Britta Velten
| Snapshot Date: 2025-12-07 13:40 -0500 (Sun, 07 Dec 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 2025-12-08 11:35 -0500 (Mon, 08 Dec 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" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4576 |
| 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 914/2331 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.27.0 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: graper |
| Version: 1.27.0 |
| Command: /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: 2025-12-07 20:15:40 -0500 (Sun, 07 Dec 2025) |
| EndedAt: 2025-12-07 20:16:12 -0500 (Sun, 07 Dec 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=-849.129
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-600.044
ELB improved by 249.085
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-542.561
ELB improved by 57.4825
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-493.39
ELB improved by 49.1711
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.624
ELB improved by 29.766
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.547
ELB improved by 14.0774
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.036
ELB improved by 7.51123
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.208
ELB improved by 5.82818
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.632
ELB improved by 5.57509
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.979
ELB improved by 5.65317
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.373
ELB improved by 5.60671
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.295
ELB improved by 5.07728
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.23
ELB improved by 4.0648
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.285
ELB improved by 2.94537
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.239
ELB improved by 2.04633
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.793
ELB improved by 1.44551
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.714
ELB improved by 1.07882
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.853
ELB improved by 0.861516
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.123
ELB improved by 0.730373
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.476
ELB improved by 0.64607
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.89
ELB improved by 0.586125
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.352
ELB improved by 0.538352
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.855
ELB improved by 0.496579
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.397
ELB improved by 0.458124
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.975
ELB improved by 0.422267
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.586
ELB improved by 0.389284
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.226
ELB improved by 0.359849
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.891
ELB improved by 0.33471
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.577
ELB improved by 0.314588
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.276
ELB improved by 0.300197
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.984
ELB improved by 0.292285
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.693
ELB improved by 0.291472
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.395
ELB improved by 0.297535
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.087
ELB improved by 0.307968
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.77
ELB improved by 0.31721
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.451
ELB improved by 0.319367
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.138
ELB improved by 0.312876
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.837
ELB improved by 0.300352
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.553
ELB improved by 0.28458
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.286
ELB improved by 0.266807
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.039
ELB improved by 0.247424
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.812
ELB improved by 0.226711
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.607
ELB improved by 0.20509
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.424
ELB improved by 0.183109
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.262
ELB improved by 0.16137
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.122
ELB improved by 0.140445
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.001
ELB improved by 0.120821
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.898
ELB improved by 0.102864
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.811
ELB improved by 0.0868017
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.739
ELB improved by 0.0727333
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.678
ELB improved by 0.0606418
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.628
ELB improved by 0.0504197
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.586
ELB improved by 0.0418977
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.551
ELB improved by 0.0348726
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.522
ELB improved by 0.0291312
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.497
ELB improved by 0.0244674
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.476
ELB improved by 0.0206932
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.459
ELB improved by 0.0176442
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.444
ELB improved by 0.0151806
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.43
ELB improved by 0.0131865
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.419
ELB improved by 0.0115674
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.409
ELB improved by 0.0102469
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.399
ELB improved by 0.0091642
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-855.367
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-577.255
ELB improved by 278.111
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-518.486
ELB improved by 58.7694
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-480.91
ELB improved by 37.5761
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.613
ELB improved by 16.2968
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.725
ELB improved by 5.88844
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.409
ELB improved by 3.31562
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.518
ELB improved by 2.89074
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.749
ELB improved by 2.76917
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.017
ELB improved by 2.73207
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.282
ELB improved by 2.73552
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.516
ELB improved by 2.76532
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.715
ELB improved by 2.80155
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.919
ELB improved by 2.7954
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.251
ELB improved by 2.66841
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.896
ELB improved by 2.35496
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.019
ELB improved by 1.87734
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.66
ELB improved by 1.35822
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.737
ELB improved by 0.923264
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.118
ELB improved by 0.619016
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.691
ELB improved by 0.426927
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.381
ELB improved by 0.310327
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.142
ELB improved by 0.239118
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.948
ELB improved by 0.193999
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.784
ELB improved by 0.163818
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.641
ELB improved by 0.14242
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.515
ELB improved by 0.126434
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.401
ELB improved by 0.113979
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.297
ELB improved by 0.103963
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.201
ELB improved by 0.0957189
