Britta Velten
| Snapshot Date: 2025-09-28 13:45 -0400 (Sun, 28 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: 82b0592 |
| git_last_commit_date: 2025-06-24 03:15:40 -0400 (Tue, 24 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-29 12:04 -0400 (Mon, 29 Sep 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" | 4833 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4621 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4566 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
| 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 913/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.25.2 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.25.2 |
| 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_1.25.2.tar.gz |
| StartedAt: 2025-09-28 21:40:42 -0400 (Sun, 28 Sep 2025) |
| EndedAt: 2025-09-28 21:42:01 -0400 (Sun, 28 Sep 2025) |
| EllapsedTime: 79.4 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_1.25.2.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 ‘1.25.2’
* 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 ‘1.25.2’ ** 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=-883.371
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-573.766
ELB improved by 309.605
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-517.127
ELB improved by 56.6382
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-484.897
ELB improved by 32.2299
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.12
ELB improved by 14.7772
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.708
ELB improved by 7.41257
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.902
ELB improved by 5.80575
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.203
ELB improved by 5.69874
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.438
ELB improved by 5.76569
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.943
ELB improved by 5.49493
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.245
ELB improved by 4.69809
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.642
ELB improved by 3.6026
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.067
ELB improved by 2.57451
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.271
ELB improved by 1.7967
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.996
ELB improved by 1.27449
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.054
ELB improved by 0.94209
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.323
ELB improved by 0.731012
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.73
ELB improved by 0.59278
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.232
ELB improved by 0.498041
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.802
ELB improved by 0.430087
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.423
ELB improved by 0.379436
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.082
ELB improved by 0.340563
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.772
ELB improved by 0.310283
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.485
ELB improved by 0.286935
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.215
ELB improved by 0.269745
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.957
ELB improved by 0.258259
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.705
ELB improved by 0.252022
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.454
ELB improved by 0.250531
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.201
ELB improved by 0.253316
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.941
ELB improved by 0.260017
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.671
ELB improved by 0.270417
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.386
ELB improved by 0.284428
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.084
ELB improved by 0.302075
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.761
ELB improved by 0.323448
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.412
ELB improved by 0.348658
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.034
ELB improved by 0.377756
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.624
ELB improved by 0.410635
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.177
ELB improved by 0.446891
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.691
ELB improved by 0.48556
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.167
ELB improved by 0.524453
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.608
ELB improved by 0.55853
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.03
ELB improved by 0.577861
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.46
ELB improved by 0.570325
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.927
ELB improved by 0.533038
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.45
ELB improved by 0.477358
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.033
ELB improved by 0.417025
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.673
ELB improved by 0.35958
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.365
ELB improved by 0.307813
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.103
ELB improved by 0.262261
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.88
ELB improved by 0.222554
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.692
ELB improved by 0.188344
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.532
ELB improved by 0.159648
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.396
ELB improved by 0.136668
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.276
ELB improved by 0.119545
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.168
ELB improved by 0.108335
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.065
ELB improved by 0.103073
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.961
ELB improved by 0.103777
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.851
ELB improved by 0.110365
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.728
ELB improved by 0.122418
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.59
ELB improved by 0.138063
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.439
ELB improved by 0.151434
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.287
ELB improved by 0.152232
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.153
ELB improved by 0.133535
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.052
ELB improved by 0.101112
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.983
ELB improved by 0.0684996
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.939
ELB improved by 0.0444932
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.909
ELB improved by 0.0298521
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.887
ELB improved by 0.0216774
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.87
ELB improved by 0.0171145
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.856
ELB improved by 0.0143813
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.843
ELB improved by 0.012559
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.832
ELB improved by 0.0112135
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.822
ELB improved by 0.0101444
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.813
ELB improved by 0.00925578
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-856.799
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-545.841
ELB improved by 310.958
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-493.845
ELB improved by 51.9955
