Britta Velten
| Snapshot Date: 2025-09-26 13:45 -0400 (Fri, 26 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: 82b0592 |
| git_last_commit_date: 2025-06-24 03:15:40 -0400 (Tue, 24 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-27 12:04 -0400 (Sat, 27 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4832 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4620 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4565 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
| 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 913/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.25.2 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: graper |
| Version: 1.25.2 |
| 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_1.25.2.tar.gz |
| StartedAt: 2025-09-26 21:37:07 -0400 (Fri, 26 Sep 2025) |
| EndedAt: 2025-09-26 21:38:25 -0400 (Fri, 26 Sep 2025) |
| EllapsedTime: 78.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.25.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.25.2’
* 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 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) predict.graper.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:23-24: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.25.2’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.1.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fit_graper.cpp -o fit_graper.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-graper/00new/graper/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (graper)
graper.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(graper)
>
> test_check("graper")
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-873.657
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-572.759
ELB improved by 300.898
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-513.104
ELB improved by 59.6552
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.185
ELB improved by 39.9185
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.088
ELB improved by 18.0975
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.781
ELB improved by 8.30644
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.719
ELB improved by 6.0622
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.676
ELB improved by 6.04295
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.003
ELB improved by 6.67345
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.626
ELB improved by 7.3768
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.278
ELB improved by 7.34846
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.23
ELB improved by 6.04764
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.103
ELB improved by 4.12653
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.502
ELB improved by 2.60177
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.846
ELB improved by 1.65604
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.782
ELB improved by 1.06326
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.079
ELB improved by 0.703343
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.582
ELB improved by 0.497176
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.205
ELB improved by 0.377214
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.903
ELB improved by 0.301233
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.656
ELB improved by 0.247614
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.449
ELB improved by 0.207064
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.272
ELB improved by 0.176241
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.119
ELB improved by 0.153429
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.982
ELB improved by 0.136849
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.857
ELB improved by 0.124766
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.742
ELB improved by 0.115876
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.632
ELB improved by 0.109367
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.527
ELB improved by 0.104807
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.425
ELB improved by 0.102005
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.324
ELB improved by 0.100924
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.223
ELB improved by 0.101619
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.119
ELB improved by 0.104213
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.01
ELB improved by 0.108921
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.894
ELB improved by 0.116164
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.767
ELB improved by 0.1268
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.624
ELB improved by 0.142419
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.459
ELB improved by 0.165583
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.258
ELB improved by 0.200237
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.005
ELB improved by 0.253786
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.662
ELB improved by 0.342898
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.171
ELB improved by 0.490766
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.488
ELB improved by 0.683166
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.599
ELB improved by 0.889296
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.421
ELB improved by 1.17754
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.912
ELB improved by 1.50902
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.218
ELB improved by 1.69357
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.43
ELB improved by 1.788
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.593
ELB improved by 1.8378
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.796
ELB improved by 1.79682
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.193
ELB improved by 1.60233
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.979
ELB improved by 1.21456
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.194
ELB improved by 0.784509
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.724
ELB improved by 0.470832
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.442
ELB improved by 0.28134
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.269
ELB improved by 0.173486
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.157
ELB improved by 0.112158
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.08
ELB improved by 0.0763743
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.026
ELB improved by 0.0547059
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.984
ELB improved by 0.0410333
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.952
ELB improved by 0.0320358
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.927
ELB improved by 0.0258633
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.905
ELB improved by 0.0214544
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.887
ELB improved by 0.0181834
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.871
ELB improved by 0.0156716
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.858
ELB improved by 0.0136849
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.846
ELB improved by 0.0120746
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.835
ELB improved by 0.0107436
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.825
ELB improved by 0.00962657
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-846.457
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-565.659
ELB improved by 280.798
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-505.81
ELB improved by 59.8495
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.985
ELB improved by 38.8245
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.929
ELB improved by 16.0564
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.558
ELB improved by 6.3705
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.754
ELB improved by 3.80483
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.48
ELB improved by 3.2736
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.292
ELB improved by 3.18789
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.028
ELB improved by 3.26443
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.6
ELB improved by 3.42775
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.968
ELB improved by 3.63193
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.181
ELB improved by 3.78654
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.464
ELB improved by 3.71711
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.2
ELB improved by 3.2645
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.707
ELB improved by 2.49319
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.022
ELB improved by 1.68488
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.95
ELB improved by 1.07139
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.261
ELB improved by 0.68929
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.791
ELB improved by 0.470384
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.445
