Britta Velten
| Snapshot Date: 2025-12-18 13:45 -0500 (Thu, 18 Dec 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 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-22 12:05 -0500 (Mon, 22 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4883 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 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: 1.26.0 |
| 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: 2025-12-20 05:14:36 -0500 (Sat, 20 Dec 2025) |
| EndedAt: 2025-12-20 05:16:19 -0500 (Sat, 20 Dec 2025) |
| EllapsedTime: 103.2 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 4.5.2 Patched (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 ‘1.26.0’
* 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-1500.0.40.1)’
* 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-1500.0.40.1)’ 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 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
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=-857.766
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-589.396
ELB improved by 268.37
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-528.895
ELB improved by 60.5019
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-479.643
ELB improved by 49.252
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.7
ELB improved by 24.9426
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.862
ELB improved by 9.83745
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.549
ELB improved by 5.31361
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.566
ELB improved by 3.98294
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.933
ELB improved by 3.63322
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.359
ELB improved by 3.5742
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.793
ELB improved by 3.56551
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.324
ELB improved by 3.46878
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.131
ELB improved by 3.19336
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.402
ELB improved by 2.72887
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.241
ELB improved by 2.16094
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.631
ELB improved by 1.61007
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.477
ELB improved by 1.15358
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.666
ELB improved by 0.811839
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.087
ELB improved by 0.578608
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.654
ELB improved by 0.433194
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.306
ELB improved by 0.347729
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.007
ELB improved by 0.298907
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.735
ELB improved by 0.272172
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.475
ELB improved by 0.259925
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.216
ELB improved by 0.258896
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.948
ELB improved by 0.26828
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.66
ELB improved by 0.288287
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.341
ELB improved by 0.318361
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.986
ELB improved by 0.355398
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.591
ELB improved by 0.39443
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.159
ELB improved by 0.432861
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.685
ELB improved by 0.473236
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.163
ELB improved by 0.522417
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.57
ELB improved by 0.592833
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.861
ELB improved by 0.709526
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.943
ELB improved by 0.917345
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.707
ELB improved by 1.23627
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.2
ELB improved by 1.50732
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.643
ELB improved by 1.5567
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.143
ELB improved by 1.49969
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.719
ELB improved by 1.42435
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.403
ELB improved by 1.31551
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.254
ELB improved by 1.14932
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.321
ELB improved by 0.933471
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.612
ELB improved by 0.708417
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.095
ELB improved by 0.517486
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.713
ELB improved by 0.38207
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.409
ELB improved by 0.303591
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.131
ELB improved by 0.277602
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.832
ELB improved by 0.299178
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.489
ELB improved by 0.343541
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.135
ELB improved by 0.353242
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.83
ELB improved by 0.305114
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.601
ELB improved by 0.229491
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.445
ELB improved by 0.156177
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.343
ELB improved by 0.101834
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.275
ELB improved by 0.0680822
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.226
ELB improved by 0.0485284
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.189
ELB improved by 0.0369869
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.159
ELB improved by 0.0296916
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.135
ELB improved by 0.0246953
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.114
ELB improved by 0.0210315
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.096
ELB improved by 0.0182072
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.08
ELB improved by 0.0159544
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.065
ELB improved by 0.0141154
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.053
ELB improved by 0.0125904
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.042
ELB improved by 0.0113115
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.031
ELB improved by 0.0102301
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.022
ELB improved by 0.00930997
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-858.973
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-546.281
ELB improved by 312.692
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-482.464
ELB improved by 63.817
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.895
ELB improved by 37.5685
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.765
ELB improved by 16.1303
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.609
ELB improved by 7.15622
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.314
ELB improved by 4.29456
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.552
ELB improved by 2.76193
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.741
ELB improved by 1.81118
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.516
ELB improved by 1.22514
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.652
ELB improved by 0.864082
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.014
ELB improved by 0.637661
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.523
ELB improved by 0.491002
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.131
ELB improved by 0.392413
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.807
ELB improved by 0.323757
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.533
ELB improved by 0.274454
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.294
ELB improved by 0.238127
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.084
ELB improved by 0.210784
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.894
ELB improved by 0.18984
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.72
ELB improved by 0.173561
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.56
ELB improved by 0.160751
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.409
ELB improved by 0.150564
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.267
ELB improved by 0.142384
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.131
ELB improved by 0.135757
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.001
ELB improved by 0.130338
