Britta Velten
| Snapshot Date: 2026-05-24 13:45 -0400 (Sun, 24 May 2026) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: ba611e2 |
| git_last_commit_date: 2026-04-28 08:49:19 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-25 11:36 -0400 (Mon, 25 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4937 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There" | 4639 |
| 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 933/2379 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.29.0 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | 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: 1.29.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings graper_1.29.0.tar.gz |
| StartedAt: 2026-05-25 00:39:12 -0400 (Mon, 25 May 2026) |
| EndedAt: 2026-05-25 00:40:47 -0400 (Mon, 25 May 2026) |
| EllapsedTime: 95.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings graper_1.29.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.24-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: 2026-05-25 04:39:12 UTC
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.29.0’
* 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 6.2Mb
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 ... 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-3.24-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.29.0’ ** 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-3.24-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.24-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-3.24-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.24-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-3.24-bioc/R/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -llapack -L/home/biocbuild/bbs-3.24-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.24-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.24-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=-865.347
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-561.733
ELB improved by 303.613
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-504.367
ELB improved by 57.3665
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.114
ELB improved by 32.2526
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.604
ELB improved by 14.5101
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.001
ELB improved by 6.60297
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.352
ELB improved by 4.64928
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.16
ELB improved by 4.19131
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.089
ELB improved by 4.07112
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.066
ELB improved by 4.02305
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.152
ELB improved by 3.91451
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.503
ELB improved by 3.64887
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.311
ELB improved by 3.19175
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.677
ELB improved by 2.63444
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.518
ELB improved by 2.15815
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.672
ELB improved by 1.84652
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.147
ELB improved by 1.52513
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.044
ELB improved by 1.10249
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.341
ELB improved by 0.703743
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.909
ELB improved by 0.43155
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.621
ELB improved by 0.288201
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.404
ELB improved by 0.216885
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.227
ELB improved by 0.176978
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.076
ELB improved by 0.150809
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.945
ELB improved by 0.131413
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.829
ELB improved by 0.115892
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.726
ELB improved by 0.102923
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.634
ELB improved by 0.0918333
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.552
ELB improved by 0.0822363
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.478
ELB improved by 0.0738787
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.411
ELB improved by 0.066572
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.351
ELB improved by 0.0601639
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.297
ELB improved by 0.0545261
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.247
ELB improved by 0.0495498
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.202
ELB improved by 0.0451423
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.161
ELB improved by 0.0412252
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.123
ELB improved by 0.0377322
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.088
ELB improved by 0.0346078
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.057
ELB improved by 0.0318048
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.027
ELB improved by 0.0292832
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411
ELB improved by 0.0270093
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.975
ELB improved by 0.0249537
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.952
ELB improved by 0.0230916
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.931
ELB improved by 0.0214013
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.911
ELB improved by 0.0198639
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.893
ELB improved by 0.018463
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.875
ELB improved by 0.0171843
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.859
ELB improved by 0.016015
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.844
ELB improved by 0.0149441
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.83
ELB improved by 0.0139617
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.817
ELB improved by 0.0130591
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.805
ELB improved by 0.0122287
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.794
ELB improved by 0.0114636
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.783
ELB improved by 0.0107576
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.773
ELB improved by 0.0101055
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.763
ELB improved by 0.00950225
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-896
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-584.142
ELB improved by 311.858
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-523.012
ELB improved by 61.13
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-485.544
ELB improved by 37.4677
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.761
ELB improved by 15.783
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.232
ELB improved by 7.52944
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.86
ELB improved by 5.37122
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.786
ELB improved by 5.07485
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.477
ELB improved by 5.30847
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.896
ELB improved by 5.58067
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.34
ELB improved by 5.5559
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.278
ELB improved by 5.06231
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.153
ELB improved by 4.12502
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.148
ELB improved by 3.00527
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.055
ELB improved by 2.09292
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.515
ELB improved by 1.54037
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.238
ELB improved by 1.27692
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.088
ELB improved by 1.14983
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.085
ELB improved by 1.00255
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.291
ELB improved by 0.794754
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.707
ELB improved by 0.58327
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.283
ELB improved by 0.42379