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.607
ELB improved by 27.2381
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.638
ELB improved by 10.9693
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.291
ELB improved by 5.34744
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.1
ELB improved by 4.19063
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.026
ELB improved by 4.07369
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.617
ELB improved by 4.40888
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.605
ELB improved by 5.01214
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.945
ELB improved by 5.66026
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.992
ELB improved by 5.95324
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.431
ELB improved by 5.56019
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.945
ELB improved by 4.48661
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.878
ELB improved by 3.06721
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.942
ELB improved by 1.93522
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.693
ELB improved by 1.24915
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.819
ELB improved by 0.874619
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.122
ELB improved by 0.696735
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.481
ELB improved by 0.640863
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.834
ELB improved by 0.64659
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.178
ELB improved by 0.656787
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.539
ELB improved by 0.63902
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.94
ELB improved by 0.599044
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.383
ELB improved by 0.556834
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.859
ELB improved by 0.52418
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.359
ELB improved by 0.499796
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.879
ELB improved by 0.479664
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.417
ELB improved by 0.462416
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.968
ELB improved by 0.44903
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.526
ELB improved by 0.442157
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.079
ELB improved by 0.446761
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.606
ELB improved by 0.472755
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.068
ELB improved by 0.538532
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.411
ELB improved by 0.656588
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.646
ELB improved by 0.765371
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.872
ELB improved by 0.773042
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.142
ELB improved by 0.730759
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.448
ELB improved by 0.694085
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.784
ELB improved by 0.6636
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.147
ELB improved by 0.637139
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.527
ELB improved by 0.620152
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.905
ELB improved by 0.62202
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.258
ELB improved by 0.647085
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.584
ELB improved by 0.673679
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.917
ELB improved by 0.667402
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.267
ELB improved by 0.649939
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.619
ELB improved by 0.647669
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.033
ELB improved by 0.585717
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.614
ELB improved by 0.419599
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.353
ELB improved by 0.260728
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.191
ELB improved by 0.162419
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.083
ELB improved by 0.107343
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.007
ELB improved by 0.0757079
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.951
ELB improved by 0.0564484
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.907
ELB improved by 0.0439705
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.872
ELB improved by 0.0354141
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.842
ELB improved by 0.0292541
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.818
ELB improved by 0.0246366
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.797
ELB improved by 0.0210605
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.778
ELB improved by 0.0182177
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.763
ELB improved by 0.0159111
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.749
ELB improved by 0.0140093
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.736
ELB improved by 0.0124218
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.725
ELB improved by 0.0110836
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.715
ELB improved by 0.00994708
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-832.784
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-586.177
ELB improved by 246.607
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-529.618
ELB improved by 56.5588
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-484.564
ELB improved by 45.0538
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.294
ELB improved by 26.2706
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.074
ELB improved by 12.2203
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.249
ELB improved by 6.82469
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.371
ELB improved by 5.87749
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.784
ELB improved by 6.58784
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.828
ELB improved by 7.95573
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.896
ELB improved by 8.93231
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.696
ELB improved by 8.19946
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.79
ELB improved by 5.90563
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.096
ELB improved by 3.69446
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.765
ELB improved by 2.33087
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.163
ELB improved by 1.60192
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.935
ELB improved by 1.22808
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.874
ELB improved by 1.06131
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.874
ELB improved by 0.999886
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.96
ELB improved by 0.913995
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.173
ELB improved by 0.786927
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.465
ELB improved by 0.708271
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.779
ELB improved by 0.685391
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.085
ELB improved by 0.694467
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.362
ELB improved by 0.722821
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.597
ELB improved by 0.765088
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.779
ELB improved by 0.818179
