Britta Velten
| Snapshot Date: 2025-11-20 13:40 -0500 (Thu, 20 Nov 2025) |
| 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 2025-11-21 11:39 -0500 (Fri, 21 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4829 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4602 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4566 |
| 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 913/2327 | 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 | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.27.0.tar.gz |
| StartedAt: 2025-11-20 20:17:24 -0500 (Thu, 20 Nov 2025) |
| EndedAt: 2025-11-20 20:17:56 -0500 (Thu, 20 Nov 2025) |
| EllapsedTime: 31.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.27.0’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.1.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fit_graper.cpp -o fit_graper.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o graper.so RcppExports.o fit_graper.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/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) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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=-858.326
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-582.995
ELB improved by 275.331
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-522.961
ELB improved by 60.0347
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-480.063
ELB improved by 42.8977
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.976
ELB improved by 22.0871
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.318
ELB improved by 9.65838
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.9
ELB improved by 5.4173
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.665
ELB improved by 4.23529
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.633
ELB improved by 4.03149
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.437
ELB improved by 4.19655
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.014
ELB improved by 4.42318
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.543
ELB improved by 4.47058
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.412
ELB improved by 4.13155
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.064
ELB improved by 3.34804
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.71
ELB improved by 2.35386
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.176
ELB improved by 1.53412
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.163
ELB improved by 1.0125
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.451
ELB improved by 0.712494
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.911
ELB improved by 0.539808
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.476
ELB improved by 0.434365
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.111
ELB improved by 0.365465
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.792
ELB improved by 0.318554
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.506
ELB improved by 0.286029
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.243
ELB improved by 0.263108
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.997
ELB improved by 0.246525
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.763
ELB improved by 0.234086
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.538
ELB improved by 0.224348
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.322
ELB improved by 0.216357
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.112
ELB improved by 0.209477
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.909
ELB improved by 0.203293
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.712
ELB improved by 0.197571
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.519
ELB improved by 0.192233
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.332
ELB improved by 0.187362
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.149
ELB improved by 0.183193
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.969
ELB improved by 0.180132
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.79
ELB improved by 0.178789
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.61
ELB improved by 0.180044
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.425
ELB improved by 0.185133
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.229
ELB improved by 0.195604
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.016
ELB improved by 0.21277
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.78
ELB improved by 0.236026
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.52
ELB improved by 0.260608
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.241
ELB improved by 0.278764
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.955
ELB improved by 0.286308
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.669
ELB improved by 0.285698
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.388
ELB improved by 0.281438
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.111
ELB improved by 0.276358
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.84
ELB improved by 0.271635
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.572
ELB improved by 0.267633
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.307
ELB improved by 0.264413
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.045
ELB improved by 0.262013
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.785
ELB improved by 0.260592
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.524
ELB improved by 0.26043
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.263
ELB improved by 0.261715
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.999
ELB improved by 0.264195
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.731
ELB improved by 0.267179
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.461
ELB improved by 0.270599
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.184
ELB improved by 0.276653
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.894
ELB improved by 0.290164
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.577
ELB improved by 0.317025
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.216
ELB improved by 0.361263
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.798
ELB improved by 0.417773
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.34
ELB improved by 0.458272
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.901
ELB improved by 0.438977
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.542
ELB improved by 0.358574
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.278
ELB improved by 0.263932
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.089
ELB improved by 0.188881
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.95
ELB improved by 0.13966
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.839
ELB improved by 0.11077
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.744
ELB improved by 0.0951232
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.657
ELB improved by 0.0870316
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.574
ELB improved by 0.082727
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.493
ELB improved by 0.0804353
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.414
ELB improved by 0.0796169
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.335
ELB improved by 0.079293
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.258
ELB improved by 0.0770154
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.187
ELB improved by 0.0701425
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.129
ELB improved by 0.0585803
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.084
ELB improved by 0.0452665
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.05
ELB improved by 0.0334476
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.026
ELB improved by 0.0245473
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.007
ELB improved by 0.0184073
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.993
ELB improved by 0.0143072
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.981
ELB improved by 0.0115618
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.972
ELB improved by 0.00968049
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-831.626
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-573.119
ELB improved by 258.507