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.961
ELB improved by 0.322582
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.702
ELB improved by 0.2586
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.488
ELB improved by 0.214481
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.306
ELB improved by 0.181359
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.151
ELB improved by 0.155168
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.017
ELB improved by 0.133897
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.901
ELB improved by 0.116366
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.799
ELB improved by 0.101776
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.71
ELB improved by 0.0895325
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.631
ELB improved by 0.0791804
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.56
ELB improved by 0.0703647
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.497
ELB improved by 0.0628067
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.441
ELB improved by 0.0562867
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.39
ELB improved by 0.0506295
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.345
ELB improved by 0.0456951
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.303
ELB improved by 0.0413702
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.266
ELB improved by 0.0375628
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.232
ELB improved by 0.0341972
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.2
ELB improved by 0.031211
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.172
ELB improved by 0.0285522
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.146
ELB improved by 0.0261775
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.122
ELB improved by 0.02405
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.099
ELB improved by 0.0221389
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.079
ELB improved by 0.0204177
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.06
ELB improved by 0.0188638
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.043
ELB improved by 0.0174579
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.027
ELB improved by 0.016183
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.012
ELB improved by 0.0150248
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.998
ELB improved by 0.0139705
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.985
ELB improved by 0.0130092
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.972
ELB improved by 0.0121311
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.961
ELB improved by 0.0113279
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.951
ELB improved by 0.0105919
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.941
ELB improved by 0.00991671
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-867.65
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-544.453
ELB improved by 323.196
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-492.765
ELB improved by 51.6879
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.462
ELB improved by 26.3039
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.547
ELB improved by 11.9143
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.467
ELB improved by 6.08068
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.589
ELB improved by 3.87718
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.552
ELB improved by 3.03744
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.813
ELB improved by 2.73887
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.174
ELB improved by 2.63871
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.581
ELB improved by 2.5931
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.053
ELB improved by 2.52806
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.677
ELB improved by 2.37655
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.59
ELB improved by 2.08655
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.899
ELB improved by 1.69066
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.603
ELB improved by 1.29627
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.617
ELB improved by 0.985657
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.841
ELB improved by 0.776432
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.192
ELB improved by 0.649308
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.614
ELB improved by 0.57757
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.075
ELB improved by 0.539498
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.554
ELB improved by 0.520388
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.043
ELB improved by 0.510973
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.538
ELB improved by 0.505582
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.037
ELB improved by 0.501001
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.541
ELB improved by 0.495911
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.05
ELB improved by 0.490471
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.565
ELB improved by 0.485755
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.082
ELB improved by 0.483032
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.599
ELB improved by 0.48307
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.113
ELB improved by 0.485634
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.624
ELB improved by 0.489256
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.132
ELB improved by 0.491327
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.644
ELB improved by 0.488547
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.166
ELB improved by 0.477735
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.709
ELB improved by 0.456822
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.284
ELB improved by 0.425649
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.897
ELB improved by 0.386142
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.556
ELB improved by 0.341723
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.259
ELB improved by 0.296233
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.007
ELB improved by 0.252924
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.793
ELB improved by 0.213906
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.612
ELB improved by 0.180133
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.461
ELB improved by 0.151704
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.333
ELB improved by 0.128244
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.223
ELB improved by 0.109183
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.129
ELB improved by 0.0939149
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.048
ELB improved by 0.0818589
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.975
ELB improved by 0.0724577
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.91
ELB improved by 0.0651542
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.851
ELB improved by 0.0593805
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.796
ELB improved by 0.054597
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.746
ELB improved by 0.0503976
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.699
ELB improved by 0.0466347
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.655
ELB improved by 0.0434777
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.614
ELB improved by 0.0413834
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.573
ELB improved by 0.0410962
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.529
ELB improved by 0.0438862
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.477
ELB improved by 0.0523349
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.404
ELB improved by 0.0723231
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.287
ELB improved by 0.117328
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.075
ELB improved by 0.211907
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.715
ELB improved by 0.360309
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.265
ELB improved by 0.449838
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.887
ELB improved by 0.377981
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.651
ELB improved by 0.236537
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.535