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.9
ELB improved by 0.878783
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.959
ELB improved by 0.941156
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.965
ELB improved by 0.99353
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.95
ELB improved by 1.01512
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.965
ELB improved by 0.984931
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.065
ELB improved by 0.900418
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.287
ELB improved by 0.777494
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.65
ELB improved by 0.637707
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.149
ELB improved by 0.501114
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.767
ELB improved by 0.381513
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.482
ELB improved by 0.284785
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.271
ELB improved by 0.210903
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.115
ELB improved by 0.156628
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.997
ELB improved by 0.117573
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.908
ELB improved by 0.0895725
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.838
ELB improved by 0.0693354
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.784
ELB improved by 0.0545075
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.74
ELB improved by 0.0434801
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.705
ELB improved by 0.0351639
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.676
ELB improved by 0.0288128
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.652
ELB improved by 0.0239072
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.632
ELB improved by 0.0200779
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.615
ELB improved by 0.0170587
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.601
ELB improved by 0.0146548
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.588
ELB improved by 0.0127225
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.577
ELB improved by 0.0111542
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.567
ELB improved by 0.00986938
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-849.419
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-566.471
ELB improved by 282.948
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-506.925
ELB improved by 59.5462
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.685
ELB improved by 37.2398
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.877
ELB improved by 16.8081
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.036
ELB improved by 7.84125
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.085
ELB improved by 4.95109
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.857
ELB improved by 4.22772
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.575
ELB improved by 4.28148
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.913
ELB improved by 4.66231
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.854
ELB improved by 5.05908
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.773
ELB improved by 5.08061
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.328
ELB improved by 4.44525
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.97
ELB improved by 3.35849
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.672
ELB improved by 2.29818
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.176
ELB improved by 1.49515
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.213
ELB improved by 0.96345
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.566
ELB improved by 0.647119
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.1
ELB improved by 0.46576
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.743
ELB improved by 0.357477
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.455
ELB improved by 0.287469
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.217
ELB improved by 0.238414
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.015
ELB improved by 0.201795
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.842
ELB improved by 0.17321
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.691
ELB improved by 0.150203
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.56
ELB improved by 0.131284
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.445
ELB improved by 0.115486
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.343
ELB improved by 0.102142
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.252
ELB improved by 0.0907686
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.171
ELB improved by 0.0810036
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.098
ELB improved by 0.072567
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.033
ELB improved by 0.0652378
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.974
ELB improved by 0.0588394
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.921
ELB improved by 0.0532282
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.873
ELB improved by 0.0482869
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.829
ELB improved by 0.0439188
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.789
ELB improved by 0.0400433
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.752
ELB improved by 0.0365935
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.719
ELB improved by 0.033513
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.688
ELB improved by 0.0307541
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.66
ELB improved by 0.0282767
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.633
ELB improved by 0.0260461
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.609
ELB improved by 0.0240332
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.587
ELB improved by 0.0222124
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.567
ELB improved by 0.020562
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.548
ELB improved by 0.0190631
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.53
ELB improved by 0.0176992
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.513
ELB improved by 0.0164559
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.498
ELB improved by 0.0153207
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.484
ELB improved by 0.0142825
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.471
ELB improved by 0.0133317
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.458
ELB improved by 0.0124595
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.446
ELB improved by 0.0116584
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.435
ELB improved by 0.0109216
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.425
ELB improved by 0.0102432
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.416
ELB improved by 0.00961771
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.864 0.281 3.171
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.053 | 0.016 | 0.069 | |
| getPIPs | 0.046 | 0.016 | 0.062 | |
| graper | 0.080 | 0.020 | 0.101 | |
| makeExampleData | 0.012 | 0.001 | 0.012 | |
| makeExampleDataWithUnequalGroups | 0.014 | 0.001 | 0.015 | |
| plotELBO | 0.359 | 0.020 | 0.382 | |
| plotGroupPenalties | 1.425 | 0.060 | 1.498 | |
| plotPosterior | 0.829 | 0.025 | 0.860 | |
| predict.graper | 1.921 | 0.095 | 2.033 | |
| print.graper | 0.047 | 0.013 | 0.060 | |