Britta Velten
| Snapshot Date: 2025-11-24 13:45 -0500 (Mon, 24 Nov 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 2025-11-27 12:04 -0500 (Thu, 27 Nov 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" | 4876 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4656 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4602 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 | NA | |||||||||
| 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: 2025-11-26 07:31:53 -0500 (Wed, 26 Nov 2025) |
| EndedAt: 2025-11-26 07:33:46 -0500 (Wed, 26 Nov 2025) |
| EllapsedTime: 113.7 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=-827.073
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-589.05
ELB improved by 238.023
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-526.587
ELB improved by 62.4631
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-477.328
ELB improved by 49.2588
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.117
ELB improved by 25.2117
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.028
ELB improved by 10.0885
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.269
ELB improved by 4.75943
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.297
ELB improved by 2.97174
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.871
ELB improved by 2.42551
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.59
ELB improved by 2.28165
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.31
ELB improved by 2.27938
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.992
ELB improved by 2.31845
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.65
ELB improved by 2.34163
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.346
ELB improved by 2.30416
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.165
ELB improved by 2.18157
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.18
ELB improved by 1.98492
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.43
ELB improved by 1.74916
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.918
ELB improved by 1.51254
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.62
ELB improved by 1.29782
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.508
ELB improved by 1.11249
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.527
ELB improved by 0.980321
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.618
ELB improved by 0.909605
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.735
ELB improved by 0.882618
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.856
ELB improved by 0.878721
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.974
ELB improved by 0.882491
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.093
ELB improved by 0.880584
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.231
ELB improved by 0.86215
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.405
ELB improved by 0.825801
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.628
ELB improved by 0.777765
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.905
ELB improved by 0.722258
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.245
ELB improved by 0.660403
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.651
ELB improved by 0.593891
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.125
ELB improved by 0.525892
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.665
ELB improved by 0.459867
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.267
ELB improved by 0.398435
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.924
ELB improved by 0.342966
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.63
ELB improved by 0.293774
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.379
ELB improved by 0.250557
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.167
ELB improved by 0.212792
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.987
ELB improved by 0.179945
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.835
ELB improved by 0.151553
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.708
ELB improved by 0.127251
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.601
ELB improved by 0.106751
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.511
ELB improved by 0.0897858
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.435
ELB improved by 0.076044
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.37
ELB improved by 0.0651473
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.314
ELB improved by 0.0566631
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.263
ELB improved by 0.0501368
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.218
ELB improved by 0.0451194
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.177
ELB improved by 0.0411851
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.139
ELB improved by 0.0379472
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.104
ELB improved by 0.0350789
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.072
ELB improved by 0.0323404
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.042
ELB improved by 0.0296007
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.015
ELB improved by 0.0268374
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.991
ELB improved by 0.0241082
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.97
ELB improved by 0.0215049
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.951
ELB improved by 0.0191102
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.934
ELB improved by 0.0169747
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.918
ELB improved by 0.0151132
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.905
ELB improved by 0.0135149
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.893
ELB improved by 0.012155
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.882
ELB improved by 0.0110041
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.872
ELB improved by 0.0100337
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.863
ELB improved by 0.00921855
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-890.663
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-618.118
ELB improved by 272.545
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-561.159
ELB improved by 56.9592
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-513.287
ELB improved by 47.872
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-485.241
ELB improved by 28.0462
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.53
ELB improved by 12.711
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.794
ELB improved by 7.73531
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.984
ELB improved by 6.81017
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.004
ELB improved by 6.97957
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.553
ELB improved by 7.45194
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.169
ELB improved by 7.38374
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.951
ELB improved by 6.21824
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.5
ELB improved by 4.45059
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.552
ELB improved by 2.94838
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.578
ELB improved by 1.97383
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.181
ELB improved by 1.39657
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.118
ELB improved by 1.063
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.242
ELB improved by 0.876313
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.453
ELB improved by 0.788656
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.662
ELB improved by 0.791204
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.763
ELB improved by 0.899377
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.683
ELB improved by 1.07969
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.502
ELB improved by 1.1809
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.341
ELB improved by 1.16122
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.2
ELB improved by 1.14106
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.049
ELB improved by 1.1508
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.88
ELB improved by 1.16926
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.694
ELB improved by 1.18589
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.495
ELB improved by 1.19924
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.287
ELB improved by 1.20717
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.084
ELB improved by 1.20293
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.908
ELB improved by 1.17644
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.789
ELB improved by 1.11882
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.762