ELB improved by 0.115414
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.477
ELB improved by 0.0576934
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.44
ELB improved by 0.0371321
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.412
ELB improved by 0.0281491
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.389
ELB improved by 0.0228835
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.37
ELB improved by 0.0193337
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.353
ELB improved by 0.0168101
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.338
ELB improved by 0.0149692
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.325
ELB improved by 0.0136002
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.312
ELB improved by 0.0125591
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.3
ELB improved by 0.0117421
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.289
ELB improved by 0.0110718
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.279
ELB improved by 0.0104905
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.269
ELB improved by 0.00995625
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-877.493
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-576.585
ELB improved by 300.907
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-517.505
ELB improved by 59.0805
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-481.215
ELB improved by 36.2899
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.273
ELB improved by 13.9421
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.004
ELB improved by 6.26895
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.378
ELB improved by 4.62568
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.038
ELB improved by 4.34032
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.519
ELB improved by 4.51868
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.752
ELB improved by 4.76763
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.03
ELB improved by 4.72221
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.918
ELB improved by 4.11128
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.822
ELB improved by 3.0965
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.69
ELB improved by 2.13221
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.226
ELB improved by 1.46324
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.172
ELB improved by 1.05392
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.37
ELB improved by 0.80256
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.727
ELB improved by 0.642541
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.189
ELB improved by 0.537929
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.722
ELB improved by 0.46732
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.305
ELB improved by 0.417248
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.925
ELB improved by 0.379731
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.574
ELB improved by 0.350663
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.246
ELB improved by 0.328244
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.935
ELB improved by 0.311565
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.635
ELB improved by 0.299804
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.343
ELB improved by 0.292079
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.055
ELB improved by 0.287586
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.769
ELB improved by 0.285731
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.483
ELB improved by 0.286172
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.194
ELB improved by 0.288803
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.901
ELB improved by 0.293689
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.6
ELB improved by 0.30093
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.289
ELB improved by 0.310439
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.968
ELB improved by 0.321658
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.634
ELB improved by 0.333427
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.29
ELB improved by 0.344417
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.936
ELB improved by 0.354204
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.572
ELB improved by 0.364134
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.195
ELB improved by 0.377006
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.798
ELB improved by 0.396167
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.373
ELB improved by 0.425477
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.903
ELB improved by 0.470343
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.366
ELB improved by 0.536892
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.747
ELB improved by 0.618222
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.083
ELB improved by 0.664698
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.461
ELB improved by 0.62131
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.942
ELB improved by 0.519254
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.528
ELB improved by 0.414271
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.203
ELB improved by 0.325246
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.949
ELB improved by 0.253732
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.751
ELB improved by 0.198
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.595
ELB improved by 0.155479
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.472
ELB improved by 0.123353
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.373
ELB improved by 0.0990499
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.293
ELB improved by 0.0805181
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.226
ELB improved by 0.0662614
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.171
ELB improved by 0.0552337
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.124
ELB improved by 0.0467053
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.084
ELB improved by 0.0401564
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.049
ELB improved by 0.035212
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.017
ELB improved by 0.0316066
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.988
ELB improved by 0.0291694
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.96
ELB improved by 0.0278221
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.933
ELB improved by 0.0275845
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.904
ELB improved by 0.0285853
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.873
ELB improved by 0.0310604
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.838
ELB improved by 0.0352964
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.796
ELB improved by 0.0414225
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.747
ELB improved by 0.0489432
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.691
ELB improved by 0.0561362
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.631
ELB improved by 0.0600987
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.573
ELB improved by 0.0583592
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.522
ELB improved by 0.0510302
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.481
ELB improved by 0.0408181
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.45
ELB improved by 0.0308089
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.428
ELB improved by 0.022716
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.411
ELB improved by 0.016825
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.398
ELB improved by 0.0127316
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.388
ELB improved by 0.00991521
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.416 0.198 2.603
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.054 | 0.005 | 0.058 | |
| getPIPs | 0.073 | 0.014 | 0.087 | |
| graper | 0.081 | 0.003 | 0.084 | |
| makeExampleData | 0.010 | 0.001 | 0.009 | |
| makeExampleDataWithUnequalGroups | 0.012 | 0.000 | 0.012 | |
| plotELBO | 0.303 | 0.019 | 0.322 | |
| plotGroupPenalties | 1.624 | 0.005 | 2.046 | |
| plotPosterior | 1.858 | 0.055 | 2.676 | |
| predict.graper | 2.066 | 0.004 | 2.070 | |
| print.graper | 0.045 | 0.006 | 0.051 | |