Britta Velten
| Snapshot Date: 2026-04-12 13:40 -0400 (Sun, 12 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 2026-04-13 11:36 -0400 (Mon, 13 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) | 4632 |
| 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: 2026-04-12 20:03:54 -0400 (Sun, 12 Apr 2026) |
| EndedAt: 2026-04-12 20:04:25 -0400 (Sun, 12 Apr 2026) |
| EllapsedTime: 31.4 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: 2026-04-13 00:03:54 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=-901.048
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-573.925
ELB improved by 327.123
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-517.71
ELB improved by 56.2157
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-486.585
ELB improved by 31.1245
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.179
ELB improved by 13.4062
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.059
ELB improved by 8.11958
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.352
ELB improved by 7.70754
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.164
ELB improved by 8.18806
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.948
ELB improved by 8.21587
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.58
ELB improved by 7.36742
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.465
ELB improved by 6.11575
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.489
ELB improved by 4.97561
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.423
ELB improved by 4.06622
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.339
ELB improved by 3.08405
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.214
ELB improved by 2.12535
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.716
ELB improved by 1.49733
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.565
ELB improved by 1.15168
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.609
ELB improved by 0.955263
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.829
ELB improved by 0.780339
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.221
ELB improved by 0.608088
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.735
ELB improved by 0.48551
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.323
ELB improved by 0.412269
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.956
ELB improved by 0.367098
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.62
ELB improved by 0.335975
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.308
ELB improved by 0.312135
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.015
ELB improved by 0.29234
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.741
ELB improved by 0.274922
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.482
ELB improved by 0.258985
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.238
ELB improved by 0.244063
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.008
ELB improved by 0.229952
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.791
ELB improved by 0.216601
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.587
ELB improved by 0.204043
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.395
ELB improved by 0.192347
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.213
ELB improved by 0.181583
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.041
ELB improved by 0.171809
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.878
ELB improved by 0.163062
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.723
ELB improved by 0.155362
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.574
ELB improved by 0.148718
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.431
ELB improved by 0.143131
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.292
ELB improved by 0.138608
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.157
ELB improved by 0.135168
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.024
ELB improved by 0.132853
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.893
ELB improved by 0.131742
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.761
ELB improved by 0.131966
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.627
ELB improved by 0.13374
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.489
ELB improved by 0.137407
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.346
ELB improved by 0.143524
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.193
ELB improved by 0.15303
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.025
ELB improved by 0.167576
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.835
ELB improved by 0.190187
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.609
ELB improved by 0.226343
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.324
ELB improved by 0.284369
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.956
ELB improved by 0.368284
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.503
ELB improved by 0.453056
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.018
ELB improved by 0.485118
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.56
ELB improved by 0.457838
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.152
ELB improved by 0.407763
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.8
ELB improved by 0.35263
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.504
ELB improved by 0.295712
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.264
ELB improved by 0.239958
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.075
ELB improved by 0.18931
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.928
ELB improved by 0.146743
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.815
ELB improved by 0.113345
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.726
ELB improved by 0.0886532
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.655
ELB improved by 0.0713937
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.595
ELB improved by 0.0600418
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.541
ELB improved by 0.0530678
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.492
ELB improved by 0.0489895
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.446
ELB improved by 0.0464216
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.402
ELB improved by 0.044251
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.36
ELB improved by 0.0418919
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.32
ELB improved by 0.0394265
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.283
ELB improved by 0.0375187
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.246
ELB improved by 0.0372774
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.205
ELB improved by 0.0404677
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.155
ELB improved by 0.0506505
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.078
ELB improved by 0.0764853
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.939
ELB improved by 0.138768
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.674
ELB improved by 0.265724
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.268
ELB improved by 0.405303
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.791
ELB improved by 0.477581
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.154
ELB improved by 0.636311
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.466
ELB improved by 0.688692
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.03
ELB improved by 0.435329
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.827
ELB improved by 0.203827
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.734
ELB improved by 0.0921294
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.69
ELB improved by 0.0443975
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.666
ELB improved by 0.0237198
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.652
ELB improved by 0.0141556
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.643
ELB improved by 0.00933393
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-862.357
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-576.269
ELB improved by 286.088
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-517.927
ELB improved by 58.3422
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-475.267
ELB improved by 42.6597
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.331
ELB improved by 19.9365
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.356
ELB improved by 7.97465
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.035
ELB improved by 5.32145
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.806
ELB improved by 5.22913
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.968
ELB improved by 5.83726
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.156
ELB improved by 6.81276
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.462
