Britta Velten
| Snapshot Date: 2026-03-06 13:40 -0500 (Fri, 06 Mar 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 2026-03-07 11:33 -0500 (Sat, 07 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4453 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-02-28 r89501) -- "Unsuffered Consequences" | 3376 |
| 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 926/2357 | 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 | | ||||||||
| 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: 1.27.0 |
| 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: 2026-03-07 00:55:36 -0500 (Sat, 07 Mar 2026) |
| EndedAt: 2026-03-07 00:57:10 -0500 (Sat, 07 Mar 2026) |
| EllapsedTime: 94.1 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) (2026-03-05 r89546)
* 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
* current time: 2026-03-07 05:55:37 UTC
* 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 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) predict.graper.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:23-24: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.27.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c fit_graper.cpp -o fit_graper.o g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -llapack -L/home/biocbuild/bbs-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-graper/00new/graper/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (graper)
graper.Rcheck/tests/testthat.Rout
R Under development (unstable) (2026-03-05 r89546) -- "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=-869.102
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-599.405
ELB improved by 269.697
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-538.435
ELB improved by 60.9701
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-489.108
ELB improved by 49.3272
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.64
ELB improved by 28.4679
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.537
ELB improved by 12.1031
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.158
ELB improved by 5.37902
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.986
ELB improved by 3.17162
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.708
ELB improved by 2.27778
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.849
ELB improved by 1.85912
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.21
ELB improved by 1.63865
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.712
ELB improved by 1.49858
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.32
ELB improved by 1.39171
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.02
ELB improved by 1.29993
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.806
ELB improved by 1.2142
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.678
ELB improved by 1.12752
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.644
ELB improved by 1.03414
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.713
ELB improved by 0.931147
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.893
ELB improved by 0.819915
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.187
ELB improved by 0.705957
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.59
ELB improved by 0.596792
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.091
ELB improved by 0.499062
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.675
ELB improved by 0.41659
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.325
ELB improved by 0.350114
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.027
ELB improved by 0.298168
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.768
ELB improved by 0.258227
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.541
ELB improved by 0.227574
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.337
ELB improved by 0.203774
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.152
ELB improved by 0.184892
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.983
ELB improved by 0.16955
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.826
ELB improved by 0.156889
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.679
ELB improved by 0.146445
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.541
ELB improved by 0.137992
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.41
ELB improved by 0.131396
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.283
ELB improved by 0.126533
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.16
ELB improved by 0.123273
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.039
ELB improved by 0.121487
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.917
ELB improved by 0.121065
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.796
ELB improved by 0.12193
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.671
ELB improved by 0.124044
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.544
ELB improved by 0.127407
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.412
ELB improved by 0.132057
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.274
ELB improved by 0.13807
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.128
ELB improved by 0.145553
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.974
ELB improved by 0.154645
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.808
ELB improved by 0.165506
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.63
ELB improved by 0.178312
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.437
ELB improved by 0.193253
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.226
ELB improved by 0.210543
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.996
ELB improved by 0.230469
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.742
ELB improved by 0.253488
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.462
ELB improved by 0.280397
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.149
ELB improved by 0.312553
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.797
ELB improved by 0.352106
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.395
ELB improved by 0.402129
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.929
ELB improved by 0.466353
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.381
ELB improved by 0.5478
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.735
ELB improved by 0.645598
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.984
ELB improved by 0.751596
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.131
ELB improved by 0.852217
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.197
ELB improved by 0.934912
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.207
ELB improved by 0.989165
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.203
ELB improved by 1.0044
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.227
ELB improved by 0.975594
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.316
ELB improved by 0.911623
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.486
ELB improved by 0.829672
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.747
ELB improved by 0.738627
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.116
ELB improved by 0.63155
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.613
ELB improved by 0.502805
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.24
ELB improved by 0.372727
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.973
ELB improved by 0.267247
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.781
ELB improved by 0.192211
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.64
ELB improved by 0.140996
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.534
ELB improved by 0.105786
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.453
ELB improved by 0.0809712
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.39
ELB improved by 0.063039
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.34
ELB improved by 0.0498397
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.3
ELB improved by 0.0400072
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.268
ELB improved by 0.0326193
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.241
ELB improved by 0.0270207
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.218
ELB improved by 0.0227348
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.198
ELB improved by 0.0194134
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.182
ELB improved by 0.016804
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.167
ELB improved by 0.0147243
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.154
ELB improved by 0.0130432
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.142
ELB improved by 0.0116665
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.132
ELB improved by 0.0105255
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.122
ELB improved by 0.0095699
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-864.104
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-574.901
ELB improved by 289.203
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-512.211
ELB improved by 62.6899
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.223
ELB improved by 40.9878
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.15