ELB improved by 1.02723
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.855
ELB improved by 0.906814
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.086
ELB improved by 0.769056
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.457
ELB improved by 0.628664
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.958
ELB improved by 0.499501
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.568
ELB improved by 0.390199
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.265
ELB improved by 0.302976
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.028
ELB improved by 0.236931
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.836
ELB improved by 0.191419
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.67
ELB improved by 0.166112
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.511
ELB improved by 0.158943
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.348
ELB improved by 0.16356
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.179
ELB improved by 0.168504
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.018
ELB improved by 0.161706
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.88
ELB improved by 0.137921
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.776
ELB improved by 0.103204
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.706
ELB improved by 0.0701029
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.66
ELB improved by 0.0460824
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.629
ELB improved by 0.0308993
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.608
ELB improved by 0.0216707
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.592
ELB improved by 0.0160042
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.579
ELB improved by 0.0124234
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.569
ELB improved by 0.0100798
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.561
ELB improved by 0.00848795
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-889.803
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-574.93
ELB improved by 314.872
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-516.389
ELB improved by 58.5414
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-482.715
ELB improved by 33.674
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.626
ELB improved by 16.0891
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.197
ELB improved by 8.42821
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.546
ELB improved by 6.65154
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.036
ELB improved by 6.5098
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.582
ELB improved by 6.45389
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.766
ELB improved by 5.81584
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.2
ELB improved by 4.5659
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.989
ELB improved by 3.21101
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.818
ELB improved by 2.17135
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.324
ELB improved by 1.49432
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.26
ELB improved by 1.06348
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.477
ELB improved by 0.783177
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.875
ELB improved by 0.602372
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.387
ELB improved by 0.487622
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.971
ELB improved by 0.416298
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.594
ELB improved by 0.377104
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.229
ELB improved by 0.365129
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.858
ELB improved by 0.370509
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.49
ELB improved by 0.367954
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.153
ELB improved by 0.336976
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.861
ELB improved by 0.292305
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.604
ELB improved by 0.257304
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.367
ELB improved by 0.236828
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.141
ELB improved by 0.226138
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.92
ELB improved by 0.220679
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.702
ELB improved by 0.217822
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.486
ELB improved by 0.216177
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.271
ELB improved by 0.214949
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.057
ELB improved by 0.21362
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.845
ELB improved by 0.211816
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.636
ELB improved by 0.209297
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.43
ELB improved by 0.205967
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.228
ELB improved by 0.201899
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.031
ELB improved by 0.197308
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.839
ELB improved by 0.192494
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.651
ELB improved by 0.187774
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.467
ELB improved by 0.183419
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.288
ELB improved by 0.179638
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.111
ELB improved by 0.176566
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.937
ELB improved by 0.174279
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.764
ELB improved by 0.172793
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.592
ELB improved by 0.172076
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.42
ELB improved by 0.172046
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.247
ELB improved by 0.172565
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.074
ELB improved by 0.173431
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.9
ELB improved by 0.174371
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.725
ELB improved by 0.175035
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.55
ELB improved by 0.175009
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.376
ELB improved by 0.173836
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.205
ELB improved by 0.171066
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.038
ELB improved by 0.166325
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.879
ELB improved by 0.159388
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.729
ELB improved by 0.150246
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.59
ELB improved by 0.139129
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.463
ELB improved by 0.126491
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.35
ELB improved by 0.112939
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.251
ELB improved by 0.0991393
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.165
ELB improved by 0.0857145
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.092
ELB improved by 0.073169
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.03
ELB improved by 0.0618463
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.978
ELB improved by 0.0519247
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.935
ELB improved by 0.0434407
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.899
ELB improved by 0.0363266
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.868
ELB improved by 0.0304501
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.842
ELB improved by 0.0256491
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.821
ELB improved by 0.0217558
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.802
ELB improved by 0.0186132
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.786
ELB improved by 0.016083
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.772
ELB improved by 0.0140494
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.76
ELB improved by 0.0124184
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.748
ELB improved by 0.0111168
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.738
ELB improved by 0.0100897
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.729
ELB improved by 0.00929933
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-876.06
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-564.363
ELB improved by 311.697
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-506.885
ELB improved by 57.4785
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-474.496
ELB improved by 32.3888
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.69
