Britta Velten
| Snapshot Date: 2026-04-10 13:40 -0400 (Fri, 10 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: 95474d7 |
| git_last_commit_date: 2025-10-29 10:49:21 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-11 11:37 -0400 (Sat, 11 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4919 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4631 |
| 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 936/2390 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.27.0 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| See other builds for graper in R Universe. | ||||||||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: graper |
| Version: 1.27.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.27.0.tar.gz |
| StartedAt: 2026-04-10 20:28:44 -0400 (Fri, 10 Apr 2026) |
| EndedAt: 2026-04-10 20:29:14 -0400 (Fri, 10 Apr 2026) |
| EllapsedTime: 30.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck’
* using R version 4.6.0 alpha (2026-04-08 r89818)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-11 00:28:44 UTC
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.27.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) predict.graper.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:23-24: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.27.0’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’ using SDK: ‘MacOSX26.2.sdk’ clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o graper.so RcppExports.o fit_graper.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.6/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 4.6.0 alpha (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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=-877.794
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-579.224
ELB improved by 298.57
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-516.392
ELB improved by 62.8316
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-475.135
ELB improved by 41.2571
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.327
ELB improved by 19.8084
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.56
ELB improved by 8.76629
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.904
ELB improved by 5.65617
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.818
ELB improved by 5.08666
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.366
ELB improved by 5.45187
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.163
ELB improved by 6.20297
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.427
ELB improved by 6.73528
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.125
ELB improved by 6.30226
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.305
ELB improved by 4.82024
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.147
ELB improved by 3.15764
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.163
ELB improved by 1.98468
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.845
ELB improved by 1.31816
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.886
ELB improved by 0.958543
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.128
ELB improved by 0.75772
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.49
ELB improved by 0.638307
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.927
ELB improved by 0.562809
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.414
ELB improved by 0.512894
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.935
ELB improved by 0.47943
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.477
ELB improved by 0.457871
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.031
ELB improved by 0.445546
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.592
ELB improved by 0.439014
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.16
ELB improved by 0.431931
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.743
ELB improved by 0.417558
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.347
ELB improved by 0.395641
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.975
ELB improved by 0.372167
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.623
ELB improved by 0.352089
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.286
ELB improved by 0.336987
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.959
ELB improved by 0.327057
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.636
ELB improved by 0.32253
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.312
ELB improved by 0.324049
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.98
ELB improved by 0.332706
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.63
ELB improved by 0.349681
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.256
ELB improved by 0.374473
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.855
ELB improved by 0.400025
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.447
ELB improved by 0.408426
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.063
ELB improved by 0.383784
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.728
ELB improved by 0.335024
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.444
ELB improved by 0.283785
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.204
ELB improved by 0.240421
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.998
ELB improved by 0.205717
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.82
ELB improved by 0.178756
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.66
ELB improved by 0.159195
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.513
ELB improved by 0.147231
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.37
ELB improved by 0.143156
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.224
ELB improved by 0.14634
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.07
ELB improved by 0.153408
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.913
ELB improved by 0.157433
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.761
ELB improved by 0.151758
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.625
ELB improved by 0.136211
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.508
ELB improved by 0.116522
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.41
ELB improved by 0.0979857
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.328
ELB improved by 0.082594
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.257
ELB improved by 0.0702638
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.197
ELB improved by 0.0603342
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.145
ELB improved by 0.0521931
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.1
ELB improved by 0.0454017
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.06
ELB improved by 0.0396625
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.025
ELB improved by 0.0347696
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.995
ELB improved by 0.0305728
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.968
ELB improved by 0.0269572
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.944
ELB improved by 0.0238314
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.923
ELB improved by 0.0211209
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.904
ELB improved by 0.0187641
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.887
ELB improved by 0.0167097
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.872
ELB improved by 0.0149146
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.859
ELB improved by 0.0133424
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.847
ELB improved by 0.0119622
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.836
ELB improved by 0.0107481
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.827
ELB improved by 0.00967779
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-862.172
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-598.869
ELB improved by 263.303
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-540.421
ELB improved by 58.448
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-489.94
ELB improved by 50.4814
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.677
ELB improved by 28.2628
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.13
ELB improved by 11.5472
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.489
ELB improved by 5.64077
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.434
ELB improved by 4.05494
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.684
ELB improved by 3.74961
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.814
ELB improved by 3.8708
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.594
ELB improved by 4.21995
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.854
ELB improved by 4.73962
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.575
ELB improved by 5.2786