ELB improved by 19.0731
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.117
ELB improved by 9.03316
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.344
ELB improved by 6.77277
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.433
ELB improved by 6.91169
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.648
ELB improved by 7.78463
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.382
ELB improved by 8.26579
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.953
ELB improved by 7.42951
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.292
ELB improved by 5.66104
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.214
ELB improved by 4.07825
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.205
ELB improved by 3.00862
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.04
ELB improved by 2.16471
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.497
ELB improved by 1.54362
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.333
ELB improved by 1.16366
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.416
ELB improved by 0.917305
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.685
ELB improved by 0.730634
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.093
ELB improved by 0.591642
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.595
ELB improved by 0.498483
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.156
ELB improved by 0.438419
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.757
ELB improved by 0.398997
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.385
ELB improved by 0.372683
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.029
ELB improved by 0.355448
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.684
ELB improved by 0.345097
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.344
ELB improved by 0.34036
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.003
ELB improved by 0.340445
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.659
ELB improved by 0.344792
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.306
ELB improved by 0.352916
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.941
ELB improved by 0.364286
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.563
ELB improved by 0.378257
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.169
ELB improved by 0.394034
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.758
ELB improved by 0.410675
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.331
ELB improved by 0.427089
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.889
ELB improved by 0.442014
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.435
ELB improved by 0.454008
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.974
ELB improved by 0.46152
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.511
ELB improved by 0.463122
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.053
ELB improved by 0.457942
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.607
ELB improved by 0.446235
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.177
ELB improved by 0.429935
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.764
ELB improved by 0.412837
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.364
ELB improved by 0.400002
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.968
ELB improved by 0.395668
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.57
ELB improved by 0.397641
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.18
ELB improved by 0.390172
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.825
ELB improved by 0.355456
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.528
ELB improved by 0.29715
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.296
ELB improved by 0.231745
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.123
ELB improved by 0.173212
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.995
ELB improved by 0.127563
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.901
ELB improved by 0.093941
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.832
ELB improved by 0.0695117
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.78
ELB improved by 0.0518061
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.741
ELB improved by 0.038991
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.711
ELB improved by 0.0297141
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.688
ELB improved by 0.022977
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.67
ELB improved by 0.0180537
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.656
ELB improved by 0.0144253
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.644
ELB improved by 0.0117254
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.634
ELB improved by 0.00969567
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-873.677
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-586.472
ELB improved by 287.205
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-524.849
ELB improved by 61.6231
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-482.365
ELB improved by 42.4843
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.105
ELB improved by 19.26
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.772
ELB improved by 7.33255
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.521
ELB improved by 4.25104
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.137
ELB improved by 3.3845
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.111
ELB improved by 3.02622
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.284
ELB improved by 2.82693
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.627
ELB improved by 2.65659
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.16
ELB improved by 2.46674
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.918
ELB improved by 2.24201
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.933
ELB improved by 1.98546
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.218
ELB improved by 1.71471
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.767
ELB improved by 1.45066
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.562
ELB improved by 1.20543
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.578
ELB improved by 0.983924
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.789
ELB improved by 0.788979
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.166
ELB improved by 0.623297
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.677
ELB improved by 0.488959
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.292
ELB improved by 0.385234
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.983
ELB improved by 0.308097
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.732
ELB improved by 0.251863
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.521
ELB improved by 0.21099
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.34
ELB improved by 0.180996
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.181
ELB improved by 0.158625
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.039
ELB improved by 0.141646
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.911
ELB improved by 0.12857
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.792
ELB improved by 0.118406
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.682
ELB improved by 0.11049
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.578
ELB improved by 0.104367
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.478
ELB improved by 0.0997194
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.382
ELB improved by 0.096319
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.287
ELB improved by 0.0940019
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.195
ELB improved by 0.0926488
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.103
ELB improved by 0.0921739
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.01
ELB improved by 0.0925173
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.917
ELB improved by 0.0936401
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.821
ELB improved by 0.0955205
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.723
ELB improved by 0.098152
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.621
ELB improved by 0.101541
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.516
ELB improved by 0.105705
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.405
ELB improved by 0.110673
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.288
ELB improved by 0.116479
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.165
ELB improved by 0.123163
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.035
ELB improved by 0.130765
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.895
ELB improved by 0.139319
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.746
ELB improved by 0.148841
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.587
ELB improved by 0.159325
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.416
ELB improved by 0.170723
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.233
ELB improved by 0.18294
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.038
ELB improved by 0.195816
