Britta Velten
| Snapshot Date: 2026-01-23 13:40 -0500 (Fri, 23 Jan 2026) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: 95474d7 |
| git_last_commit_date: 2025-10-29 10:49:21 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-24 11:34 -0500 (Sat, 24 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4811 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4545 |
| 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 921/2345 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.27.0 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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: 1.27.0 |
| 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_1.27.0.tar.gz |
| StartedAt: 2026-01-24 00:13:29 -0500 (Sat, 24 Jan 2026) |
| EndedAt: 2026-01-24 00:15:00 -0500 (Sat, 24 Jan 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_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.27.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... 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 ‘1.27.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-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++17 -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++17 -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 Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
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=-874.964
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-581.125
ELB improved by 293.839
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-519.839
ELB improved by 61.2857
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-479.476
ELB improved by 40.3635
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.247
ELB improved by 18.2287
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.842
ELB improved by 8.40517
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.501
ELB improved by 5.34136
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.848
ELB improved by 4.65223
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.126
ELB improved by 4.72184
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.151
ELB improved by 4.97551
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.106
ELB improved by 5.04494
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.507
ELB improved by 4.59883
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.857
ELB improved by 3.65025
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.229
ELB improved by 2.62776
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.364
ELB improved by 1.86529
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.002
ELB improved by 1.36147
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.976
ELB improved by 1.02607
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.164
ELB improved by 0.811869
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.48
ELB improved by 0.684405
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.866
ELB improved by 0.614191
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.287
ELB improved by 0.578593
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.728
ELB improved by 0.558911
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.183
ELB improved by 0.545877
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.636
ELB improved by 0.546259
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.063
ELB improved by 0.57293
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.429
ELB improved by 0.634326
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.693
ELB improved by 0.736408
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.805
ELB improved by 0.887205
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.707
ELB improved by 1.0986
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.319
ELB improved by 1.38756
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.538
ELB improved by 1.78141
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.22
ELB improved by 2.31756
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.308
ELB improved by 2.91204
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.129
ELB improved by 3.17899
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.182
ELB improved by 2.94771
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.905
ELB improved by 2.27663
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.396
ELB improved by 1.50897
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.443
ELB improved by 0.953272
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.825
ELB improved by 0.617497
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.404
ELB improved by 0.420765
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.104
ELB improved by 0.300806
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.88
ELB improved by 0.223346
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.709
ELB improved by 0.170751
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.576
ELB improved by 0.133615
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.469
ELB improved by 0.106581
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.383
ELB improved by 0.0864075
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.312
ELB improved by 0.0710387
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.253
ELB improved by 0.0591207
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.203
ELB improved by 0.0497351
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.161
ELB improved by 0.0422434
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.125
ELB improved by 0.0361915
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.093
ELB improved by 0.0312508
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.066
ELB improved by 0.0271789
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.042
ELB improved by 0.0237945
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.021
ELB improved by 0.02096
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.003
ELB improved by 0.0185698
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.986
ELB improved by 0.0165418
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.971
ELB improved by 0.0148112
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.958
ELB improved by 0.0133269
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.946
ELB improved by 0.0120479
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.935
ELB improved by 0.0109409
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.925
ELB improved by 0.00997899
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-901.469
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-575.279
ELB improved by 326.189
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-517.685
ELB improved by 57.5944
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-484.177
ELB improved by 33.5078
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.783
ELB improved by 14.3944
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.375
ELB improved by 7.40814
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.993
ELB improved by 5.38194
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.003
ELB improved by 4.98952
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.069
ELB improved by 4.93444
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.349
ELB improved by 4.71956
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.176
ELB improved by 4.17314
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.735
ELB improved by 3.4412
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.936
ELB improved by 2.7988
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.621
ELB improved by 2.31483
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.776
ELB improved by 1.84505
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.397
ELB improved by 1.3792
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.369
ELB improved by 1.02809
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.558
ELB improved by 0.810806
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.861
ELB improved by 0.697287
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.208
ELB improved by 0.652728
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.583
ELB improved by 0.624708
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.025
ELB improved by 0.557883
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.569
ELB improved by 0.456071
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.213
ELB improved by 0.356503
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.937
ELB improved by 0.27577
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.72
ELB improved by 0.217011
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.542
ELB improved by 0.177769
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.39
ELB improved by 0.152511
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.254
ELB improved by 0.136058
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.129
