Britta Velten
| Snapshot Date: 2025-10-29 19:52 -0400 (Wed, 29 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: RELEASE_3_22 |
| git_last_commit: 76fc31b |
| git_last_commit_date: 2025-10-29 10:49:21 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-30 12:35 -0400 (Thu, 30 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 922/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.26.0 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| 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: 1.26.0 |
| 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_1.26.0.tar.gz |
| StartedAt: 2025-10-30 04:23:56 -0400 (Thu, 30 Oct 2025) |
| EndedAt: 2025-10-30 04:25:15 -0400 (Thu, 30 Oct 2025) |
| EllapsedTime: 79.0 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_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.26.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.22-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/4.5-x86_64/Resources/library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.26.0’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.1.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fit_graper.cpp -o fit_graper.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/x86_64-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/4.5-x86_64/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 version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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=-846.231
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-585.599
ELB improved by 260.632
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-525.454
ELB improved by 60.1449
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-481.198
ELB improved by 44.2555
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.047
ELB improved by 24.1511
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.422
ELB improved by 10.6254
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.987
ELB improved by 5.4349
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.158
ELB improved by 3.82895
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.909
ELB improved by 3.24931
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.976
ELB improved by 2.93316
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.339
ELB improved by 2.63622
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.057
ELB improved by 2.28251
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.178
ELB improved by 1.87898
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.707
ELB improved by 1.47116
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.598
ELB improved by 1.10855
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.777
ELB improved by 0.821423
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.163
ELB improved by 0.613655
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.692
ELB improved by 0.471188
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.317
ELB improved by 0.375138
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.007
ELB improved by 0.309668
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.743
ELB improved by 0.263902
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.512
ELB improved by 0.231041
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.305
ELB improved by 0.206969
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.116
ELB improved by 0.189191
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.94
ELB improved by 0.176164
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.773
ELB improved by 0.166914
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.612
ELB improved by 0.16083
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.454
ELB improved by 0.157543
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.298
ELB improved by 0.156867
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.139
ELB improved by 0.158765
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.976
ELB improved by 0.163332
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.805
ELB improved by 0.170804
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.623
ELB improved by 0.181565
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.427
ELB improved by 0.196177
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.212
ELB improved by 0.215417
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.971
ELB improved by 0.240328
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.699
ELB improved by 0.272286
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.386
ELB improved by 0.313078
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.021
ELB improved by 0.365003
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.59
ELB improved by 0.431001
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.075
ELB improved by 0.514819
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.454
ELB improved by 0.621119
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.699
ELB improved by 0.755128
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.778
ELB improved by 0.92055
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.664
ELB improved by 1.11381
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.349
ELB improved by 1.31568
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.861
ELB improved by 1.48788
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.277
ELB improved by 1.58412
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.692
ELB improved by 1.58495
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.149
ELB improved by 1.54307
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.594
ELB improved by 1.55474
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.072
ELB improved by 1.52228
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.805
ELB improved by 1.26673
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.85
ELB improved by 0.955266
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.176
ELB improved by 0.673495
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.743
ELB improved by 0.43291
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.48
ELB improved by 0.262887
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.315
ELB improved by 0.164996
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.202
ELB improved by 0.112954
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.118
ELB improved by 0.0842481
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.051
ELB improved by 0.0669188
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.996
ELB improved by 0.0553912
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.949
ELB improved by 0.0470893
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.908
ELB improved by 0.0407641
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.872
ELB improved by 0.0357622
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.841
ELB improved by 0.0317134
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.812
ELB improved by 0.028394
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.787
ELB improved by 0.025662
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.763
ELB improved by 0.0234264
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.741
ELB improved by 0.0216302
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.721
ELB improved by 0.020243
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.702
ELB improved by 0.0192564
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.683
ELB improved by 0.0186808
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.665
ELB improved by 0.0185402
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.646
ELB improved by 0.0188569
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.626
ELB improved by 0.0196199
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.606
ELB improved by 0.0207265
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.584
ELB improved by 0.0219096
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.561
ELB improved by 0.0227049
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.538
ELB improved by 0.0225609
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.517
ELB improved by 0.0211273
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.499
ELB improved by 0.0185349
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.483
ELB improved by 0.0153634
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.471
ELB improved by 0.0122893
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.461
ELB improved by 0.0097506
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-869.103
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-575.819
ELB improved by 293.284
