| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-12 11:36 -0400 (Tue, 12 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4994 |
| 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 944/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.28.0 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 24.04.4 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: 1.28.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings graper_1.28.0.tar.gz |
| StartedAt: 2026-05-12 00:41:56 -0400 (Tue, 12 May 2026) |
| EndedAt: 2026-05-12 00:43:27 -0400 (Tue, 12 May 2026) |
| EllapsedTime: 91.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings graper_1.28.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-12 04:41:56 UTC
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.28.0’
* 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 ... OK
* 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 ... INFO
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: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.28.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-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++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-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++20 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -llapack -L/home/biocbuild/bbs-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.23-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 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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=-850.599
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-559.737
ELB improved by 290.862
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-497.47
ELB improved by 62.2671
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.787
ELB improved by 40.6826
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.497
ELB improved by 16.2898
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.075
ELB improved by 6.42291
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.293
ELB improved by 3.78151
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.246
ELB improved by 3.04657
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.371
ELB improved by 2.87579
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.373
ELB improved by 2.99729
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.047
ELB improved by 3.32666
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.264
ELB improved by 3.78308
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.08
ELB improved by 4.18409
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.816
ELB improved by 4.26369
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.913
ELB improved by 3.90263
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.673
ELB improved by 3.24038
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.217
ELB improved by 2.45617
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.425
ELB improved by 1.79157
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.044
ELB improved by 1.38111
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.875
ELB improved by 1.16931
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.806
ELB improved by 1.06902
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.781
ELB improved by 1.02488
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.773
ELB improved by 1.00817
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.768
ELB improved by 1.00468
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.761
ELB improved by 1.00728
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.747
ELB improved by 1.01324
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.72
ELB improved by 1.02772
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.645
ELB improved by 1.07476
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.46
ELB improved by 1.18476
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.224
ELB improved by 1.23596
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.175
ELB improved by 1.04969
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.381
ELB improved by 0.794068
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.796
ELB improved by 0.584056
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.373
ELB improved by 0.423206
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.068
ELB improved by 0.305452
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.844
ELB improved by 0.223476
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.676
ELB improved by 0.16881
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.542
ELB improved by 0.133984
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.428
ELB improved by 0.113702
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.323
ELB improved by 0.104575
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.22
ELB improved by 0.103469
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.115
ELB improved by 0.104513
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.017
ELB improved by 0.098721
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.935
ELB improved by 0.0819668
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.874
ELB improved by 0.0607924
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.83
ELB improved by 0.0436058
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.797
ELB improved by 0.0328021
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.771
ELB improved by 0.0267615
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.747
ELB improved by 0.023401
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.726
ELB improved by 0.0213455
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.706
ELB improved by 0.0198372
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.688
ELB improved by 0.0184736
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.671
ELB improved by 0.0170584
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.655
ELB improved by 0.015539
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.641
ELB improved by 0.0139627
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.629
ELB improved by 0.012424
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.618
ELB improved by 0.0110119
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.608
ELB improved by 0.00977963
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-870.668
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-599.24
ELB improved by 271.427
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-542.035
ELB improved by 57.2054
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-495.072
ELB improved by 46.9635
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.803
ELB improved by 26.2686
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.219
ELB improved by 10.5841
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.725
ELB improved by 5.494
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.108
ELB improved by 4.6171
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.313
ELB improved by 4.79517
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.067
ELB improved by 5.24596
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.635
ELB improved by 5.4313
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.687
ELB improved by 4.94879
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.801
ELB improved by 3.88591
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.086
ELB improved by 2.7146
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.293
ELB improved by 1.79271
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.086
ELB improved by 1.20726
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.192
ELB improved by 0.894484
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.411
ELB improved by 0.78021
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.557
ELB improved by 0.854648
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.47
ELB improved by 1.08643
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.291
ELB improved by 1.17948
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.324
ELB improved by 0.967056
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.624
ELB improved by 0.699868
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.098
ELB improved by 0.525481
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.666
ELB improved by 0.432052