ELB improved by 0.124953
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.012
ELB improved by 0.117211
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.9
ELB improved by 0.111754
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.792
ELB improved by 0.107984
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.686
ELB improved by 0.105557
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.582
ELB improved by 0.104255
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.478
ELB improved by 0.103936
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.374
ELB improved by 0.104501
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.268
ELB improved by 0.105877
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.16
ELB improved by 0.108014
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.049
ELB improved by 0.110879
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.934
ELB improved by 0.114453
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.816
ELB improved by 0.118732
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.692
ELB improved by 0.123731
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.562
ELB improved by 0.129482
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.426
ELB improved by 0.136044
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.283
ELB improved by 0.143501
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.131
ELB improved by 0.151976
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.969
ELB improved by 0.161627
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.797
ELB improved by 0.172654
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.611
ELB improved by 0.185299
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.411
ELB improved by 0.199837
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.195
ELB improved by 0.216562
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.959
ELB improved by 0.235752
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.702
ELB improved by 0.257618
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.419
ELB improved by 0.28221
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.11
ELB improved by 0.309296
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.772
ELB improved by 0.3382
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.404
ELB improved by 0.367635
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.009
ELB improved by 0.39555
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.59
ELB improved by 0.41908
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.155
ELB improved by 0.434704
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.716
ELB improved by 0.438802
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.287
ELB improved by 0.428721
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.883
ELB improved by 0.40409
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.516
ELB improved by 0.367649
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.191
ELB improved by 0.324856
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.909
ELB improved by 0.282188
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.664
ELB improved by 0.244976
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.447
ELB improved by 0.21611
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.251
ELB improved by 0.1963
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.066
ELB improved by 0.185226
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.885
ELB improved by 0.181432
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.705
ELB improved by 0.179618
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.535
ELB improved by 0.170151
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.387
ELB improved by 0.147865
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.268
ELB improved by 0.118798
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.177
ELB improved by 0.0914912
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.107
ELB improved by 0.0693806
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.055
ELB improved by 0.052528
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.015
ELB improved by 0.0400722
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.984
ELB improved by 0.0310099
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.959
ELB improved by 0.0244357
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.94
ELB improved by 0.0196333
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.923
ELB improved by 0.016081
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.91
ELB improved by 0.0134143
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.899
ELB improved by 0.0113822
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.889
ELB improved by 0.00981153
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-824.406
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-562.454
ELB improved by 261.952
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-500.457
ELB improved by 61.9971
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.56
ELB improved by 43.8971
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.083
ELB improved by 19.4766
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.843
ELB improved by 8.23953
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.251
ELB improved by 4.59241
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.736
ELB improved by 3.51519
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.338
ELB improved by 3.39798
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.668
ELB improved by 3.66974
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.631
ELB improved by 4.03677
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.437
ELB improved by 4.19434
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.579
ELB improved by 3.85823
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.535
ELB improved by 3.04329
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.416
ELB improved by 2.11902
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395
ELB improved by 1.41675
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.009
ELB improved by 0.990486
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.256
ELB improved by 0.752702
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.635
ELB improved by 0.621561
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.085
ELB improved by 0.550299
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.571
ELB improved by 0.513922
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.075
ELB improved by 0.495456
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.596
ELB improved by 0.47891
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.143
ELB improved by 0.453546
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.722
ELB improved by 0.42081
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.334
ELB improved by 0.388184
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.973
ELB improved by 0.360666
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.633
ELB improved by 0.340533
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.303
ELB improved by 0.329268
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.976
ELB improved by 0.32746
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.644
ELB improved by 0.332351
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.308
ELB improved by 0.335439
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.981
ELB improved by 0.327474
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.672
ELB improved by 0.308934
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.384
ELB improved by 0.287757
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.115
ELB improved by 0.269078
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.861
ELB improved by 0.253634
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.621
ELB improved by 0.240601
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.392
ELB improved by 0.228998
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.174
ELB improved by 0.217963
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.967
ELB improved by 0.206788
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.772
ELB improved by 0.194936
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.59
ELB improved by 0.182089
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.422
ELB improved by 0.168166
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.268
ELB improved by 0.153325
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.13
ELB improved by 0.137917
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.008
ELB improved by 0.122406
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.901
ELB improved by 0.107286
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.808
ELB improved by 0.0929926
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.728