ELB improved by 7.6939
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.786
ELB improved by 7.67558
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.362
ELB improved by 6.42401
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.706
ELB improved by 4.65643
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.579
ELB improved by 3.12615
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.473
ELB improved by 2.10598
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.001
ELB improved by 1.47218
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.999
ELB improved by 1.00275
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.321
ELB improved by 0.677507
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.828
ELB improved by 0.493067
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.434
ELB improved by 0.393545
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.097
ELB improved by 0.337171
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.794
ELB improved by 0.302843
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.514
ELB improved by 0.280283
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.25
ELB improved by 0.264207
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.998
ELB improved by 0.251724
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.757
ELB improved by 0.241201
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.525
ELB improved by 0.231721
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.302
ELB improved by 0.222811
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.088
ELB improved by 0.214268
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.882
ELB improved by 0.206056
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.684
ELB improved by 0.198226
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.493
ELB improved by 0.190866
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.309
ELB improved by 0.18407
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.131
ELB improved by 0.177919
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.959
ELB improved by 0.172476
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.791
ELB improved by 0.167787
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.627
ELB improved by 0.163884
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.466
ELB improved by 0.160792
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.308
ELB improved by 0.158537
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.15
ELB improved by 0.157153
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.994
ELB improved by 0.156681
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.837
ELB improved by 0.157169
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.678
ELB improved by 0.158641
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.517
ELB improved by 0.161066
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.353
ELB improved by 0.164279
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.185
ELB improved by 0.167903
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.013
ELB improved by 0.171302
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.84
ELB improved by 0.173627
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.666
ELB improved by 0.17399
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.494
ELB improved by 0.171698
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.328
ELB improved by 0.166439
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.169
ELB improved by 0.158322
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.022
ELB improved by 0.147793
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.886
ELB improved by 0.135503
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.764
ELB improved by 0.122186
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.655
ELB improved by 0.108556
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.56
ELB improved by 0.095236
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.477
ELB improved by 0.0827136
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.406
ELB improved by 0.0713142
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.345
ELB improved by 0.0612056
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.292
ELB improved by 0.0524212
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.248
ELB improved by 0.0448963
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.209
ELB improved by 0.0385079
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.176
ELB improved by 0.0331082
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.147
ELB improved by 0.0285497
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.123
ELB improved by 0.0246993
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.101
ELB improved by 0.0214437
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.083
ELB improved by 0.0186893
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.066
ELB improved by 0.016358
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.052
ELB improved by 0.014384
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.039
ELB improved by 0.0127099
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.028
ELB improved by 0.0112853
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.018
ELB improved by 0.0100662
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.009
ELB improved by 0.00901476
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-909.462
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-588.302
ELB improved by 321.16
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-527.648
ELB improved by 60.6532
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-489.189
ELB improved by 38.459
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.318
ELB improved by 16.8711
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.432
ELB improved by 7.88582
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.298
ELB improved by 5.13463
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.846
ELB improved by 4.4515
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.299
ELB improved by 4.54731
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.276
ELB improved by 5.02339
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.659
ELB improved by 5.61655
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.731
ELB improved by 5.92829
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.16
ELB improved by 5.57084
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.542
ELB improved by 4.61823
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.998
ELB improved by 3.54327
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.393
ELB improved by 2.60551
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.529
ELB improved by 1.86379
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.179
ELB improved by 1.35042
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.153
ELB improved by 1.02567
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.328
ELB improved by 0.824791
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.625
ELB improved by 0.703034
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.989
ELB improved by 0.636026
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.378
ELB improved by 0.611113
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.755
ELB improved by 0.623446
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.082
ELB improved by 0.672319
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.329
ELB improved by 0.753497
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.479
ELB improved by 0.849332
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.55
ELB improved by 0.929443
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.559
ELB improved by 0.99123
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.484
ELB improved by 1.07514
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.28
ELB improved by 1.20409
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.904
ELB improved by 1.37568
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.325
ELB improved by 1.57861
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.541
ELB improved by 1.78455
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.612
ELB improved by 1.9285
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.688
ELB improved by 1.92407
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.955
ELB improved by 1.73344
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.554
ELB improved by 1.40073
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.53
ELB improved by 1.02355
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.833
ELB improved by 0.697109
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.371
ELB improved by 0.462406
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.06
