Britta Velten
| Snapshot Date: 2025-10-31 13:45 -0400 (Fri, 31 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 2025-11-01 12:04 -0400 (Sat, 01 Nov 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: 2025-10-31 20:09:29 -0400 (Fri, 31 Oct 2025) |
| EndedAt: 2025-10-31 20:09:57 -0400 (Fri, 31 Oct 2025) |
| EllapsedTime: 28.3 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: 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 13.7.7
* 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 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 ... 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-arm64/Resources/library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.26.0’ ** 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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-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 version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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=-865.071
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-600.744
ELB improved by 264.327
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-540.834
ELB improved by 59.9105
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-492.439
ELB improved by 48.3949
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.729
ELB improved by 25.7105
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.846
ELB improved by 10.8823
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.772
ELB improved by 5.07446
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.729
ELB improved by 3.04243
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.428
ELB improved by 2.30132
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.474
ELB improved by 1.95436
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.722
ELB improved by 1.75197
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.11
ELB improved by 1.61211
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.606
ELB improved by 1.50358
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.196
ELB improved by 1.40953
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.881
ELB improved by 1.31563
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.672
ELB improved by 1.20928
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.588
ELB improved by 1.08365
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.647
ELB improved by 0.940645
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.858
ELB improved by 0.789207
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.217
ELB improved by 0.641522
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.706
ELB improved by 0.510163
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.302
ELB improved by 0.404486
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.975
ELB improved by 0.327334
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.699
ELB improved by 0.275573
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.456
ELB improved by 0.243397
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.23
ELB improved by 0.225142
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.014
ELB improved by 0.216468
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.8
ELB improved by 0.214414
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.582
ELB improved by 0.217064
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.359
ELB improved by 0.223199
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.127
ELB improved by 0.232037
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.884
ELB improved by 0.243087
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.628
ELB improved by 0.256071
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.357
ELB improved by 0.270901
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.069
ELB improved by 0.287698
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.763
ELB improved by 0.306824
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.434
ELB improved by 0.328936
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.079
ELB improved by 0.355027
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.692
ELB improved by 0.386416
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.268
ELB improved by 0.424607
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.797
ELB improved by 0.47075
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.273
ELB improved by 0.524293
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.692
ELB improved by 0.580721
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.061
ELB improved by 0.63047
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.399
ELB improved by 0.66291
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.726
ELB improved by 0.672965
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.064
ELB improved by 0.661713
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.431
ELB improved by 0.632607
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.841
ELB improved by 0.590446
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.299
ELB improved by 0.542148
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.803
ELB improved by 0.495554
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.348
ELB improved by 0.455547
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.928
ELB improved by 0.41961
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.549
ELB improved by 0.378502
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.223
ELB improved by 0.32692
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.951
ELB improved by 0.271248
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.729
ELB improved by 0.222559
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.541
ELB improved by 0.187956
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.372
ELB improved by 0.16923
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.207
ELB improved by 0.164959
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.035
ELB improved by 0.171988
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.849
ELB improved by 0.185215
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.652
ELB improved by 0.19757
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.448
ELB improved by 0.203496
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.243
ELB improved by 0.204839
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.034
ELB improved by 0.209835
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.811
ELB improved by 0.223105
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.575
ELB improved by 0.235316
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.351
ELB improved by 0.223871
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.172
ELB improved by 0.179673
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.047
ELB improved by 0.124228
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.967
ELB improved by 0.0803133
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.914
ELB improved by 0.052627
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.878
ELB improved by 0.0366935
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.85
ELB improved by 0.0276093
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.828
ELB improved by 0.0222047
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.809
ELB improved by 0.018745
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.793
ELB improved by 0.0163404
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.778
ELB improved by 0.0145416
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.765
ELB improved by 0.0131179
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.753
ELB improved by 0.0119461
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.742
ELB improved by 0.010956
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.732
ELB improved by 0.010105
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.723
ELB improved by 0.00936501
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-857.351
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-555.059
ELB improved by 302.292
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-499.467
ELB improved by 55.592
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.165
ELB improved by 27.3014
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.456
ELB improved by 11.7091
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.234
ELB improved by 6.22242
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.918
ELB improved by 4.31611
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.023
ELB improved by 3.89502