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.113
ELB improved by 0.0888125
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.03
ELB improved by 0.0829481
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.952
ELB improved by 0.0779139
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.878
ELB improved by 0.0735522
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.808
ELB improved by 0.0697422
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.742
ELB improved by 0.0663888
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.679
ELB improved by 0.0634159
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.618
ELB improved by 0.0607615
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.559
ELB improved by 0.0583748
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.503
ELB improved by 0.0562135
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.449
ELB improved by 0.0542424
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.397
ELB improved by 0.0524324
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.346
ELB improved by 0.0507589
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.297
ELB improved by 0.0492021
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.249
ELB improved by 0.0477454
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.203
ELB improved by 0.0463757
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.157
ELB improved by 0.0450825
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.114
ELB improved by 0.0438575
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.071
ELB improved by 0.0426944
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.029
ELB improved by 0.0415882
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.989
ELB improved by 0.0405348
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.949
ELB improved by 0.0395306
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.911
ELB improved by 0.0385718
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.873
ELB improved by 0.0376541
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.836
ELB improved by 0.0367723
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.8
ELB improved by 0.0359197
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.765
ELB improved by 0.0350887
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.731
ELB improved by 0.0342702
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.697
ELB improved by 0.0334548
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.665
ELB improved by 0.0326328
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.633
ELB improved by 0.0317955
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.602
ELB improved by 0.0309359
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.572
ELB improved by 0.0300492
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.543
ELB improved by 0.0291335
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.515
ELB improved by 0.0281895
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.488
ELB improved by 0.0272204
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.461
ELB improved by 0.0262313
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.436
ELB improved by 0.0252287
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.412
ELB improved by 0.0242196
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.389
ELB improved by 0.0232112
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.366
ELB improved by 0.0222103
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.345
ELB improved by 0.0212231
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.325
ELB improved by 0.0202553
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.306
ELB improved by 0.0193114
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.287
ELB improved by 0.0183953
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.27
ELB improved by 0.0175101
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.253
ELB improved by 0.0166582
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.237
ELB improved by 0.0158411
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.222
ELB improved by 0.0150599
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.208
ELB improved by 0.0143153
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.194
ELB improved by 0.0136073
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.181
ELB improved by 0.0129356
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.169
ELB improved by 0.0122998
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.157
ELB improved by 0.0116989
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.146
ELB improved by 0.0111319
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.136
ELB improved by 0.0105977
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.125
ELB improved by 0.010095
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.116
ELB improved by 0.0096225
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-889.102
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-560.761
ELB improved by 328.34
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-498.286
ELB improved by 62.4759
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.044
ELB improved by 31.2419
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.735
ELB improved by 11.3091
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.067
ELB improved by 5.66712
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.911
ELB improved by 4.15672
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.172
ELB improved by 3.73923
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.356
ELB improved by 3.81504
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.193
ELB improved by 4.16324
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.551
ELB improved by 4.64207
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.561
ELB improved by 4.99017
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.768
ELB improved by 4.79269
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.85
ELB improved by 3.91783
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.059
ELB improved by 2.79185
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.185
ELB improved by 1.87385
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.917
ELB improved by 1.2674
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.055
ELB improved by 0.862769
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.464
ELB improved by 0.590405
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.042
ELB improved by 0.42265
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.722
ELB improved by 0.319956
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.47
ELB improved by 0.251724
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.267
ELB improved by 0.203159
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.099
ELB improved by 0.167574
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.958
ELB improved by 0.141076
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.837
ELB improved by 0.120925
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.732
ELB improved by 0.105199
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.639
ELB improved by 0.0926133
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.557
ELB improved by 0.082326
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.483
ELB improved by 0.0737811
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.417
ELB improved by 0.0665968
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.356
ELB improved by 0.0604996
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.301
ELB improved by 0.0552857
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.25
ELB improved by 0.0507979
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.203
ELB improved by 0.0469128
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.16
ELB improved by 0.0435311
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.119
ELB improved by 0.0405723
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.081
ELB improved by 0.0379704
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.045
ELB improved by 0.0356705
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.012
ELB improved by 0.0336271
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.98
ELB improved by 0.0318017
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.95
