Britta Velten
| Snapshot Date: 2026-03-29 13:45 -0400 (Sun, 29 Mar 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 2026-03-30 11:57 -0400 (Mon, 30 Mar 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" | 4893 |
| 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: 2026-03-30 00:35:52 -0400 (Mon, 30 Mar 2026) |
| EndedAt: 2026-03-30 00:37:24 -0400 (Mon, 30 Mar 2026) |
| EllapsedTime: 92.1 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=-868.858
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-576.314
ELB improved by 292.543
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-517.166
ELB improved by 59.1486
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-478.854
ELB improved by 38.3119
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.741
ELB improved by 18.1131
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.459
ELB improved by 9.28174
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.639
ELB improved by 7.81994
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.277
ELB improved by 8.36222
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.722
ELB improved by 8.55472
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.417
ELB improved by 7.30511
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.246
ELB improved by 5.17079
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.904
ELB improved by 3.34208
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.677
ELB improved by 2.22702
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.041
ELB improved by 1.63626
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.711
ELB improved by 1.3293
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.548
ELB improved by 1.16302
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.474
ELB improved by 1.07422
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.442
ELB improved by 1.03272
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.424
ELB improved by 1.01782
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.406
ELB improved by 1.01739
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.377
ELB improved by 1.02891
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.318
ELB improved by 1.05903
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.196
ELB improved by 1.12277
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.961
ELB improved by 1.23448
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.587
ELB improved by 1.37367
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.106
ELB improved by 1.48175
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.558
ELB improved by 1.54724
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.955
ELB improved by 1.60325
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.254
ELB improved by 1.70105
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.444
ELB improved by 1.80999
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.7
ELB improved by 1.74424
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.879
ELB improved by 1.8206
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.279
ELB improved by 1.6004
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.297
ELB improved by 0.982021
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.67
ELB improved by 0.627023
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.179
ELB improved by 0.491287
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.704
ELB improved by 0.474316
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.191
ELB improved by 0.513595
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.58
ELB improved by 0.610853
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.7
ELB improved by 0.879518
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.707
ELB improved by 0.993257
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.984
ELB improved by 0.723127
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.496
ELB improved by 0.487672
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.17
ELB improved by 0.325831
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.939
ELB improved by 0.231456
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.755
ELB improved by 0.183585
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.597
ELB improved by 0.158621
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.453
ELB improved by 0.143273
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.323
ELB improved by 0.130221
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.208
ELB improved by 0.11555
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.109
ELB improved by 0.0987396
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.027
ELB improved by 0.0817838
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.96
ELB improved by 0.0668032
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.906
ELB improved by 0.0545861
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.861
ELB improved by 0.0448728
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.824
ELB improved by 0.0371047
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.793
ELB improved by 0.0308201
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.767
ELB improved by 0.025715
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.746
ELB improved by 0.0215815
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.727
ELB improved by 0.0182525
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.712
ELB improved by 0.0155788
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.698
ELB improved by 0.0134287
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.687
ELB improved by 0.0116906
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.676
ELB improved by 0.0102744
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.667
ELB improved by 0.00910964
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-847.774
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-554.091
ELB improved by 293.683
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-499.449
ELB improved by 54.642
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.814
ELB improved by 31.6353
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.355
ELB improved by 14.4593
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.43
ELB improved by 5.92434
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.241
ELB improved by 3.18894
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.812
ELB improved by 2.42979
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.577
ELB improved by 2.23493
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.305
ELB improved by 2.27216
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.87
ELB improved by 2.43442
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.198
ELB improved by 2.67214
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.26
ELB improved by 2.93836
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.12
ELB improved by 3.14
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.02
ELB improved by 3.09978
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.336
ELB improved by 2.68341
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.307
ELB improved by 2.0295
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.896
ELB improved by 1.41126
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.938
ELB improved by 0.958195
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.276
ELB improved by 0.661733
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.799
ELB improved by 0.476717
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.436
ELB improved by 0.363207
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.143
ELB improved by 0.292886
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.895
ELB improved by 0.24787
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.677
ELB improved by 0.21779
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.48
ELB improved by 0.196845
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.299
ELB improved by 0.181757
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.128
ELB improved by 0.170599
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.966
ELB improved by 0.162166