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.129
ELB improved by 3.89389
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.409
ELB improved by 3.71937
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.29
ELB improved by 3.11912
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.03
ELB improved by 2.26007
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.529
ELB improved by 1.50122
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.523
ELB improved by 1.00554
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.803
ELB improved by 0.720925
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.246
ELB improved by 0.556124
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.791
ELB improved by 0.455896
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.396
ELB improved by 0.394905
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.033
ELB improved by 0.362968
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.673
ELB improved by 0.35944
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.28
ELB improved by 0.392883
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.805
ELB improved by 0.475622
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.215
ELB improved by 0.589277
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.561
ELB improved by 0.653981
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.931
ELB improved by 0.630737
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.368
ELB improved by 0.563231
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.886
ELB improved by 0.481052
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.478
ELB improved by 0.408104
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.121
ELB improved by 0.357594
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.797
ELB improved by 0.324009
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.497
ELB improved by 0.299474
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.217
ELB improved by 0.280299
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.951
ELB improved by 0.266
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.693
ELB improved by 0.257871
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.435
ELB improved by 0.258354
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.164
ELB improved by 0.270618
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.867
ELB improved by 0.296734
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.534
ELB improved by 0.333398
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.161
ELB improved by 0.37259
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.742
ELB improved by 0.419212
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.238
ELB improved by 0.504391
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.584
ELB improved by 0.65333
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.792
ELB improved by 0.792407
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.951
ELB improved by 0.840807
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.053
ELB improved by 0.89805
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.031
ELB improved by 1.02217
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.869
ELB improved by 1.16192
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.627
ELB improved by 1.24169
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.35
ELB improved by 1.2776
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.031
ELB improved by 1.31841
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.737
ELB improved by 1.29478
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.675
ELB improved by 1.06116
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.946
ELB improved by 0.729328
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.481
ELB improved by 0.465128
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.187
ELB improved by 0.294398
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.994
ELB improved by 0.19283
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.86
ELB improved by 0.13385
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.761
ELB improved by 0.0988784
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.684
ELB improved by 0.0770345
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.622
ELB improved by 0.0624498
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.57
ELB improved by 0.0520497
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.525
ELB improved by 0.044213
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.487
ELB improved by 0.0380569
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.454
ELB improved by 0.0330754
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.425
ELB improved by 0.0289604
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.4
ELB improved by 0.0255112
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.377
ELB improved by 0.0225899
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.357
ELB improved by 0.0200959
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.339
ELB improved by 0.0179538
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.323
ELB improved by 0.0161048
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.308
ELB improved by 0.0145021
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.295
ELB improved by 0.013108
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.283
ELB improved by 0.0118915
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.273
ELB improved by 0.0108268
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.263
ELB improved by 0.00989274
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-884.907
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-571.315
ELB improved by 313.592
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-511.999
ELB improved by 59.3163
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-477.798
ELB improved by 34.2011
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.732
ELB improved by 14.0653
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.248
ELB improved by 6.48412
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.848
ELB improved by 4.40047
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.897
ELB improved by 3.95055
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.843
ELB improved by 4.0537
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.431
ELB improved by 4.41192
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.621
ELB improved by 4.81083
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.678
ELB improved by 4.94292
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.129
ELB improved by 4.54897
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.405
ELB improved by 3.72387
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.58
ELB improved by 2.82442
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.512
ELB improved by 2.06805
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.03
ELB improved by 1.48254
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.967
ELB improved by 1.06262
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.191
ELB improved by 0.775827
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.616
ELB improved by 0.57548
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.183
ELB improved by 0.433316
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.848
ELB improved by 0.334691
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.581
ELB improved by 0.266694
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.363
ELB improved by 0.218366
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.18
ELB improved by 0.18246
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.026
ELB improved by 0.154733
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.893
ELB improved by 0.132709
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.778
ELB improved by 0.114859
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.678
ELB improved by 0.100174
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.59
ELB improved by 0.0879511
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.512
ELB improved by 0.0776773
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.443
ELB improved by 0.0689694
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.382
ELB improved by 0.061534
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.327
ELB improved by 0.0551434
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.277
ELB improved by 0.0496179
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.232
ELB improved by 0.0448147
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.192