ELB improved by 0.0301619
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.921
ELB improved by 0.0286803
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.894
ELB improved by 0.0273335
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.868
ELB improved by 0.0261015
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.843
ELB improved by 0.024967
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.819
ELB improved by 0.0239156
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.796
ELB improved by 0.0229346
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.774
ELB improved by 0.0220135
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.753
ELB improved by 0.021143
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.732
ELB improved by 0.0203157
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.713
ELB improved by 0.0195251
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.694
ELB improved by 0.0187661
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.676
ELB improved by 0.0180343
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.659
ELB improved by 0.0173263
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.642
ELB improved by 0.0166397
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.626
ELB improved by 0.0159725
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.611
ELB improved by 0.0153232
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.596
ELB improved by 0.0146911
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.582
ELB improved by 0.0140757
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.569
ELB improved by 0.0134768
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.556
ELB improved by 0.0128945
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.543
ELB improved by 0.0123291
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.532
ELB improved by 0.0117809
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.52
ELB improved by 0.0112502
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.51
ELB improved by 0.0107377
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.499
ELB improved by 0.0102435
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.49
ELB improved by 0.00976801
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-878.243
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-567.083
ELB improved by 311.16
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-506.921
ELB improved by 60.1625
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.129
ELB improved by 33.7913
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.849
ELB improved by 13.2805
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.631
ELB improved by 6.21775
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.351
ELB improved by 4.28024
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.49
ELB improved by 3.86125
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.38
ELB improved by 4.10926
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.641
ELB improved by 4.73932
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.183
ELB improved by 5.45826
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.543
ELB improved by 5.64015
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.758
ELB improved by 4.78484
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.391
ELB improved by 3.3666
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.164
ELB improved by 2.22659
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.569
ELB improved by 1.59523
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.282
ELB improved by 1.28738
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.154
ELB improved by 1.12763
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.126
ELB improved by 1.02796
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.178
ELB improved by 0.948777
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.304
ELB improved by 0.873947
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.504
ELB improved by 0.799808
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.775
ELB improved by 0.728368
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.112
ELB improved by 0.662917
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.507
ELB improved by 0.605871
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.948
ELB improved by 0.558267
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.428
ELB improved by 0.520004
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.938
ELB improved by 0.490241
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.47
ELB improved by 0.467682
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.02
ELB improved by 0.450737
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.582
ELB improved by 0.437612
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.156
ELB improved by 0.426383
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.741
ELB improved by 0.415105
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.339
ELB improved by 0.401989
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.953
ELB improved by 0.385663
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.587
ELB improved by 0.36547
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.246
ELB improved by 0.341721
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.93
ELB improved by 0.315732
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.641
ELB improved by 0.289457
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.376
ELB improved by 0.264524
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.136
ELB improved by 0.2405
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.922
ELB improved by 0.213591
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.742
ELB improved by 0.17985
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.6
ELB improved by 0.142206
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.491
ELB improved by 0.109045
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.406
ELB improved by 0.0851352
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.336
ELB improved by 0.0696163
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.276
ELB improved by 0.0597838
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.223
ELB improved by 0.0534273
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.174
ELB improved by 0.0491609
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.128
ELB improved by 0.0461645
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.084
ELB improved by 0.0439333
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.041
ELB improved by 0.042117
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.001
ELB improved by 0.0404294
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.962
ELB improved by 0.0386119
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.926
ELB improved by 0.0364512
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.892
ELB improved by 0.0338326
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.861
ELB improved by 0.0307876
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.834
ELB improved by 0.0274852
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.81
ELB improved by 0.0241629
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.789
ELB improved by 0.0210387
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.77
ELB improved by 0.0182559
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.755
ELB improved by 0.0158739
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.741
ELB improved by 0.0138891
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.728
ELB improved by 0.0122626
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.717
ELB improved by 0.010943
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.708
ELB improved by 0.00987874
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
1.040 0.089 1.145
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.014 | 0.006 | 0.021 | |
| getPIPs | 0.012 | 0.005 | 0.018 | |
| graper | 0.019 | 0.009 | 0.028 | |
| makeExampleData | 0.001 | 0.000 | 0.002 | |
| makeExampleDataWithUnequalGroups | 0.002 | 0.001 | 0.002 | |
| plotELBO | 0.112 | 0.008 | 0.125 | |
| plotGroupPenalties | 0.362 | 0.008 | 0.383 | |
| plotPosterior | 0.311 | 0.016 | 0.332 | |
| predict.graper | 0.215 | 0.034 | 0.250 | |
| print.graper | 0.011 | 0.005 | 0.015 | |