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.81
ELB improved by 0.155657
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.66
ELB improved by 0.15051
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.513
ELB improved by 0.146317
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.371
ELB improved by 0.142778
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.231
ELB improved by 0.139677
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.094
ELB improved by 0.136857
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.96
ELB improved by 0.134217
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.828
ELB improved by 0.131692
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.699
ELB improved by 0.129249
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.572
ELB improved by 0.12688
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.448
ELB improved by 0.124588
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.325
ELB improved by 0.122385
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.205
ELB improved by 0.120285
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.087
ELB improved by 0.1183
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.97
ELB improved by 0.116432
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.855
ELB improved by 0.114677
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.742
ELB improved by 0.113021
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.631
ELB improved by 0.111439
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.521
ELB improved by 0.1099
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.413
ELB improved by 0.108366
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.306
ELB improved by 0.106793
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.201
ELB improved by 0.10514
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.097
ELB improved by 0.103365
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.996
ELB improved by 0.101433
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.897
ELB improved by 0.0993174
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.8
ELB improved by 0.0970057
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.705
ELB improved by 0.0945003
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.613
ELB improved by 0.0918215
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.524
ELB improved by 0.0890092
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.438
ELB improved by 0.086123
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.355
ELB improved by 0.0832419
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.275
ELB improved by 0.0804632
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.197
ELB improved by 0.0778997
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.121
ELB improved by 0.0756732
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.047
ELB improved by 0.0738989
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.974
ELB improved by 0.0726504
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.903
ELB improved by 0.0718892
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.831
ELB improved by 0.071356
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.761
ELB improved by 0.0704732
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.692
ELB improved by 0.0684115
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.628
ELB improved by 0.0644803
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.569
ELB improved by 0.0586849
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.517
ELB improved by 0.0518705
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.472
ELB improved by 0.0451768
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.433
ELB improved by 0.0393695
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.398
ELB improved by 0.0346554
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.367
ELB improved by 0.0309009
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.339
ELB improved by 0.0278836
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.314
ELB improved by 0.025416
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.29
ELB improved by 0.0233699
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.269
ELB improved by 0.0216639
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.249
ELB improved by 0.0202462
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.229
ELB improved by 0.0190824
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.211
ELB improved by 0.0181479
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.194
ELB improved by 0.0174226
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.177
ELB improved by 0.0168873
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.16
ELB improved by 0.0165191
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.144
ELB improved by 0.0162872
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.128
ELB improved by 0.0161473
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.112
ELB improved by 0.0160377
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.096
ELB improved by 0.0158791
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.081
ELB improved by 0.0155827
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.065
ELB improved by 0.0150686
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.051
ELB improved by 0.0142903
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.038
ELB improved by 0.0132557
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.026
ELB improved by 0.0120289
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.015
ELB improved by 0.0107107
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.006
ELB improved by 0.00940559
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-878.907
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-588.568
ELB improved by 290.338
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-531.727
ELB improved by 56.8416
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-490.141
ELB improved by 41.5856
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.408
ELB improved by 21.7336
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.892
ELB improved by 9.5161
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.612
ELB improved by 5.27951
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.358
ELB improved by 4.2539
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.173
ELB improved by 4.18493
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.791
ELB improved by 4.38182
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.179
ELB improved by 4.61233
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.551
ELB improved by 4.62862
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.405
ELB improved by 4.14562
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.248
ELB improved by 3.15704
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.145
ELB improved by 2.10295
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.783
ELB improved by 1.362
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.829
ELB improved by 0.953582
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.072
ELB improved by 0.75771
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.393
ELB improved by 0.678179
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.732
ELB improved by 0.661772
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.05
ELB improved by 0.681799
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.325
ELB improved by 0.725025
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.54
ELB improved by 0.784673
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.683
ELB improved by 0.857069
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.743
ELB improved by 0.940032
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.711
ELB improved by 1.03199
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.58
ELB improved by 1.13137
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.344
ELB improved by 1.23575
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.004
ELB improved by 1.33979
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.572
ELB improved by 1.43224
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.077