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-510.666
ELB improved by 62.4523
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.285
ELB improved by 40.3809
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.93
ELB improved by 16.3555
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.865
ELB improved by 7.06516
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.035
ELB improved by 4.8295
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.545
ELB improved by 4.4904
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.711
ELB improved by 4.83376
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.191
ELB improved by 5.52053
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.952
ELB improved by 6.23827
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.442
ELB improved by 6.5101
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.51
ELB improved by 5.93243
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.066
ELB improved by 4.44338
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.229
ELB improved by 2.83755
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.469
ELB improved by 1.75948
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.34
ELB improved by 1.12905
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.577
ELB improved by 0.763506
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.031
ELB improved by 0.546121
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.62
ELB improved by 0.410758
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.298
ELB improved by 0.321597
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.039
ELB improved by 0.259615
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.824
ELB improved by 0.214549
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.644
ELB improved by 0.180615
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.489
ELB improved by 0.154364
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.356
ELB improved by 0.133622
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.239
ELB improved by 0.11695
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.135
ELB improved by 0.103353
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.043
ELB improved by 0.0921281
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.96
ELB improved by 0.0827587
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.886
ELB improved by 0.074862
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.817
ELB improved by 0.0681475
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.755
ELB improved by 0.0623917
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.698
ELB improved by 0.0574202
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.644
ELB improved by 0.0530955
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.595
ELB improved by 0.0493079
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.549
ELB improved by 0.045969
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.506
ELB improved by 0.0430072
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.466
ELB improved by 0.0403637
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.428
ELB improved by 0.0379903
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.392
ELB improved by 0.0358469
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.358
ELB improved by 0.0339001
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.326
ELB improved by 0.0321222
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.295
ELB improved by 0.0304898
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.266
ELB improved by 0.0289831
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.239
ELB improved by 0.0275858
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.213
ELB improved by 0.0262839
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.188
ELB improved by 0.0250657
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.164
ELB improved by 0.0239213
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.141
ELB improved by 0.0228424
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.119
ELB improved by 0.0218221
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.098
ELB improved by 0.0208545
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.078
ELB improved by 0.0199348
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.059
ELB improved by 0.0190589
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.041
ELB improved by 0.0182235
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.023
ELB improved by 0.0174257
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.007
ELB improved by 0.0166631
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.991
ELB improved by 0.0159339
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.976
ELB improved by 0.0152364
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.961
ELB improved by 0.0145692
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.947
ELB improved by 0.013931
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.934
ELB improved by 0.0133208
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.921
ELB improved by 0.0127377
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.909
ELB improved by 0.0121808
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.897
ELB improved by 0.0116493
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.886
ELB improved by 0.0111423
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.875
ELB improved by 0.0106592
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.865
ELB improved by 0.0101991
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.855
ELB improved by 0.00976141
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-891.301
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-590.762
ELB improved by 300.539
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-529.532
ELB improved by 61.2294
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-486.224
ELB improved by 43.3078
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.993
ELB improved by 19.2318
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.467
ELB improved by 8.52536
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.364
ELB improved by 6.10335
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.555
ELB improved by 5.80898
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.389
ELB improved by 6.16548
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.918
ELB improved by 6.47127
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.735
ELB improved by 6.18333
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.631
ELB improved by 5.10348
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.994
ELB improved by 3.63747
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.584
ELB improved by 2.40951
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.951
ELB improved by 1.63281
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.753
ELB improved by 1.19852
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.797
ELB improved by 0.955883
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.997
ELB improved by 0.799722
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.315
ELB improved by 0.682769
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.724
ELB improved by 0.590412
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.221
ELB improved by 0.503552
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.802
ELB improved by 0.418236
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.451
ELB improved by 0.35105
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.141
ELB improved by 0.310375
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.848
ELB improved by 0.292723
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.556
ELB improved by 0.292043
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.252
ELB improved by 0.303807
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.927
ELB improved by 0.324908
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.575
ELB improved by 0.352736
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.19
ELB improved by 0.385215
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.768
ELB improved by 0.421752
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.304
ELB improved by 0.463672
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.791
ELB improved by 0.513405
