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.794
ELB improved by 0.81771
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.798
ELB improved by 0.996192
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.496
ELB improved by 1.3015
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.783
ELB improved by 1.71356
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.737
ELB improved by 2.04528
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.615
ELB improved by 2.12273
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.429
ELB improved by 2.18586
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.893
ELB improved by 2.53619
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.679
ELB improved by 3.21377
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.525
ELB improved by 3.15338
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.257
ELB improved by 2.26878
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.68
ELB improved by 1.57662
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.388
ELB improved by 1.29243
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.986
ELB improved by 1.40125
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.505
ELB improved by 1.48146
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.387
ELB improved by 1.1179
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.585
ELB improved by 0.802022
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.92
ELB improved by 0.665124
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.317
ELB improved by 0.602813
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.843
ELB improved by 0.474278
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.517
ELB improved by 0.325682
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.278
ELB improved by 0.238754
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.076
ELB improved by 0.201896
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.877
ELB improved by 0.198969
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.646
ELB improved by 0.23135
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.34
ELB improved by 0.305977
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.952
ELB improved by 0.38769
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.567
ELB improved by 0.384924
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.259
ELB improved by 0.308085
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.017
ELB improved by 0.242132
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.817
ELB improved by 0.200294
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.653
ELB improved by 0.163689
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.526
ELB improved by 0.127226
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.431
ELB improved by 0.0954997
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.36
ELB improved by 0.0707472
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.307
ELB improved by 0.0526432
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.267
ELB improved by 0.0402022
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.235
ELB improved by 0.0321789
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.208
ELB improved by 0.0272531
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.183
ELB improved by 0.0242606
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.161
ELB improved by 0.0222969
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.14
ELB improved by 0.0207043
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.121
ELB improved by 0.0190448
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.104
ELB improved by 0.0171061
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.089
ELB improved by 0.0149068
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.077
ELB improved by 0.0126407
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.066
ELB improved by 0.0105538
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.057
ELB improved by 0.00882299
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-889.123
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-621.268
ELB improved by 267.854
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-563.014
ELB improved by 58.254
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-514.1
ELB improved by 48.9143
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-486.285
ELB improved by 27.8153
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-475.124
ELB improved by 11.1609
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.184
ELB improved by 4.94006
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.799
ELB improved by 3.38496
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.66
ELB improved by 3.13841
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.385
ELB improved by 3.27583
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.904
ELB improved by 3.48031
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.355
ELB improved by 3.5495
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.007
ELB improved by 3.34745
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.14
ELB improved by 2.86724
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.914
ELB improved by 2.22581
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.324
ELB improved by 1.59048
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.233
ELB improved by 1.09083
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.469
ELB improved by 0.76443
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.888
ELB improved by 0.580736
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.396
ELB improved by 0.49198
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.934
ELB improved by 0.462226
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.461
ELB improved by 0.472562
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.944
ELB improved by 0.516617
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.349
ELB improved by 0.595205
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.638
ELB improved by 0.711432
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.771
ELB improved by 0.866699
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.714
ELB improved by 1.05732
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.449
ELB improved by 1.26463
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.996
ELB improved by 1.45272
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.392
ELB improved by 1.60433
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.672
ELB improved by 1.71987
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.941
ELB improved by 1.73149
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.401
ELB improved by 1.53988
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.143
ELB improved by 1.25786
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.079
ELB improved by 1.06378
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.074
ELB improved by 1.00503
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.106
ELB improved by 0.968443
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.276
ELB improved by 0.8298
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.587
ELB improved by 0.688615
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.958
ELB improved by 0.62891
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.366
ELB improved by 0.591914
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.864
ELB improved by 0.502718
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.472
ELB improved by 0.392214
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.158
ELB improved by 0.313695
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.878
ELB improved by 0.27966
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.586
ELB improved by 0.291724
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.243
ELB improved by 0.343521
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.856
ELB improved by 0.387099
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.503
ELB improved by 0.35283
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.236
ELB improved by 0.266775
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.04
ELB improved by 0.196503
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.885
ELB improved by 0.154526
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.755
ELB improved by 0.130023
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.64
ELB improved by 0.114758
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.535
ELB improved by 0.105384
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.433
ELB improved by 0.10178
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.328
ELB improved by 0.105669
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.209
ELB improved by 0.118776
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.071
ELB improved by 0.137701
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.923
ELB improved by 0.147679
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.788
ELB improved by 0.135348