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.284
ELB improved by 0.382054
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.933
ELB improved by 0.351069
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.605
ELB improved by 0.328284
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.295
ELB improved by 0.309837
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.001
ELB improved by 0.294609
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.718
ELB improved by 0.282516
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.444
ELB improved by 0.273969
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.174
ELB improved by 0.269794
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.903
ELB improved by 0.271424
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.621
ELB improved by 0.281373
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.317
ELB improved by 0.30406
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.971
ELB improved by 0.346693
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.553
ELB improved by 0.417949
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.033
ELB improved by 0.519651
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.393
ELB improved by 0.639612
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.618
ELB improved by 0.775017
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.683
ELB improved by 0.935548
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.622
ELB improved by 1.06088
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.557
ELB improved by 1.06471
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.579
ELB improved by 0.97848
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.72
ELB improved by 0.858378
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.993
ELB improved by 0.727601
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.394
ELB improved by 0.598693
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.912
ELB improved by 0.481683
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.529
ELB improved by 0.38378
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.224
ELB improved by 0.305129
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.984
ELB improved by 0.239811
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.8
ELB improved by 0.18348
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.663
ELB improved by 0.13683
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.562
ELB improved by 0.10135
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.486
ELB improved by 0.0760204
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.428
ELB improved by 0.0583968
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.381
ELB improved by 0.0462426
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.343
ELB improved by 0.0379875
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.311
ELB improved by 0.0326028
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.281
ELB improved by 0.0293907
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.254
ELB improved by 0.0277981
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.226
ELB improved by 0.0272586
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.199
ELB improved by 0.0270952
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.173
ELB improved by 0.0265723
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.148
ELB improved by 0.0251387
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.125
ELB improved by 0.0226998
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.105
ELB improved by 0.0196332
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.089
ELB improved by 0.0164992
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.075
ELB improved by 0.0137243
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.064
ELB improved by 0.0114861
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.054
ELB improved by 0.00977458
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-833.876
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-573.099
ELB improved by 260.777
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-512.428
ELB improved by 60.6713
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.525
ELB improved by 42.9032
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.833
ELB improved by 20.6918
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.216
ELB improved by 7.61695
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.511
ELB improved by 3.70445
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.905
ELB improved by 2.60646
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.672
ELB improved by 2.23244
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.539
ELB improved by 2.13349
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.401
ELB improved by 2.13815
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.233
ELB improved by 2.1683
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.062
ELB improved by 2.17077
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.967
ELB improved by 2.09433
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.065
ELB improved by 1.90256
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.463
ELB improved by 1.60235
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.211
ELB improved by 1.25185
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.284
ELB improved by 0.926353
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.611
ELB improved by 0.672991
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.114
ELB improved by 0.49729
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.733
ELB improved by 0.38103
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.43
ELB improved by 0.303319
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.18
ELB improved by 0.249783
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.968
ELB improved by 0.212262
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.782
ELB improved by 0.185941
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.614
ELB improved by 0.167525
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.46
ELB improved by 0.154637
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.314
ELB improved by 0.145644
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.174
ELB improved by 0.13951
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.039
ELB improved by 0.135664
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.905
ELB improved by 0.133908
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.77
ELB improved by 0.134415
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.633
ELB improved by 0.137856
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.487
ELB improved by 0.145754
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.326
ELB improved by 0.161259
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.135
ELB improved by 0.190553
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.891
ELB improved by 0.244085
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.559
ELB improved by 0.332034
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.116
ELB improved by 0.442491
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.594
ELB improved by 0.522405
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.057
ELB improved by 0.537334
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.532
ELB improved by 0.524311
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.011
ELB improved by 0.52133
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.475
ELB improved by 0.535731
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.911
ELB improved by 0.564288
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.308
ELB improved by 0.602887
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.661
ELB improved by 0.646849
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.972
ELB improved by 0.689647
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.249
ELB improved by 0.722489
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.513
ELB improved by 0.735714
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.791
ELB improved by 0.722146
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.11
ELB improved by 0.680955
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.491
ELB improved by 0.619241
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.942
ELB improved by 0.549379