ELB improved by 0.310605
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.844
ELB improved by 0.216503
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.686
ELB improved by 0.158181
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.564
ELB improved by 0.121162
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.468
ELB improved by 0.0968408
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.387
ELB improved by 0.0802678
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.319
ELB improved by 0.0685889
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.259
ELB improved by 0.0601154
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.205
ELB improved by 0.0538049
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.156
ELB improved by 0.0489767
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.111
ELB improved by 0.0451619
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.069
ELB improved by 0.0420319
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.029
ELB improved by 0.039374
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.992
ELB improved by 0.0370913
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.957
ELB improved by 0.0352061
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.923
ELB improved by 0.0338528
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.89
ELB improved by 0.0332482
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.856
ELB improved by 0.0336341
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.821
ELB improved by 0.0351654
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.783
ELB improved by 0.0376962
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.743
ELB improved by 0.0404669
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.701
ELB improved by 0.041959
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.66
ELB improved by 0.040485
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.625
ELB improved by 0.0355313
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.596
ELB improved by 0.0284341
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.575
ELB improved by 0.0213144
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.56
ELB improved by 0.0155875
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.548
ELB improved by 0.0115816
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.539
ELB improved by 0.00899919
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-876.621
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-548.327
ELB improved by 328.294
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-498.205
ELB improved by 50.1215
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.161
ELB improved by 25.0449
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.105
ELB improved by 11.0553
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.159
ELB improved by 5.94611
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.664
ELB improved by 4.49487
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.514
ELB improved by 4.14985
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.442
ELB improved by 4.0727
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.461
ELB improved by 3.98049
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.718
ELB improved by 3.74361
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.395
ELB improved by 3.32275
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.633
ELB improved by 2.76159
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.463
ELB improved by 2.16994
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.806
ELB improved by 1.6577
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.54
ELB improved by 1.26602
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.533
ELB improved by 1.00663
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.667
ELB improved by 0.866017
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.853
ELB improved by 0.813845
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.028
ELB improved by 0.825061
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.15
ELB improved by 0.878176
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.205
ELB improved by 0.944733
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.21
ELB improved by 0.994817
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.189
ELB improved by 1.02135
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.153
ELB improved by 1.03639
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.11
ELB improved by 1.04298
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.076
ELB improved by 1.03376
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.07
ELB improved by 1.00567
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.107
ELB improved by 0.962879
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.197
ELB improved by 0.91062
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.345
ELB improved by 0.851938
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.557
ELB improved by 0.788115
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.837
ELB improved by 0.719594
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.19
ELB improved by 0.646922
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.619
ELB improved by 0.57151
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.123
ELB improved by 0.495721
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.7
ELB improved by 0.422393
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.346
ELB improved by 0.354395
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.052
ELB improved by 0.294269
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.808
ELB improved by 0.243809
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.604
ELB improved by 0.203714
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.431
ELB improved by 0.17356
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.279
ELB improved by 0.152064
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.141
ELB improved by 0.137452
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.013
ELB improved by 0.127775
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.892
ELB improved by 0.121188
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.776
ELB improved by 0.116241
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.664
ELB improved by 0.112125
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.555
ELB improved by 0.108709
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.449
ELB improved by 0.106272
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.344
ELB improved by 0.10513
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.238
ELB improved by 0.105426
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.131
ELB improved by 0.10721
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.02
ELB improved by 0.110878
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.902
ELB improved by 0.118079
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.769
ELB improved by 0.132809
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.609
ELB improved by 0.160156
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.414
ELB improved by 0.194852
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.211
ELB improved by 0.203611
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.049
ELB improved by 0.161376
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.947
ELB improved by 0.102488
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.886
ELB improved by 0.0611001
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.847
ELB improved by 0.038461
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.821
ELB improved by 0.0267216
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.8
ELB improved by 0.0204097
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.783
ELB improved by 0.016742
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.769
ELB improved by 0.0144088
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.756
ELB improved by 0.0127959
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.745
ELB improved by 0.0116054
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.734
ELB improved by 0.0106846
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.724
ELB improved by 0.00994994
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
1.074 0.081 1.157
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.029 | 0.006 | 0.035 | |
| getPIPs | 0.027 | 0.006 | 0.034 | |
| graper | 0.047 | 0.009 | 0.057 | |
| makeExampleData | 0.006 | 0.000 | 0.007 | |
| makeExampleDataWithUnequalGroups | 0.007 | 0.001 | 0.008 | |
| plotELBO | 0.125 | 0.008 | 0.135 | |
| plotGroupPenalties | 0.336 | 0.007 | 0.344 | |
| plotPosterior | 0.248 | 0.005 | 0.252 | |
| predict.graper | 1.048 | 0.040 | 1.100 | |
| print.graper | 0.027 | 0.004 | 0.032 | |