Britta Velten
| Snapshot Date: 2026-04-07 13:45 -0400 (Tue, 07 Apr 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 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-04-08 11:57 -0400 (Wed, 08 Apr 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" | 4897 |
| 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: 2026-04-08 00:07:21 -0400 (Wed, 08 Apr 2026) |
| EndedAt: 2026-04-08 00:08:52 -0400 (Wed, 08 Apr 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 24.04.4 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 13.3.0-6ubuntu2~24.04.1) 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 13.3.0-6ubuntu2~24.04.1) 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=-836.771
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-572.781
ELB improved by 263.99
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-510.981
ELB improved by 61.8005
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.753
ELB improved by 40.2283
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.404
ELB improved by 19.3487
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.166
ELB improved by 9.23759
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.021
ELB improved by 6.14522
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.08
ELB improved by 5.94129
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.465
ELB improved by 6.61533
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.301
ELB improved by 7.16396
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.509
ELB improved by 6.79163
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.033
ELB improved by 5.47582
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.09
ELB improved by 3.94297
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.362
ELB improved by 2.72857
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.425
ELB improved by 1.9369
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.939
ELB improved by 1.48591
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.769
ELB improved by 1.16955
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.933
ELB improved by 0.836677
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.361
ELB improved by 0.571411
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.952
ELB improved by 0.409228
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.64
ELB improved by 0.31149
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.393
ELB improved by 0.24729
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.192
ELB improved by 0.201616
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.024
ELB improved by 0.16745
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.883
ELB improved by 0.141103
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.763
ELB improved by 0.120362
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.659
ELB improved by 0.103768
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.569
ELB improved by 0.090309
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.489
ELB improved by 0.0792536
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.419
ELB improved by 0.0700628
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.357
ELB improved by 0.0623304
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.301
ELB improved by 0.0557448
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.251
ELB improved by 0.0500652
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.206
ELB improved by 0.045105
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.165
ELB improved by 0.0407221
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.128
ELB improved by 0.0368118
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.095
ELB improved by 0.0333008
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.065
ELB improved by 0.0301404
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.038
ELB improved by 0.0272991
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.013
ELB improved by 0.0247547
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.99
ELB improved by 0.0224883
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.97
ELB improved by 0.0204799
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.951
ELB improved by 0.018707
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.934
ELB improved by 0.017145
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.918
ELB improved by 0.0157688
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.904
ELB improved by 0.0145543
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.89
ELB improved by 0.0134794
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.878
ELB improved by 0.0125245
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.866
ELB improved by 0.0116732
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.855
ELB improved by 0.0109113
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.845
ELB improved by 0.0102273
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.835
ELB improved by 0.00961131
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-907.566
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-588.586
ELB improved by 318.979
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-526.509
ELB improved by 62.0775
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-488.604
ELB improved by 37.9047
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.282
ELB improved by 16.3218
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.103
ELB improved by 7.17947
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.15
ELB improved by 4.95266
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.822
ELB improved by 4.32861
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.663
ELB improved by 4.15907
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.651
ELB improved by 4.01111
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.023
ELB improved by 3.62807
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.039
ELB improved by 2.98474
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.778
ELB improved by 2.26046
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.132
ELB improved by 1.6463
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.921
ELB improved by 1.21068
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.991
ELB improved by 0.929896
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.235
ELB improved by 0.756706
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.587
ELB improved by 0.648017
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.017
ELB improved by 0.569193
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.516
ELB improved by 0.50157
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.072
ELB improved by 0.443949
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.672
ELB improved by 0.399603
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.305
ELB improved by 0.367758
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.959
ELB improved by 0.345074
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.631
ELB improved by 0.328418
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.315
ELB improved by 0.315729
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.009
ELB improved by 0.305911
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.711
ELB improved by 0.298609
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.417
ELB improved by 0.294097
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.123
ELB improved by 0.293326
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.825
ELB improved by 0.298132
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.514
ELB improved by 0.311628
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.175
ELB improved by 0.338722
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.789
ELB improved by 0.385998
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.332
ELB improved by 0.457385
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.793
ELB improved by 0.538421
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.206
ELB improved by 0.587415
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.621
ELB improved by 0.584413
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.066
ELB improved by 0.55513
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.546
ELB improved by 0.519937
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.065
ELB improved by 0.481685
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.625
ELB improved by 0.43906
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.234
ELB improved by 0.391921
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.892
ELB improved by 0.341835
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.6
ELB improved by 0.291503
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.356
ELB improved by 0.243851
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.155
ELB improved by 0.20119
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.99
ELB improved by 0.164782
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.856
ELB improved by 0.134843
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.745
ELB improved by 0.110849