ELB improved by 0.0406187
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.155
ELB improved by 0.0369366
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.121
ELB improved by 0.0336921
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.09
ELB improved by 0.0308223
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.062
ELB improved by 0.0282749
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.036
ELB improved by 0.0260064
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.012
ELB improved by 0.0239801
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.99
ELB improved by 0.0221651
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.969
ELB improved by 0.020535
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.95
ELB improved by 0.0190675
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.932
ELB improved by 0.0177432
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.916
ELB improved by 0.0165456
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.9
ELB improved by 0.0154604
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.886
ELB improved by 0.0144752
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.872
ELB improved by 0.013579
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.86
ELB improved by 0.0127624
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.848
ELB improved by 0.0120171
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.836
ELB improved by 0.0113358
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.826
ELB improved by 0.010712
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.815
ELB improved by 0.0101401
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.806
ELB improved by 0.00961501
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-884.118
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-578.979
ELB improved by 305.139
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-520.055
ELB improved by 58.9243
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-480.767
ELB improved by 39.288
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.495
ELB improved by 18.2724
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.874
ELB improved by 7.62014
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.63
ELB improved by 4.24473
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.74
ELB improved by 2.88953
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.467
ELB improved by 2.27343
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.504
ELB improved by 1.963
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.727
ELB improved by 1.77642
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.08
ELB improved by 1.64686
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.535
ELB improved by 1.54564
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.083
ELB improved by 1.45175
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.738
ELB improved by 1.34461
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.53
ELB improved by 1.20879
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.487
ELB improved by 1.04261
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.626
ELB improved by 0.860886
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.94
ELB improved by 0.686544
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.401
ELB improved by 0.5382
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.978
ELB improved by 0.423746
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.636
ELB improved by 0.341811
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.349
ELB improved by 0.286403
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.099
ELB improved by 0.250712
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.87
ELB improved by 0.228997
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.653
ELB improved by 0.21709
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.44
ELB improved by 0.212206
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.228
ELB improved by 0.212569
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.011
ELB improved by 0.217046
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.786
ELB improved by 0.224864
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.551
ELB improved by 0.235412
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.302
ELB improved by 0.248114
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.04
ELB improved by 0.262367
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.763
ELB improved by 0.277542
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.47
ELB improved by 0.293073
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.161
ELB improved by 0.308611
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.837
ELB improved by 0.324257
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.496
ELB improved by 0.340838
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.136
ELB improved by 0.360244
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.75
ELB improved by 0.385906
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.326
ELB improved by 0.423733
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.842
ELB improved by 0.484097
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.256
ELB improved by 0.585349
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.503
ELB improved by 0.753917
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.509
ELB improved by 0.993537
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.277
ELB improved by 1.23232
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.854
ELB improved by 1.42313
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.224
ELB improved by 1.62951
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.308
ELB improved by 1.91574
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.13
ELB improved by 2.17793
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.069
ELB improved by 2.06168
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.37
ELB improved by 1.69831
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.93
ELB improved by 1.44067
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.585
ELB improved by 1.34483
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.541
ELB improved by 1.04411
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.927
ELB improved by 0.614024
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.584
ELB improved by 0.342932
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.383
ELB improved by 0.200895
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.255
ELB improved by 0.127475
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.167
ELB improved by 0.0879889
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.102
ELB improved by 0.0651179
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.052
ELB improved by 0.0507566
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.011
ELB improved by 0.0410857
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.976
ELB improved by 0.0342041
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.947
ELB improved by 0.0290912
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.922
ELB improved by 0.0251585
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.9
ELB improved by 0.0220469
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.88
ELB improved by 0.019527
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.863
ELB improved by 0.0174471
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.847
ELB improved by 0.0157033
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.833
ELB improved by 0.0142231
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.82
ELB improved by 0.0129536
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.808
ELB improved by 0.0118559
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.797
ELB improved by 0.0109004
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.787
ELB improved by 0.0100639
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.778
ELB improved by 0.00932821
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
1.002 0.073 1.072
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.028 | 0.006 | 0.033 | |
| getPIPs | 0.027 | 0.005 | 0.033 | |
| graper | 0.050 | 0.009 | 0.058 | |
| makeExampleData | 0.003 | 0.000 | 0.004 | |
| makeExampleDataWithUnequalGroups | 0.004 | 0.000 | 0.005 | |
| plotELBO | 0.134 | 0.008 | 0.141 | |
| plotGroupPenalties | 0.448 | 0.012 | 0.465 | |
| plotPosterior | 0.221 | 0.008 | 0.230 | |
| predict.graper | 1.034 | 0.021 | 1.055 | |
| print.graper | 0.027 | 0.003 | 0.031 | |