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-516.391
ELB improved by 59.4283
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-480.541
ELB improved by 35.8506
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.156
ELB improved by 15.3851
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.213
ELB improved by 6.94297
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.637
ELB improved by 4.57508
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.765
ELB improved by 3.87249
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.019
ELB improved by 3.74635
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.149
ELB improved by 3.8696
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.078
ELB improved by 4.07138
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.912
ELB improved by 4.1661
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.971
ELB improved by 3.94066
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.632
ELB improved by 3.33861
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.05
ELB improved by 2.58239
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.108
ELB improved by 1.94144
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.637
ELB improved by 1.47126
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.539
ELB improved by 1.09839
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.743
ELB improved by 0.796193
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.166
ELB improved by 0.576094
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.734
ELB improved by 0.432015
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.393
ELB improved by 0.341508
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.11
ELB improved by 0.282949
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.868
ELB improved by 0.241989
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.657
ELB improved by 0.21069
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.472
ELB improved by 0.185195
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.308
ELB improved by 0.163854
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.162
ELB improved by 0.145995
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.031
ELB improved by 0.13123
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.912
ELB improved by 0.119189
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.802
ELB improved by 0.109469
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.701
ELB improved by 0.101683
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.605
ELB improved by 0.095494
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.515
ELB improved by 0.0906276
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.428
ELB improved by 0.0868738
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.344
ELB improved by 0.084076
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.262
ELB improved by 0.08212
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.181
ELB improved by 0.0809259
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.1
ELB improved by 0.0804419
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.02
ELB improved by 0.0806404
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.938
ELB improved by 0.0815157
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.855
ELB improved by 0.0830842
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.77
ELB improved by 0.0853845
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.681
ELB improved by 0.0884803
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.589
ELB improved by 0.0924628
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.491
ELB improved by 0.0974559
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.388
ELB improved by 0.103621
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.276
ELB improved by 0.111164
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.156
ELB improved by 0.120341
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.025
ELB improved by 0.131463
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.88
ELB improved by 0.144901
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.719
ELB improved by 0.161078
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.538
ELB improved by 0.180459
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.335
ELB improved by 0.203519
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.104
ELB improved by 0.230699
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.842
ELB improved by 0.262339
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.543
ELB improved by 0.298618
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.203
ELB improved by 0.339498
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.819
ELB improved by 0.384694
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.385
ELB improved by 0.433639
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.9
ELB improved by 0.485338
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.362
ELB improved by 0.538062
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.772
ELB improved by 0.589259
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.135
ELB improved by 0.637091
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.45
ELB improved by 0.685417
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.699
ELB improved by 0.750534
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.848
ELB improved by 0.850938
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.912
ELB improved by 0.936757
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.019
ELB improved by 0.892835
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.271
ELB improved by 0.748074
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.675
ELB improved by 0.596188
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.193
ELB improved by 0.481671
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.78
ELB improved by 0.413439
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.418
ELB improved by 0.361068
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.133
ELB improved by 0.285055
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.937
ELB improved by 0.195955
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.811
ELB improved by 0.126736
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.727
ELB improved by 0.0837307
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.668
ELB improved by 0.058477
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.625
ELB improved by 0.0432188
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.592
ELB improved by 0.0334357
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.565
ELB improved by 0.0267677
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.543
ELB improved by 0.0219844
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.525
ELB improved by 0.0184122
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.509
ELB improved by 0.0156584
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.496
ELB improved by 0.0134805
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.484
ELB improved by 0.0117218
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.474
ELB improved by 0.0102778
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.464
ELB improved by 0.0090768
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-870.128
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-560.35
ELB improved by 309.778
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-497.938
ELB improved by 62.412
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.135
ELB improved by 36.8027
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.087
ELB improved by 14.0489
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.149
ELB improved by 5.93724
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.332
ELB improved by 3.81699
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.23
ELB improved by 3.1026
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.276
ELB improved by 2.95344
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.186
ELB improved by 3.09011
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.771
ELB improved by 3.41551
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.906
ELB improved by 3.86504
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.615
ELB improved by 4.29094
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.199
ELB improved by 4.4158
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.161
ELB improved by 4.0382
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.8
ELB improved by 3.36045
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.012
ELB improved by 2.78804
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.579