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.118
ELB improved by 5.45772
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.222
ELB improved by 4.89525
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.494
ELB improved by 3.72867
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.954
ELB improved by 2.54018
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.267
ELB improved by 1.68626
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.124
ELB improved by 1.14378
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.314
ELB improved by 0.809991
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.701
ELB improved by 0.612853
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.21
ELB improved by 0.490473
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.809
ELB improved by 0.401167
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.478
ELB improved by 0.330573
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.201
ELB improved by 0.277275
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.962
ELB improved by 0.239315
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.749
ELB improved by 0.212697
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.555
ELB improved by 0.193705
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.376
ELB improved by 0.179775
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.206
ELB improved by 0.169328
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.045
ELB improved by 0.161411
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.89
ELB improved by 0.155443
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.738
ELB improved by 0.151071
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.59
ELB improved by 0.148088
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.444
ELB improved by 0.146396
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.298
ELB improved by 0.14599
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.151
ELB improved by 0.146948
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.002
ELB improved by 0.149457
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.848
ELB improved by 0.153834
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.687
ELB improved by 0.16058
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.517
ELB improved by 0.170426
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.332
ELB improved by 0.184305
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.129
ELB improved by 0.203085
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.902
ELB improved by 0.226903
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.648
ELB improved by 0.254545
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.364
ELB improved by 0.284325
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.047
ELB improved by 0.316664
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.692
ELB improved by 0.355044
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.288
ELB improved by 0.403957
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.821
ELB improved by 0.466445
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.28
ELB improved by 0.541613
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.657
ELB improved by 0.622611
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.958
ELB improved by 0.699612
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.192
ELB improved by 0.766099
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.373
ELB improved by 0.818666
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.523
ELB improved by 0.850339
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.675
ELB improved by 0.847891
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.875
ELB improved by 0.799888
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.166
ELB improved by 0.709068
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.572
ELB improved by 0.593568
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.097
ELB improved by 0.475481
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.726
ELB improved by 0.370292
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.442
ELB improved by 0.284359
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.224
ELB improved by 0.217611
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.057
ELB improved by 0.167066
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.928
ELB improved by 0.129138
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.827
ELB improved by 0.100668
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.748
ELB improved by 0.079181
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.685
ELB improved by 0.0628379
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.635
ELB improved by 0.0503016
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.595
ELB improved by 0.0406038
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.562
ELB improved by 0.033041
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.534
ELB improved by 0.0270987
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.512
ELB improved by 0.022397
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.493
ELB improved by 0.0186529
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.478
ELB improved by 0.0156538
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.464
ELB improved by 0.0132382
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.453
ELB improved by 0.0112826
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.444
ELB improved by 0.00969167
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-869.028
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-592.987
ELB improved by 276.041
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-535.039
ELB improved by 57.9477
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-491.962
ELB improved by 43.0771
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.406
ELB improved by 24.5558
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.7
ELB improved by 12.7064
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.997
ELB improved by 7.70234
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.35
ELB improved by 6.64754
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.341
ELB improved by 7.00913
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.65
ELB improved by 7.69056
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.844
ELB improved by 7.80606
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.066
ELB improved by 6.77819
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.042
ELB improved by 5.02366
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.731
ELB improved by 3.31112
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.66
ELB improved by 2.07164
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.348
ELB improved by 1.31188
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.473
ELB improved by 0.874229
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.85
ELB improved by 0.623528
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.374
ELB improved by 0.476081
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.988
ELB improved by 0.385421
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.662
ELB improved by 0.326768
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.375
ELB improved by 0.286888
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.116
ELB improved by 0.25849
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.879
ELB improved by 0.237358
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.658
ELB improved by 0.220925
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.45
ELB improved by 0.207553
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.254
ELB improved by 0.196168
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.068
ELB improved by 0.186067
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.891
ELB improved by 0.176799
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.723
ELB improved by 0.168105
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.563
ELB improved by 0.159866
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.411
ELB improved by 0.15207
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.267
ELB improved by 0.144779
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.128
ELB improved by 0.138112
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.996
ELB improved by 0.132223
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.869
ELB improved by 0.127302
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.745
ELB improved by 0.123578
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.624
ELB improved by 0.121358
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.503
ELB improved by 0.121096
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.379
ELB improved by 0.123543