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.676
ELB improved by 0.112399
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.576
ELB improved by 0.099754
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.467
ELB improved by 0.109036
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.309
ELB improved by 0.158128
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.013
ELB improved by 0.29552
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.47
ELB improved by 0.54359
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.844
ELB improved by 0.625344
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.438
ELB improved by 0.406325
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.23
ELB improved by 0.207538
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.122
ELB improved by 0.108419
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.059
ELB improved by 0.0634741
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.016
ELB improved by 0.0425613
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.984
ELB improved by 0.0322588
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.957
ELB improved by 0.0269908
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.932
ELB improved by 0.0244666
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.909
ELB improved by 0.0237605
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.884
ELB improved by 0.0245303
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.857
ELB improved by 0.026625
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.828
ELB improved by 0.0297217
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.795
ELB improved by 0.0328698
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.761
ELB improved by 0.0342614
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.728
ELB improved by 0.0320551
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.702
ELB improved by 0.0262107
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.683
ELB improved by 0.0189827
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.67
ELB improved by 0.0128644
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.662
ELB improved by 0.00879779
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-876.548
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-585.494
ELB improved by 291.055
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-525.831
ELB improved by 59.6625
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-489.549
ELB improved by 36.2821
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.965
ELB improved by 17.5845
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.477
ELB improved by 9.48773
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.74
ELB improved by 7.73652
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.394
ELB improved by 8.34643
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.42
ELB improved by 8.97365
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.497
ELB improved by 7.92378
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.891
ELB improved by 5.60511
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.241
ELB improved by 3.65001
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.767
ELB improved by 2.474
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.032
ELB improved by 1.7358
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.791
ELB improved by 1.24077
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.859
ELB improved by 0.931762
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.108
ELB improved by 0.751371
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.46
ELB improved by 0.647759
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.89
ELB improved by 0.570502
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.408
ELB improved by 0.481642
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.018
ELB improved by 0.389599
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.701
ELB improved by 0.317583
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.433
ELB improved by 0.267359
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.202
ELB improved by 0.231491
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.997
ELB improved by 0.204557
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.813
ELB improved by 0.183773
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.646
ELB improved by 0.16771
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.49
ELB improved by 0.155537
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.344
ELB improved by 0.146686
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.203
ELB improved by 0.140723
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.066
ELB improved by 0.13732
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.929
ELB improved by 0.136245
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.792
ELB improved by 0.137369
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.651
ELB improved by 0.140658
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.505
ELB improved by 0.14617
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.351
ELB improved by 0.154054
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.186
ELB improved by 0.164538
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.009
ELB improved by 0.177909
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.814
ELB improved by 0.194468
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.6
ELB improved by 0.214444
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.362
ELB improved by 0.237903
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.097
ELB improved by 0.264798
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.802
ELB improved by 0.295268
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.472
ELB improved by 0.329964
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.103
ELB improved by 0.369111
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.694
ELB improved by 0.408729
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.257
ELB improved by 0.436838
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.817
ELB improved by 0.440471
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.397
ELB improved by 0.419974
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.011
ELB improved by 0.385976
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.664
ELB improved by 0.347061
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.356
ELB improved by 0.307625
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.086
ELB improved by 0.270154
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.85
ELB improved by 0.236205
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.643
ELB improved by 0.206552
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.462
ELB improved by 0.181214
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.302
ELB improved by 0.159581
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.162
ELB improved by 0.140659
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.038
ELB improved by 0.123439
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.931
ELB improved by 0.107278
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.839
ELB improved by 0.0920648
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.761
ELB improved by 0.0780633
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.695
ELB improved by 0.065595
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.64
ELB improved by 0.0548303
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.595
ELB improved by 0.045754
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.556
ELB improved by 0.0382242
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.524
ELB improved by 0.0320412
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.497
ELB improved by 0.0269942
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.474
ELB improved by 0.0228868
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.455
ELB improved by 0.0195477
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.438
ELB improved by 0.0168331
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.423
ELB improved by 0.0146258
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.411
ELB improved by 0.0128311
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.399
ELB improved by 0.0113739
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.389
ELB improved by 0.0101951
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.38
ELB improved by 0.00924857
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.382 0.176 2.548
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.053 | 0.002 | 0.055 | |
| getPIPs | 0.048 | 0.004 | 0.053 | |
| graper | 0.091 | 0.018 | 0.109 | |
| makeExampleData | 0.013 | 0.005 | 0.019 | |
| makeExampleDataWithUnequalGroups | 0.017 | 0.005 | 0.022 | |
| plotELBO | 0.359 | 0.081 | 0.441 | |
| plotGroupPenalties | 1.166 | 0.064 | 1.231 | |
| plotPosterior | 0.653 | 0.010 | 0.665 | |
| predict.graper | 2.049 | 0.019 | 2.069 | |
| print.graper | 0.047 | 0.009 | 0.056 | |