ELB improved by 2.43351
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.404
ELB improved by 2.17492
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.423
ELB improved by 1.98084
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.565
ELB improved by 1.85829
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.767
ELB improved by 1.79742
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.982
ELB improved by 1.78545
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.179
ELB improved by 1.80272
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.359
ELB improved by 1.82017
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.553
ELB improved by 1.80537
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.822
ELB improved by 1.73165
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.231
ELB improved by 1.59044
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.828
ELB improved by 1.40306
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.621
ELB improved by 1.207
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.601
ELB improved by 1.02041
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.763
ELB improved by 0.83836
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.098
ELB improved by 0.664965
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.575
ELB improved by 0.522279
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.144
ELB improved by 0.430973
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.75
ELB improved by 0.393891
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.359
ELB improved by 0.391414
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.976
ELB improved by 0.382833
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.643
ELB improved by 0.332764
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.391
ELB improved by 0.252076
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.215
ELB improved by 0.176317
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.093
ELB improved by 0.121824
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.007
ELB improved by 0.0866366
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.942
ELB improved by 0.0644213
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.892
ELB improved by 0.050098
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.852
ELB improved by 0.0404621
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.818
ELB improved by 0.0336428
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.789
ELB improved by 0.0285722
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.765
ELB improved by 0.0246389
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.743
ELB improved by 0.0214854
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.724
ELB improved by 0.018895
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.708
ELB improved by 0.0167304
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.693
ELB improved by 0.0148996
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.679
ELB improved by 0.0133378
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.667
ELB improved by 0.0119971
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.657
ELB improved by 0.0108407
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.647
ELB improved by 0.00983925
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-877.403
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-571.029
ELB improved by 306.374
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-502.988
ELB improved by 68.0407
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.047
ELB improved by 41.9415
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.192
ELB improved by 17.855
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.151
ELB improved by 8.04021
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.822
ELB improved by 5.32932
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.44
ELB improved by 4.38191
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.389
ELB improved by 4.05124
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.457
ELB improved by 3.93177
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.637
ELB improved by 3.81993
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.029
ELB improved by 3.60798
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.8
ELB improved by 3.22902
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.113
ELB improved by 2.68742
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.036
ELB improved by 2.07644
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.521
ELB improved by 1.51542
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.443
ELB improved by 1.0779
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.673
ELB improved by 0.769966
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.115
ELB improved by 0.558617
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.703
ELB improved by 0.411219
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.395
ELB improved by 0.308269
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.158
ELB improved by 0.237347
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.969
ELB improved by 0.188684
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.814
ELB improved by 0.15476
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.684
ELB improved by 0.130367
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.572
ELB improved by 0.112162
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.474
ELB improved by 0.098074
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.387
ELB improved by 0.0868211
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.309
ELB improved by 0.0775941
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.239
ELB improved by 0.069866
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.176
ELB improved by 0.0632824
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.119
ELB improved by 0.0575968
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.066
ELB improved by 0.0526324
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.018
ELB improved by 0.048259
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.973
ELB improved by 0.044378
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.932
ELB improved by 0.0409131
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.895
ELB improved by 0.0378039
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.86
ELB improved by 0.035002
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.827
ELB improved by 0.0324678
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.797
ELB improved by 0.0301683
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.769
ELB improved by 0.0280759
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.743
ELB improved by 0.0261674
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.718
ELB improved by 0.0244226
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.695
ELB improved by 0.0228245
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.674
ELB improved by 0.021358
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.654
ELB improved by 0.0200101
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.635
ELB improved by 0.0187693
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.618
ELB improved by 0.0176255
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.601
ELB improved by 0.0165699
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.585
ELB improved by 0.0155945
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.571
ELB improved by 0.0146922
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.557
ELB improved by 0.0138566
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.544
ELB improved by 0.0130822
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.531
ELB improved by 0.0123638
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.52
ELB improved by 0.0116969
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.509
ELB improved by 0.0110774
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.498
ELB improved by 0.0105014
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.488
ELB improved by 0.00996573
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.786 0.271 3.090
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.049 | 0.018 | 0.070 | |
| getPIPs | 0.054 | 0.015 | 0.069 | |
| graper | 0.097 | 0.021 | 0.118 | |
| makeExampleData | 0.011 | 0.001 | 0.011 | |
| makeExampleDataWithUnequalGroups | 0.012 | 0.002 | 0.014 | |
| plotELBO | 0.314 | 0.019 | 0.334 | |
| plotGroupPenalties | 1.251 | 0.037 | 1.290 | |
| plotPosterior | 0.607 | 0.029 | 0.637 | |
| predict.graper | 1.635 | 0.064 | 1.701 | |
| print.graper | 0.038 | 0.009 | 0.047 | |