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.653
ELB improved by 0.0918976
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.576
ELB improved by 0.0770027
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.511
ELB improved by 0.0652672
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.455
ELB improved by 0.0559543
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.406
ELB improved by 0.0484946
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.364
ELB improved by 0.0424635
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.326
ELB improved by 0.0375498
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.293
ELB improved by 0.0335285
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.262
ELB improved by 0.0302399
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.235
ELB improved by 0.0275772
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.209
ELB improved by 0.0254822
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.185
ELB improved by 0.0239507
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.162
ELB improved by 0.0230551
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.139
ELB improved by 0.0229981
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.115
ELB improved by 0.0242346
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.087
ELB improved by 0.0277503
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.052
ELB improved by 0.0356776
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.999
ELB improved by 0.0524869
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.913
ELB improved by 0.0861219
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.769
ELB improved by 0.143635
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.556
ELB improved by 0.212965
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.298
ELB improved by 0.258121
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.05
ELB improved by 0.248684
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.863
ELB improved by 0.186768
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.741
ELB improved by 0.122018
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.656
ELB improved by 0.0843779
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.588
ELB improved by 0.0682247
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.524
ELB improved by 0.0637969
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.458
ELB improved by 0.0660537
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.386
ELB improved by 0.0723411
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.307
ELB improved by 0.0794285
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.224
ELB improved by 0.0820883
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.149
ELB improved by 0.0757498
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.087
ELB improved by 0.0617301
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.041
ELB improved by 0.0463351
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.006
ELB improved by 0.0343308
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.98
ELB improved by 0.0265964
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.958
ELB improved by 0.0221625
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.938
ELB improved by 0.0199884
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.918
ELB improved by 0.0194878
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.898
ELB improved by 0.0205601
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.874
ELB improved by 0.0236365
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.844
ELB improved by 0.0299607
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.802
ELB improved by 0.0423008
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.735
ELB improved by 0.0661419
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.626
ELB improved by 0.109518
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.453
ELB improved by 0.172989
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.226
ELB improved by 0.227439
iteration 99
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.993
ELB improved by 0.232185
iteration 100
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.802
ELB improved by 0.190853
iteration 101
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.666
ELB improved by 0.136391
iteration 102
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.574
ELB improved by 0.0922088
iteration 103
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.51
ELB improved by 0.0634148
iteration 104
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.465
ELB improved by 0.045906
iteration 105
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.43
ELB improved by 0.0348899
iteration 106
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.402
ELB improved by 0.027295
iteration 107
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.381
ELB improved by 0.021536
iteration 108
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.364
ELB improved by 0.0169147
iteration 109
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.351
ELB improved by 0.013168
iteration 110
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.341
ELB improved by 0.0101902
iteration 111
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.333
ELB improved by 0.00789757
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-870.922
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-590.102
ELB improved by 280.82
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-529.376
ELB improved by 60.7265
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-484.233
ELB improved by 45.1423
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.044
ELB improved by 23.1894
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.589
ELB improved by 10.4545
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.362
ELB improved by 6.22706
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.073
ELB improved by 5.28954
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.64
ELB improved by 5.4328
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.775
ELB improved by 5.86481
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.901
ELB improved by 5.87468
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.915
ELB improved by 4.98514
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.409
ELB improved by 3.50621
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.24
ELB improved by 2.16948
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.935
ELB improved by 1.30523
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.108
ELB improved by 0.826089
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.542
ELB improved by 0.566203
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.125
ELB improved by 0.417229
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.8
ELB improved by 0.324599
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.538
ELB improved by 0.262477
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.32
ELB improved by 0.218234
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.134
ELB improved by 0.185241
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.975
ELB improved by 0.15975
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.835
ELB improved by 0.139502
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.712
ELB improved by 0.123061
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.603
ELB improved by 0.109474
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.505
ELB improved by 0.0980832
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.416
ELB improved by 0.0884194
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.336
ELB improved by 0.0801384
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.263
ELB improved by 0.0729814
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.196
ELB improved by 0.0667497
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.135
ELB improved by 0.0612879
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.079
ELB improved by 0.0564729
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.026
ELB improved by 0.0522058
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.978
ELB improved by 0.048406
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.933
ELB improved by 0.0450078
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.891
ELB improved by 0.0419566
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.852
ELB improved by 0.0392071
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.815
ELB improved by 0.0367212
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.781
ELB improved by 0.034467
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.748
ELB improved by 0.0324174
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.718
ELB improved by 0.0305493
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.689
ELB improved by 0.0288434
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.661
ELB improved by 0.0272828
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.636
ELB improved by 0.0258535
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.611
ELB improved by 0.0245434