ELB improved by 0.0798517
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.66
ELB improved by 0.068061
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.602
ELB improved by 0.0576955
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.553
ELB improved by 0.0487321
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.512
ELB improved by 0.0410802
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.478
ELB improved by 0.0346105
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.449
ELB improved by 0.0291778
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.424
ELB improved by 0.0246374
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.403
ELB improved by 0.020854
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.385
ELB improved by 0.0177071
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.37
ELB improved by 0.0150919
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.357
ELB improved by 0.0129194
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.346
ELB improved by 0.0111141
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.337
ELB improved by 0.00961327
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-828.016
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-584.466
ELB improved by 243.55
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-525.247
ELB improved by 59.2197
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-478.232
ELB improved by 47.0143
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.754
ELB improved by 23.4786
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.124
ELB improved by 7.62918
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.023
ELB improved by 3.10136
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.98
ELB improved by 2.04279
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.298
ELB improved by 1.68203
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.772
ELB improved by 1.52607
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.336
ELB improved by 1.43654
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.961
ELB improved by 1.37428
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.639
ELB improved by 1.32262
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.372
ELB improved by 1.2665
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.181
ELB improved by 1.19138
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.093
ELB improved by 1.08832
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.133
ELB improved by 0.959511
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.314
ELB improved by 0.81877
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.629
ELB improved by 0.685328
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.054
ELB improved by 0.575328
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.557
ELB improved by 0.49694
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.106
ELB improved by 0.450773
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.673
ELB improved by 0.433107
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.234
ELB improved by 0.438958
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.77
ELB improved by 0.463691
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.267
ELB improved by 0.503316
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.713
ELB improved by 0.554147
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.1
ELB improved by 0.612394
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.426
ELB improved by 0.674065
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.691
ELB improved by 0.735176
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.899
ELB improved by 0.792054
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.057
ELB improved by 0.841643
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.175
ELB improved by 0.881995
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.263
ELB improved by 0.912737
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.328
ELB improved by 0.934771
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.379
ELB improved by 0.949128
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.423
ELB improved by 0.955857
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.469
ELB improved by 0.953596
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.53
ELB improved by 0.939685
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.62
ELB improved by 0.909701
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.764
ELB improved by 0.855784
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.99
ELB improved by 0.774544
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.285
ELB improved by 0.704304
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.528
ELB improved by 0.757352
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.457
ELB improved by 1.07137
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.057
ELB improved by 1.40006
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.912
ELB improved by 1.14442
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.19
ELB improved by 0.722206
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.723
ELB improved by 0.467207
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.387
ELB improved by 0.335866
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.12
ELB improved by 0.266792
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.894
ELB improved by 0.225814
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.696
ELB improved by 0.198174
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.518
ELB improved by 0.178241
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.355
ELB improved by 0.162501
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.208
ELB improved by 0.147676
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.075
ELB improved by 0.132708
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.954
ELB improved by 0.120854
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.835
ELB improved by 0.118888
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.7
ELB improved by 0.135013
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.526
ELB improved by 0.174174
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.304
ELB improved by 0.222357
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.061
ELB improved by 0.242785
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.839
ELB improved by 0.221713
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.661
ELB improved by 0.178217
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.528
ELB improved by 0.133223
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.426
ELB improved by 0.101835
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.339
ELB improved by 0.0868962
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.256
ELB improved by 0.0826151
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.174
ELB improved by 0.0826131
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.091
ELB improved by 0.08308
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.007
ELB improved by 0.083531
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.921
ELB improved by 0.0861601
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.827
ELB improved by 0.0936547
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.721
ELB improved by 0.106696
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.599
ELB improved by 0.121788
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.468
ELB improved by 0.130623
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.344
ELB improved by 0.124428
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.241
ELB improved by 0.102297
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.168
ELB improved by 0.0735176
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.119
ELB improved by 0.0488526
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.087
ELB improved by 0.0323226
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.064
ELB improved by 0.0224606
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.048
ELB improved by 0.0166655
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.035
ELB improved by 0.0130871
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.024
ELB improved by 0.0106988
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.015
ELB improved by 0.00898167
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.334 0.210 2.530
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.050 | 0.024 | 0.075 | |
| getPIPs | 0.048 | 0.012 | 0.061 | |
| graper | 0.075 | 0.023 | 0.100 | |
| makeExampleData | 0.009 | 0.000 | 0.011 | |
| makeExampleDataWithUnequalGroups | 0.011 | 0.002 | 0.013 | |
| plotELBO | 0.318 | 0.032 | 0.351 | |
| plotGroupPenalties | 1.087 | 0.037 | 1.123 | |
| plotPosterior | 0.638 | 0.014 | 0.653 | |
| predict.graper | 2.042 | 0.080 | 2.122 | |
| print.graper | 0.044 | 0.017 | 0.062 | |