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.459
ELB improved by 0.483049
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.033
ELB improved by 0.425621
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.658
ELB improved by 0.37497
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.332
ELB improved by 0.325633
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.058
ELB improved by 0.274414
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.834
ELB improved by 0.223467
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.656
ELB improved by 0.178259
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.514
ELB improved by 0.142602
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.397
ELB improved by 0.117018
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.296
ELB improved by 0.100197
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.206
ELB improved by 0.090345
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.121
ELB improved by 0.0854495
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.038
ELB improved by 0.0828264
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.959
ELB improved by 0.078946
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.888
ELB improved by 0.0708522
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.829
ELB improved by 0.0585852
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.784
ELB improved by 0.0451731
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.751
ELB improved by 0.0336519
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.725
ELB improved by 0.0251186
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.706
ELB improved by 0.0192198
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.691
ELB improved by 0.0152011
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.679
ELB improved by 0.0124215
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.668
ELB improved by 0.0104475
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.659
ELB improved by 0.00900764
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-880.954
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-559.004
ELB improved by 321.95
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-501.364
ELB improved by 57.6398
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.85
ELB improved by 31.5145
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.022
ELB improved by 13.828
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.206
ELB improved by 6.81572
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.597
ELB improved by 4.60933
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.661
ELB improved by 3.93606
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.983
ELB improved by 3.67807
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.508
ELB improved by 3.47521
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.3
ELB improved by 3.20729
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.48
ELB improved by 2.8204
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.194
ELB improved by 2.28618
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.505
ELB improved by 1.68875
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.325
ELB improved by 1.17965
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.498
ELB improved by 0.826892
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.891
ELB improved by 0.607149
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.423
ELB improved by 0.468568
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.047
ELB improved by 0.375312
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.735
ELB improved by 0.312592
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.462
ELB improved by 0.27315
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.211
ELB improved by 0.250747
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.971
ELB improved by 0.240377
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.732
ELB improved by 0.238731
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.488
ELB improved by 0.243765
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.234
ELB improved by 0.254113
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.965
ELB improved by 0.268858
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.677
ELB improved by 0.287731
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.366
ELB improved by 0.311365
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.025
ELB improved by 0.34119
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.646
ELB improved by 0.378904
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.22
ELB improved by 0.425551
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.741
ELB improved by 0.479759
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.205
ELB improved by 0.535596
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.621
ELB improved by 0.583834
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.002
ELB improved by 0.618859
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.361
ELB improved by 0.64173
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.706
ELB improved by 0.654191
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.052
ELB improved by 0.654441
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.413
ELB improved by 0.638724
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.809
ELB improved by 0.604596
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.255
ELB improved by 0.553676
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.763
ELB improved by 0.492353
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.333
ELB improved by 0.429366
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.961
ELB improved by 0.371763
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.639
ELB improved by 0.322406
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.358
ELB improved by 0.280739
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.113
ELB improved by 0.245387
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.897
ELB improved by 0.215935
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.704
ELB improved by 0.193092
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.526
ELB improved by 0.178223
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.353
ELB improved by 0.172696
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.177
ELB improved by 0.176135
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.994
ELB improved by 0.182588
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.815
ELB improved by 0.179504
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.655
ELB improved by 0.159872
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.523
ELB improved by 0.132195
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.416
ELB improved by 0.106443
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.332
ELB improved by 0.0841347
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.268
ELB improved by 0.064359
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.22
ELB improved by 0.047768
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.185
ELB improved by 0.0352561
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.158
ELB improved by 0.0266304
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.137
ELB improved by 0.0209297
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.12
ELB improved by 0.0171416
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.106
ELB improved by 0.0145292
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.093
ELB improved by 0.0126371
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.082
ELB improved by 0.0112012
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.072
ELB improved by 0.0100688
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.062
ELB improved by 0.00914841
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.381 0.192 2.557
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.045 | 0.032 | 0.077 | |
| getPIPs | 0.074 | 0.031 | 0.105 | |
| graper | 0.079 | 0.020 | 0.101 | |
| makeExampleData | 0.009 | 0.001 | 0.011 | |
| makeExampleDataWithUnequalGroups | 0.011 | 0.000 | 0.012 | |
| plotELBO | 0.299 | 0.026 | 0.325 | |
| plotGroupPenalties | 0.931 | 0.015 | 0.944 | |
| plotPosterior | 0.635 | 0.013 | 0.649 | |
| predict.graper | 2.060 | 0.081 | 2.141 | |
| print.graper | 0.054 | 0.010 | 0.064 | |