ELB improved by 1.4954
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.562
ELB improved by 1.51415
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.071
ELB improved by 1.49154
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.623
ELB improved by 1.44744
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.236
ELB improved by 1.38779
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.955
ELB improved by 1.28015
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.835
ELB improved by 1.12054
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.853
ELB improved by 0.98169
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.889
ELB improved by 0.964245
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.874
ELB improved by 1.01527
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.976
ELB improved by 0.8982
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.369
ELB improved by 0.606713
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.037
ELB improved by 0.332117
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.859
ELB improved by 0.177305
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.753
ELB improved by 0.105938
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.68
ELB improved by 0.0733788
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.623
ELB improved by 0.0568994
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.576
ELB improved by 0.0471572
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.535
ELB improved by 0.0405391
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.5
ELB improved by 0.035613
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.468
ELB improved by 0.0317522
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.439
ELB improved by 0.0286386
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.413
ELB improved by 0.0260833
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.389
ELB improved by 0.0239587
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.367
ELB improved by 0.0221692
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.347
ELB improved by 0.0206377
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.327
ELB improved by 0.0192981
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.309
ELB improved by 0.018092
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.292
ELB improved by 0.0169665
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.276
ELB improved by 0.0158754
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.262
ELB improved by 0.0147807
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.248
ELB improved by 0.0136562
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.235
ELB improved by 0.0124904
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.224
ELB improved by 0.0112905
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.214
ELB improved by 0.010081
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.205
ELB improved by 0.00890019
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-865.213
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-597.726
ELB improved by 267.487
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-539.655
ELB improved by 58.0714
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-494.147
ELB improved by 45.5075
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.938
ELB improved by 26.209
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.894
ELB improved by 11.0446
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.147
ELB improved by 5.74686
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.229
ELB improved by 4.91832
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.281
ELB improved by 4.94729
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.022
ELB improved by 5.25883
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.332
ELB improved by 5.69009
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.364
ELB improved by 5.96846
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.605
ELB improved by 5.75913
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.574
ELB improved by 5.03096
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.494
ELB improved by 4.07951
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.335
ELB improved by 3.15874
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.967
ELB improved by 2.36863
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.269
ELB improved by 1.69821
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.058
ELB improved by 1.2109
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.14
ELB improved by 0.917691
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.389
ELB improved by 0.750648
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.745
ELB improved by 0.644259
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.195
ELB improved by 0.550369
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.748
ELB improved by 0.447087
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.401
ELB improved by 0.346571
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.134
ELB improved by 0.267424
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.922
ELB improved by 0.211938
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.748
ELB improved by 0.173328
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.603
ELB improved by 0.145226
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.479
ELB improved by 0.123715
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.373
ELB improved by 0.106604
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.28
ELB improved by 0.0926388
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.199
ELB improved by 0.0810452
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.128
ELB improved by 0.0713034
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.065
ELB improved by 0.0630421
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.009
ELB improved by 0.0559835
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.959
ELB improved by 0.049914
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.914
ELB improved by 0.0446655
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.874
ELB improved by 0.0401041
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.838
ELB improved by 0.036122
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.805
ELB improved by 0.0326311
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.776
ELB improved by 0.0295593
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.749
ELB improved by 0.0268469
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.725
ELB improved by 0.0244442
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.702
ELB improved by 0.0223095
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.682
ELB improved by 0.0204076
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.663
ELB improved by 0.0187089
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.646
ELB improved by 0.017188
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.63
ELB improved by 0.0158232
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.616
ELB improved by 0.0145959
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.602
ELB improved by 0.01349
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.59
ELB improved by 0.0124915
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.578
ELB improved by 0.0115885
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.567
ELB improved by 0.0107704
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.557
ELB improved by 0.0100279
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.548
ELB improved by 0.00935295
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.461 0.182 2.628
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.054 | 0.000 | 0.054 | |
| getPIPs | 0.046 | 0.005 | 0.050 | |
| graper | 0.082 | 0.002 | 0.084 | |
| makeExampleData | 0.008 | 0.002 | 0.010 | |
| makeExampleDataWithUnequalGroups | 0.011 | 0.001 | 0.012 | |
| plotELBO | 0.328 | 0.012 | 0.340 | |
| plotGroupPenalties | 1.147 | 0.035 | 1.182 | |
| plotPosterior | 0.647 | 0.008 | 0.654 | |
| predict.graper | 2.042 | 0.015 | 2.058 | |
| print.graper | 0.046 | 0.006 | 0.051 | |