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.828
ELB improved by 0.20913
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.606
ELB improved by 0.222603
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.37
ELB improved by 0.235923
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.121
ELB improved by 0.248801
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.86
ELB improved by 0.261051
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.587
ELB improved by 0.272706
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.303
ELB improved by 0.284138
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.007
ELB improved by 0.296068
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.698
ELB improved by 0.309234
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.375
ELB improved by 0.323301
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.039
ELB improved by 0.335127
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.701
ELB improved by 0.33861
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.372
ELB improved by 0.329302
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.062
ELB improved by 0.309768
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.775
ELB improved by 0.2872
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.507
ELB improved by 0.267097
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.257
ELB improved by 0.250856
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.02
ELB improved by 0.236317
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.801
ELB improved by 0.219625
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.602
ELB improved by 0.198778
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.426
ELB improved by 0.176359
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.267
ELB improved by 0.158277
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.116
ELB improved by 0.150982
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.955
ELB improved by 0.161007
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.76
ELB improved by 0.19509
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.506
ELB improved by 0.254665
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.186
ELB improved by 0.319349
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.844
ELB improved by 0.342102
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.535
ELB improved by 0.30926
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.275
ELB improved by 0.260019
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.055
ELB improved by 0.220201
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.869
ELB improved by 0.185304
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.724
ELB improved by 0.145284
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.619
ELB improved by 0.105218
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.545
ELB improved by 0.0742209
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.491
ELB improved by 0.0535353
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.451
ELB improved by 0.0400577
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.42
ELB improved by 0.0308467
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.396
ELB improved by 0.0241621
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.377
ELB improved by 0.0191351
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.362
ELB improved by 0.015325
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.349
ELB improved by 0.0124589
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.339
ELB improved by 0.0103256
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.33
ELB improved by 0.0087477
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-802.444
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-560.509
ELB improved by 241.935
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-496.083
ELB improved by 64.4259
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.927
ELB improved by 47.1559
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.334
ELB improved by 21.5934
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.127
ELB improved by 8.20656
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.799
ELB improved by 4.32809
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.894
ELB improved by 2.90508
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.568
ELB improved by 2.32638
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.442
ELB improved by 2.1258
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.335
ELB improved by 2.10624
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.144
ELB improved by 2.19113
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.806
ELB improved by 2.33863
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.299
ELB improved by 2.50672
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.658
ELB improved by 2.64071
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.981
ELB improved by 2.67764
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.414
ELB improved by 2.56663
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.124
ELB improved by 2.29019
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.238
ELB improved by 1.88599
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.783
ELB improved by 1.45453
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.68
ELB improved by 1.10314
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.801
ELB improved by 0.879265
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.033
ELB improved by 0.768248
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.3
ELB improved by 0.733037
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.557
ELB improved by 0.742621
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.779
ELB improved by 0.778134
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.949
ELB improved by 0.830165
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.053
ELB improved by 0.895445
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.079
ELB improved by 0.974401
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.01
ELB improved by 1.06884
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.831
ELB improved by 1.17893
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.531
ELB improved by 1.29992
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.109
ELB improved by 1.42181
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.569
ELB improved by 1.54066
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.892
ELB improved by 1.67661
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.076
ELB improved by 1.81584
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.181
ELB improved by 1.89569
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-363.22
ELB improved by 1.96008
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-361.559
ELB improved by 1.66189
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-360.458
ELB improved by 1.10037
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-359.783
ELB improved by 0.674887
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-359.362
ELB improved by 0.421216
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-359.075
ELB improved by 0.287437
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-358.838
ELB improved by 0.23618
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-358.572
ELB improved by 0.266879
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-358.156
ELB improved by 0.415554
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-357.558
ELB improved by 0.597562
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-357.059
ELB improved by 0.499897
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-356.806
ELB improved by 0.252365
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-356.699
ELB improved by 0.107727
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-356.648
ELB improved by 0.0501247
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-356.62
ELB improved by 0.0288321
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-356.599
ELB improved by 0.0204431
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-356.583
ELB improved by 0.0165475
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-356.568
ELB improved by 0.0143133
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-356.555
ELB improved by 0.0127785
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-356.544
ELB improved by 0.0115945
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-356.533
ELB improved by 0.0106195
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-356.523
ELB improved by 0.00978632
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.322 0.179 2.490
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.206 | 0.042 | 0.330 | |
| getPIPs | 0.107 | 0.033 | 0.142 | |
| graper | 0.105 | 0.032 | 0.138 | |
| makeExampleData | 0.014 | 0.000 | 0.014 | |
| makeExampleDataWithUnequalGroups | 0.015 | 0.003 | 0.018 | |
| plotELBO | 0.438 | 0.027 | 0.464 | |
| plotGroupPenalties | 1.136 | 0.281 | 1.417 | |
| plotPosterior | 0.643 | 0.052 | 0.695 | |
| predict.graper | 2.044 | 0.067 | 2.110 | |
| print.graper | 0.051 | 0.011 | 0.062 | |