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.875
ELB improved by 0.125867
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.753
ELB improved by 0.12214
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.634
ELB improved by 0.119003
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.517
ELB improved by 0.116337
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.403
ELB improved by 0.114054
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.291
ELB improved by 0.11209
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.181
ELB improved by 0.110405
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.072
ELB improved by 0.108976
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.964
ELB improved by 0.107796
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.857
ELB improved by 0.106874
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.751
ELB improved by 0.106229
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.645
ELB improved by 0.105888
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.539
ELB improved by 0.105889
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.433
ELB improved by 0.106274
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.326
ELB improved by 0.107091
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.217
ELB improved by 0.108391
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.107
ELB improved by 0.110235
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.994
ELB improved by 0.112685
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.878
ELB improved by 0.115818
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.759
ELB improved by 0.119718
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.634
ELB improved by 0.124491
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.504
ELB improved by 0.130265
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.367
ELB improved by 0.137198
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.221
ELB improved by 0.145491
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.066
ELB improved by 0.155401
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.899
ELB improved by 0.167253
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.717
ELB improved by 0.181457
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.519
ELB improved by 0.19853
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.3
ELB improved by 0.219111
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.056
ELB improved by 0.243968
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.782
ELB improved by 0.274007
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.471
ELB improved by 0.310251
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.118
ELB improved by 0.353812
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.712
ELB improved by 0.405847
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.244
ELB improved by 0.467523
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.704
ELB improved by 0.540007
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.08
ELB improved by 0.62447
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.358
ELB improved by 0.722006
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.525
ELB improved by 0.833027
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.57
ELB improved by 0.955005
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.492
ELB improved by 1.07726
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.316
ELB improved by 1.17644
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.094
ELB improved by 1.22203
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.91
ELB improved by 1.18365
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.869
ELB improved by 1.04175
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.043
ELB improved by 0.825014
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.44
ELB improved by 0.603215
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.015
ELB improved by 0.425304
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.716
ELB improved by 0.299433
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.501
ELB improved by 0.214338
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.344
ELB improved by 0.156989
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.226
ELB improved by 0.117839
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.136
ELB improved by 0.0907171
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.064
ELB improved by 0.071725
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.006
ELB improved by 0.0583625
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.957
ELB improved by 0.0489865
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.914
ELB improved by 0.0424928
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.876
ELB improved by 0.0381222
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.841
ELB improved by 0.0353353
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.807
ELB improved by 0.0337256
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.774
ELB improved by 0.03296
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.741
ELB improved by 0.0327409
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.708
ELB improved by 0.0327945
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.676
ELB improved by 0.0328806
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.643
ELB improved by 0.0328135
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.61
ELB improved by 0.0324683
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.578
ELB improved by 0.0317623
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.548
ELB improved by 0.0306282
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.519
ELB improved by 0.0290144
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.492
ELB improved by 0.0269233
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.467
ELB improved by 0.0244536
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.446
ELB improved by 0.0217972
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.426
ELB improved by 0.0191801
iteration 99
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.41
ELB improved by 0.0167874
iteration 100
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.395
ELB improved by 0.0147211
iteration 101
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.382
ELB improved by 0.0130027
iteration 102
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.37
ELB improved by 0.0116013
iteration 103
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.36
ELB improved by 0.0104642
iteration 104
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.35
ELB improved by 0.00953626
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-896.837
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-542.749
ELB improved by 354.088
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-488.191
ELB improved by 54.5577
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.262
ELB improved by 23.9288
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.371
ELB improved by 10.8915
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.146
ELB improved by 7.22459
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.517
ELB improved by 6.62956
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.494
ELB improved by 7.02252
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.142
ELB improved by 7.35211
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.431
ELB improved by 6.7108
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.408
ELB improved by 5.0228
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.145
ELB improved by 3.26337
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.993
ELB improved by 2.1517
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.483
ELB improved by 1.51035
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.449
ELB improved by 1.03402
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.729
ELB improved by 0.719494
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.18
ELB improved by 0.549187
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.714
ELB improved by 0.466518
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.282
ELB improved by 0.432022
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.857
ELB improved by 0.424903
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.423
ELB improved by 0.433439
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.973
ELB improved by 0.449946
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.502
ELB improved by 0.47151
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.002
ELB improved by 0.499876
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.468
ELB improved by 0.53434