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.249
ELB improved by 0.130081
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.106
ELB improved by 0.143451
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.937
ELB improved by 0.169237
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.719
ELB improved by 0.217716
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.42
ELB improved by 0.2988
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.029
ELB improved by 0.391082
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.592
ELB improved by 0.436642
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.147
ELB improved by 0.445757
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.676
ELB improved by 0.470986
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.152
ELB improved by 0.523839
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.553
ELB improved by 0.598237
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.868
ELB improved by 0.685432
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.097
ELB improved by 0.770952
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.264
ELB improved by 0.833197
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.415
ELB improved by 0.849055
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.61
ELB improved by 0.804572
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.906
ELB improved by 0.704074
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.336
ELB improved by 0.570412
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.902
ELB improved by 0.433475
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.587
ELB improved by 0.315276
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.363
ELB improved by 0.224018
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.205
ELB improved by 0.158002
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.093
ELB improved by 0.111791
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.013
ELB improved by 0.0799103
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.955
ELB improved by 0.05804
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.912
ELB improved by 0.0430454
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.88
ELB improved by 0.0327207
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.854
ELB improved by 0.0255411
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.834
ELB improved by 0.0204698
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.817
ELB improved by 0.0168139
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.803
ELB improved by 0.0141149
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.79
ELB improved by 0.012072
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.78
ELB improved by 0.0104871
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.771
ELB improved by 0.00922916
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-855.844
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-599.934
ELB improved by 255.91
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-541.698
ELB improved by 58.2364
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-493.1
ELB improved by 48.598
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.77
ELB improved by 27.3293
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.03
ELB improved by 10.7398
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.823
ELB improved by 5.20785
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.764
ELB improved by 4.05823
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.624
ELB improved by 4.13995
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.917
ELB improved by 4.70753
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.452
ELB improved by 5.46505
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.371
ELB improved by 6.08086
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.355
ELB improved by 6.01554
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.588
ELB improved by 4.76762
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.527
ELB improved by 3.06118
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.626
ELB improved by 1.90053
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.312
ELB improved by 1.31438
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.275
ELB improved by 1.03675
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.366
ELB improved by 0.908624
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.511
ELB improved by 0.855125
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.674
ELB improved by 0.837677
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.839
ELB improved by 0.834847
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.004
ELB improved by 0.834571
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.173
ELB improved by 0.830796
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.352
ELB improved by 0.821721
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.543
ELB improved by 0.808295
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.75
ELB improved by 0.792812
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.973
ELB improved by 0.777864
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.207
ELB improved by 0.765764
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.449
ELB improved by 0.758317
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.692
ELB improved by 0.756909
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.928
ELB improved by 0.763417
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.145
ELB improved by 0.783535
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.307
ELB improved by 0.837377
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.319
ELB improved by 0.988614
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.975
ELB improved by 1.34331
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.347
ELB improved by 1.62865
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.914
ELB improved by 1.4329
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.727
ELB improved by 1.18655
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.606
ELB improved by 1.12125
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.457
ELB improved by 1.14858
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.607
ELB improved by 0.850912
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.122
ELB improved by 0.48431
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.817
ELB improved by 0.304947
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.576
ELB improved by 0.241003
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.35
ELB improved by 0.226644
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.131
ELB improved by 0.219085
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.942
ELB improved by 0.188846
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.798
ELB improved by 0.143316
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.694
ELB improved by 0.10463
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.616
ELB improved by 0.0782121
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.555
ELB improved by 0.0604071
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.507
ELB improved by 0.0479191
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.468
ELB improved by 0.0388996
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.436
ELB improved by 0.0322557
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.409
ELB improved by 0.0272619
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.385
ELB improved by 0.02342
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.365
ELB improved by 0.020393
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.347
ELB improved by 0.0179563
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.331
ELB improved by 0.0159596
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.317
ELB improved by 0.0143004
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.304
ELB improved by 0.0129069
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.292
ELB improved by 0.0117271
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.281
ELB improved by 0.0107215
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.272
ELB improved by 0.00985996
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
1.049 0.078 1.126
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.029 | 0.005 | 0.034 | |
| getPIPs | 0.027 | 0.004 | 0.031 | |
| graper | 0.044 | 0.006 | 0.050 | |
| makeExampleData | 0.004 | 0.000 | 0.004 | |
| makeExampleDataWithUnequalGroups | 0.004 | 0.001 | 0.005 | |
| plotELBO | 0.127 | 0.006 | 0.133 | |
| plotGroupPenalties | 0.340 | 0.004 | 0.345 | |
| plotPosterior | 0.307 | 0.010 | 0.318 | |
| predict.graper | 1.015 | 0.027 | 1.046 | |
| print.graper | 0.029 | 0.006 | 0.035 | |