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.588
ELB improved by 0.0233426
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.565
ELB improved by 0.0222425
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.544
ELB improved by 0.0212365
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.524
ELB improved by 0.0203192
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.504
ELB improved by 0.0194871
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.486
ELB improved by 0.0187379
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.468
ELB improved by 0.0180713
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.45
ELB improved by 0.0174885
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.433
ELB improved by 0.0169933
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.417
ELB improved by 0.0165916
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.4
ELB improved by 0.0162921
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.384
ELB improved by 0.0161068
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.368
ELB improved by 0.0160504
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.352
ELB improved by 0.0161405
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.336
ELB improved by 0.0163957
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.319
ELB improved by 0.0168321
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.301
ELB improved by 0.0174575
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.283
ELB improved by 0.0182608
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.264
ELB improved by 0.0191993
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.244
ELB improved by 0.0201843
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.223
ELB improved by 0.0210734
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.201
ELB improved by 0.0216788
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.179
ELB improved by 0.0218033
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.158
ELB improved by 0.0213008
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.138
ELB improved by 0.0201413
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.119
ELB improved by 0.018442
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.103
ELB improved by 0.016437
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.088
ELB improved by 0.0143955
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.076
ELB improved by 0.0125359
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.065
ELB improved by 0.0109789
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.055
ELB improved by 0.00974997
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-864.724
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-560.213
ELB improved by 304.511
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-501.287
ELB improved by 58.926
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.873
ELB improved by 33.4139
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.491
ELB improved by 13.3819
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.8
ELB improved by 5.69073
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.159
ELB improved by 3.6415
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.182
ELB improved by 2.97697
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.399
ELB improved by 2.78253
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.6
ELB improved by 2.79977
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.681
ELB improved by 2.91906
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.636
ELB improved by 3.04475
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.595
ELB improved by 3.04098
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.807
ELB improved by 2.78804
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.507
ELB improved by 2.29993
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.771
ELB improved by 1.73591
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.51
ELB improved by 1.26104
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.574
ELB improved by 0.93614
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.838
ELB improved by 0.73614
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.225
ELB improved by 0.613057
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.691
ELB improved by 0.533934
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.207
ELB improved by 0.48392
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.753
ELB improved by 0.45371
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.318
ELB improved by 0.434904
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.897
ELB improved by 0.421512
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.486
ELB improved by 0.410506
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.085
ELB improved by 0.401137
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.691
ELB improved by 0.394075
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.3
ELB improved by 0.390783
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.907
ELB improved by 0.393292
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.502
ELB improved by 0.404443
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.074
ELB improved by 0.428201
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.606
ELB improved by 0.468251
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.085
ELB improved by 0.52103
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.518
ELB improved by 0.567382
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.928
ELB improved by 0.58931
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.331
ELB improved by 0.597287
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.72
ELB improved by 0.611259
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.083
ELB improved by 0.637146
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.413
ELB improved by 0.669611
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.714
ELB improved by 0.699029
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.998
ELB improved by 0.716256
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.284
ELB improved by 0.713242
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.611
ELB improved by 0.673786
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.033
ELB improved by 0.577415
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.59
ELB improved by 0.442723
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.273
ELB improved by 0.317193
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.051
ELB improved by 0.222343
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.895
ELB improved by 0.155879
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.785
ELB improved by 0.110429
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.705
ELB improved by 0.0796103
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.646
ELB improved by 0.058749
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.602
ELB improved by 0.0446253
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.567
ELB improved by 0.0351016
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.538
ELB improved by 0.0288028
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.513
ELB improved by 0.0248901
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.49
ELB improved by 0.0229301
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.467
ELB improved by 0.022851
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.442
ELB improved by 0.0249899
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.412
ELB improved by 0.0302368
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.372
ELB improved by 0.0402077
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.315
ELB improved by 0.0570063
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.233
ELB improved by 0.0811482
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.127
ELB improved by 0.106059
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.012
ELB improved by 0.115353
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.914
ELB improved by 0.098521
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.846
ELB improved by 0.0677139
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.805
ELB improved by 0.0410114
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.781
ELB improved by 0.0242535
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.765
ELB improved by 0.0151267
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.755
ELB improved by 0.0103357
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.747
ELB improved by 0.00774759
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.379 0.177 2.545
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.049 | 0.004 | 0.053 | |
| getPIPs | 0.045 | 0.005 | 0.051 | |
| graper | 0.082 | 0.002 | 0.084 | |
| makeExampleData | 0.009 | 0.002 | 0.011 | |
| makeExampleDataWithUnequalGroups | 0.013 | 0.000 | 0.013 | |
| plotELBO | 0.326 | 0.019 | 0.346 | |
| plotGroupPenalties | 1.082 | 0.041 | 1.123 | |
| plotPosterior | 0.709 | 0.005 | 0.714 | |
| predict.graper | 2.048 | 0.020 | 2.069 | |
| print.graper | 0.048 | 0.010 | 0.058 | |