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.904
ELB improved by 0.563285
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.332
ELB improved by 0.572629
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.764
ELB improved by 0.567229
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.201
ELB improved by 0.563064
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.635
ELB improved by 0.566299
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.062
ELB improved by 0.573336
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.483
ELB improved by 0.579199
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.901
ELB improved by 0.581977
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.319
ELB improved by 0.582048
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.738
ELB improved by 0.580107
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.162
ELB improved by 0.576871
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.588
ELB improved by 0.573897
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.013
ELB improved by 0.574929
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.424
ELB improved by 0.588715
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.789
ELB improved by 0.635137
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.039
ELB improved by 0.74995
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.094
ELB improved by 0.94467
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.969
ELB improved by 1.12568
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.768
ELB improved by 1.20107
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.691
ELB improved by 1.07603
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.924
ELB improved by 0.767755
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.427
ELB improved by 0.496936
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.088
ELB improved by 0.338809
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.836
ELB improved by 0.252072
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.64
ELB improved by 0.195856
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.491
ELB improved by 0.149174
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.383
ELB improved by 0.108295
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.306
ELB improved by 0.0768011
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.25
ELB improved by 0.0555412
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.208
ELB improved by 0.0419377
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.175
ELB improved by 0.0330741
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.148
ELB improved by 0.0270006
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.126
ELB improved by 0.0226181
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.106
ELB improved by 0.019323
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.09
ELB improved by 0.0167688
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.075
ELB improved by 0.0147433
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.062
ELB improved by 0.0131079
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.05
ELB improved by 0.0117679
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.039
ELB improved by 0.0106559
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.03
ELB improved by 0.00972262
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-893.72
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-571.001
ELB improved by 322.719
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-509.496
ELB improved by 61.5048
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.532
ELB improved by 37.9643
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.882
ELB improved by 14.6493
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.082
ELB improved by 5.80082
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.251
ELB improved by 3.83039
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.921
ELB improved by 3.32982
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.591
ELB improved by 3.33042
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.027
ELB improved by 3.56387
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.105
ELB improved by 3.92217
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.805
ELB improved by 4.30043
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.299
ELB improved by 4.50549
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.995
ELB improved by 4.3038
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.359
ELB improved by 3.63574
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.625
ELB improved by 2.73498
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.699
ELB improved by 1.92548
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.347
ELB improved by 1.35162
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.368
ELB improved by 0.979855
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.628
ELB improved by 0.739179
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.045
ELB improved by 0.583119
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.561
ELB improved by 0.484425
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.137
ELB improved by 0.423895
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.749
ELB improved by 0.387843
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.384
ELB improved by 0.364958
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.043
ELB improved by 0.341318
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.74
ELB improved by 0.302557
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.493
ELB improved by 0.247294
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.302
ELB improved by 0.190723
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.156
ELB improved by 0.146561
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.039
ELB improved by 0.116512
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.943
ELB improved by 0.0963167
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.861
ELB improved by 0.081963
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.79
ELB improved by 0.0710579
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.727
ELB improved by 0.062343
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.672
ELB improved by 0.0551496
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.623
ELB improved by 0.0490926
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.579
ELB improved by 0.0439271
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.54
ELB improved by 0.0394831
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.504
ELB improved by 0.0356343
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.472
ELB improved by 0.0322835
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.443
ELB improved by 0.0293533
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.416
ELB improved by 0.0267809
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.391
ELB improved by 0.0245151
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.369
ELB improved by 0.0225133
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.348
ELB improved by 0.0207399
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.329
ELB improved by 0.019165
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.311
ELB improved by 0.0177635
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.295
ELB improved by 0.0165139
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.279
ELB improved by 0.0153978
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.265
ELB improved by 0.0143995
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.251
ELB improved by 0.0135055
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.239
ELB improved by 0.0127042
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.227
ELB improved by 0.0119853
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.215
ELB improved by 0.0113402
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.204
ELB improved by 0.0107611
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.194
ELB improved by 0.0102413
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.184
ELB improved by 0.00977507
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
3.173 0.263 4.870
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.035 | 0.016 | 0.052 | |
| getPIPs | 0.031 | 0.014 | 0.055 | |
| graper | 0.050 | 0.020 | 0.071 | |
| makeExampleData | 0.006 | 0.001 | 0.006 | |
| makeExampleDataWithUnequalGroups | 0.029 | 0.003 | 0.045 | |
| plotELBO | 0.357 | 0.021 | 0.453 | |
| plotGroupPenalties | 1.337 | 0.048 | 1.582 | |
| plotPosterior | 0.715 | 0.023 | 0.925 | |
| predict.graper | 0.523 | 0.093 | 0.728 | |
| print.graper | 0.030 | 0.011 | 0.042 | |