ELB improved by 13.8057
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.294
ELB improved by 6.39621
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.007
ELB improved by 4.28737
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.391
ELB improved by 3.61517
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.919
ELB improved by 3.47276
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.406
ELB improved by 3.51303
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.84
ELB improved by 3.56532
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.33
ELB improved by 3.51007
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.1
ELB improved by 3.23058
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.431
ELB improved by 2.66882
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.49
ELB improved by 1.94057
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.213
ELB improved by 1.27705
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.403
ELB improved by 0.810327
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.876
ELB improved by 0.52687
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.512
ELB improved by 0.363915
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.242
ELB improved by 0.269989
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.028
ELB improved by 0.213839
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.85
ELB improved by 0.178333
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.695
ELB improved by 0.154399
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.558
ELB improved by 0.13726
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.434
ELB improved by 0.124369
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.32
ELB improved by 0.114318
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.213
ELB improved by 0.106292
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.113
ELB improved by 0.0997804
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.019
ELB improved by 0.0944469
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.929
ELB improved by 0.0900516
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.843
ELB improved by 0.0864165
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.759
ELB improved by 0.0834038
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.678
ELB improved by 0.0809033
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.599
ELB improved by 0.078824
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.522
ELB improved by 0.0770887
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.447
ELB improved by 0.0756296
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.372
ELB improved by 0.074386
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.299
ELB improved by 0.0733032
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.227
ELB improved by 0.0723318
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.155
ELB improved by 0.0714297
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.085
ELB improved by 0.0705632
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.015
ELB improved by 0.0697086
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.946
ELB improved by 0.0688527
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.878
ELB improved by 0.0679916
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.811
ELB improved by 0.0671287
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.745
ELB improved by 0.0662725
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.679
ELB improved by 0.0654344
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.615
ELB improved by 0.0646273
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.551
ELB improved by 0.0638656
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.488
ELB improved by 0.0631648
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.425
ELB improved by 0.0625419
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.363
ELB improved by 0.0620154
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.301
ELB improved by 0.0616052
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.24
ELB improved by 0.0613329
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.179
ELB improved by 0.0612214
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.118
ELB improved by 0.0612954
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.056
ELB improved by 0.0615815
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.994
ELB improved by 0.062109
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.931
ELB improved by 0.0629102
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.867
ELB improved by 0.0640218
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.802
ELB improved by 0.0654852
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.734
ELB improved by 0.0673485
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.664
ELB improved by 0.0696666
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.592
ELB improved by 0.0725027
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.516
ELB improved by 0.0759282
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.436
ELB improved by 0.0800218
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.351
ELB improved by 0.0848671
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.261
ELB improved by 0.0905463
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.164
ELB improved by 0.09713
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.059
ELB improved by 0.10466
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.946
ELB improved by 0.113127
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.823
ELB improved by 0.122434
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.691
ELB improved by 0.132365
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.548
ELB improved by 0.142548
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.396
ELB improved by 0.152438
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.235
ELB improved by 0.161327
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.066
ELB improved by 0.168405
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.893
ELB improved by 0.172865
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.719
ELB improved by 0.174049
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.548
ELB improved by 0.171607
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.382
ELB improved by 0.165621
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.225
ELB improved by 0.156629
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.08
ELB improved by 0.145546
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.946
ELB improved by 0.133484
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.825
ELB improved by 0.121541
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.714
ELB improved by 0.110634
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.613
ELB improved by 0.101423
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.518
ELB improved by 0.0943346
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.429
ELB improved by 0.0896654
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.341
ELB improved by 0.0876824
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.253
ELB improved by 0.0884836
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.161
ELB improved by 0.0912686
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.068
ELB improved by 0.0931735
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.979
ELB improved by 0.0895962
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.901
ELB improved by 0.0779962
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.839
ELB improved by 0.0611757
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.795
ELB improved by 0.0444769
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.764
ELB improved by 0.0312025
iteration 99
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.742
ELB improved by 0.0218644
iteration 100
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.726
ELB improved by 0.0156577
iteration 101
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.715
ELB improved by 0.0115934
iteration 102
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.706
ELB improved by 0.00890403
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
3.055 0.262 5.285
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.036 | 0.016 | 0.071 | |
| getPIPs | 0.031 | 0.014 | 0.064 | |
| graper | 0.050 | 0.022 | 0.112 | |
| makeExampleData | 0.006 | 0.001 | 0.016 | |
| makeExampleDataWithUnequalGroups | 0.025 | 0.003 | 0.029 | |
| plotELBO | 0.355 | 0.020 | 0.565 | |
| plotGroupPenalties | 1.386 | 0.052 | 2.169 | |
| plotPosterior | 0.714 | 0.023 | 1.083 | |
| predict.graper | 0.540 | 0.103 | 1.009 | |
| print.graper | 0.030 | 0.012 | 0.049 | |