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.217
ELB improved by 0.573256
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.573
ELB improved by 0.644357
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.848
ELB improved by 0.72539
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.037
ELB improved by 0.810594
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.15
ELB improved by 0.887501
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.213
ELB improved by 0.936805
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.275
ELB improved by 0.938045
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.394
ELB improved by 0.880971
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.62
ELB improved by 0.774232
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.977
ELB improved by 0.64205
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.466
ELB improved by 0.511082
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.067
ELB improved by 0.399253
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.753
ELB improved by 0.313835
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.497
ELB improved by 0.256404
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.267
ELB improved by 0.230372
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.015
ELB improved by 0.251329
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.662
ELB improved by 0.352778
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.167
ELB improved by 0.495412
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.714
ELB improved by 0.452829
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.454
ELB improved by 0.26061
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.322
ELB improved by 0.131955
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.248
ELB improved by 0.073332
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.201
ELB improved by 0.0469352
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.167
ELB improved by 0.034047
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.14
ELB improved by 0.0269766
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.118
ELB improved by 0.0225914
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.098
ELB improved by 0.0195639
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.081
ELB improved by 0.0172953
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.065
ELB improved by 0.0154956
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.051
ELB improved by 0.014013
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.039
ELB improved by 0.012761
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.027
ELB improved by 0.0116863
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.016
ELB improved by 0.0107531
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.006
ELB improved by 0.00993587
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-870.752
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-575.249
ELB improved by 295.503
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-514.442
ELB improved by 60.8073
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-475.527
ELB improved by 38.915
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.608
ELB improved by 18.9184
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.019
ELB improved by 8.58934
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.355
ELB improved by 4.66437
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.976
ELB improved by 3.37876
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.929
ELB improved by 3.04711
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.809
ELB improved by 3.11987
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.382
ELB improved by 3.42667
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.575
ELB improved by 3.807
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.609
ELB improved by 3.96665
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419
ELB improved by 3.60833
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.203
ELB improved by 2.79762
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.256
ELB improved by 1.94704
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.902
ELB improved by 1.35388
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.869
ELB improved by 1.03244
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.978
ELB improved by 0.891418
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.116
ELB improved by 0.861348
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.204
ELB improved by 0.912476
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.166
ELB improved by 1.03753
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.949
ELB improved by 1.21766
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.555
ELB improved by 1.39406
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.028
ELB improved by 1.52631
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.388
ELB improved by 1.64038
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.626
ELB improved by 1.76233
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.73
ELB improved by 1.89592
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.694
ELB improved by 2.03537
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.526
ELB improved by 2.16822
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.289
ELB improved by 2.2375
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.229
ELB improved by 2.05945
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.607
ELB improved by 1.62184
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.42
ELB improved by 1.18693
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.589
ELB improved by 0.831737
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.02
ELB improved by 0.568336
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.629
ELB improved by 0.391078
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.354
ELB improved by 0.27508
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.156
ELB improved by 0.198332
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.009
ELB improved by 0.147242
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.896
ELB improved by 0.113135
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.806
ELB improved by 0.0899763
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.732
ELB improved by 0.0737078
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.67
ELB improved by 0.0617851
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.617
ELB improved by 0.0526774
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.572
ELB improved by 0.0454713
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.532
ELB improved by 0.0396118
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.498
ELB improved by 0.0347498
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.467
ELB improved by 0.030656
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.44
ELB improved by 0.0271718
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.416
ELB improved by 0.0241831
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.394
ELB improved by 0.021604
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.375
ELB improved by 0.0193678
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.357
ELB improved by 0.0174216
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.341
ELB improved by 0.0157221
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.327
ELB improved by 0.0142339
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.314
ELB improved by 0.0129273
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.302
ELB improved by 0.0117776
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.292
ELB improved by 0.0107635
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.282
ELB improved by 0.00986719
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
1.086 0.089 1.199
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.013 | 0.006 | 0.019 | |
| getPIPs | 0.012 | 0.005 | 0.017 | |
| graper | 0.025 | 0.008 | 0.033 | |
| makeExampleData | 0.002 | 0.001 | 0.002 | |
| makeExampleDataWithUnequalGroups | 0.002 | 0.000 | 0.002 | |
| plotELBO | 0.112 | 0.007 | 0.121 | |
| plotGroupPenalties | 0.439 | 0.010 | 0.465 | |
| plotPosterior | 0.214 | 0.009 | 0.229 | |
| predict.graper | 0.221 | 0.027 | 0.258 | |
| print.graper | 0.011 | 0.004 | 0.015 | |