ELB improved by 0.345346
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.174
ELB improved by 0.271201
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.949
ELB improved by 0.225061
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.754
ELB improved by 0.19507
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.579
ELB improved by 0.174784
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.419
ELB improved by 0.160259
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.27
ELB improved by 0.148721
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.132
ELB improved by 0.13816
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.005
ELB improved by 0.127366
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.889
ELB improved by 0.115992
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.784
ELB improved by 0.104399
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.691
ELB improved by 0.0932666
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.608
ELB improved by 0.0831692
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.534
ELB improved by 0.0743507
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.467
ELB improved by 0.0667582
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.407
ELB improved by 0.0601933
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.352
ELB improved by 0.0544415
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.303
ELB improved by 0.0493355
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.258
ELB improved by 0.0447654
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.217
ELB improved by 0.0406671
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.18
ELB improved by 0.0370027
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.147
ELB improved by 0.0337451
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.116
ELB improved by 0.0308668
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.087
ELB improved by 0.0283366
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.061
ELB improved by 0.0261184
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.037
ELB improved by 0.0241743
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.015
ELB improved by 0.0224666
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.994
ELB improved by 0.0209603
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.974
ELB improved by 0.0196244
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.956
ELB improved by 0.0184322
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.938
ELB improved by 0.0173617
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.922
ELB improved by 0.0163944
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.906
ELB improved by 0.0155154
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.892
ELB improved by 0.0147124
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.878
ELB improved by 0.0139754
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.864
ELB improved by 0.013296
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.852
ELB improved by 0.0126674
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.84
ELB improved by 0.0120836
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.828
ELB improved by 0.01154
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.817
ELB improved by 0.0110321
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.807
ELB improved by 0.0105565
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.796
ELB improved by 0.0101099
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.787
ELB improved by 0.00968973
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-848.835
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-568.735
ELB improved by 280.1
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-510.992
ELB improved by 57.7427
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.789
ELB improved by 38.2033
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.754
ELB improved by 17.0352
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.204
ELB improved by 6.54949
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.198
ELB improved by 4.00668
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.709
ELB improved by 3.48866
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.243
ELB improved by 3.46583
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.594
ELB improved by 3.649
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.634
ELB improved by 3.96035
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.325
ELB improved by 4.30869
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.835
ELB improved by 4.49025
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.605
ELB improved by 4.22949
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.142
ELB improved by 3.46317
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.633
ELB improved by 2.50882
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.886
ELB improved by 1.74712
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.616
ELB improved by 1.26982
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.649
ELB improved by 0.966856
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.877
ELB improved by 0.772188
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.21
ELB improved by 0.667257
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.594
ELB improved by 0.615635
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.016
ELB improved by 0.578004
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.476
ELB improved by 0.53998
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.967
ELB improved by 0.509602
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.47
ELB improved by 0.496428
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.964
ELB improved by 0.506756
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.421
ELB improved by 0.542841
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.837
ELB improved by 0.583807
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.253
ELB improved by 0.584359
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.708
ELB improved by 0.544953
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.2
ELB improved by 0.50811
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.707
ELB improved by 0.492513
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.21
ELB improved by 0.497419
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.685
ELB improved by 0.524897
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.1
ELB improved by 0.584425
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.434
ELB improved by 0.665819
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.718
ELB improved by 0.716382
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.998
ELB improved by 0.720134
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.286
ELB improved by 0.711925
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.584
ELB improved by 0.70182
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.901
ELB improved by 0.683217
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.246
ELB improved by 0.655347
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.616
ELB improved by 0.629194
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.992
ELB improved by 0.624018
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.352
ELB improved by 0.640819
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.734
ELB improved by 0.617822
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.219
ELB improved by 0.515254
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.804
ELB improved by 0.414741
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.423
ELB improved by 0.380874
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.044
ELB improved by 0.378868
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.728
ELB improved by 0.316318
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.525
ELB improved by 0.202321
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.412
ELB improved by 0.113592
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.347
ELB improved by 0.0652305
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.305
ELB improved by 0.0411714
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.277
ELB improved by 0.0287664
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.255
ELB improved by 0.0217915
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.237
ELB improved by 0.0174814
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.223
ELB improved by 0.0145926
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.21
ELB improved by 0.0125303
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.199
ELB improved by 0.0109865
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.19
ELB improved by 0.00978806
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-882.962
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-599.667
ELB improved by 283.296
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-539.508
ELB improved by 60.1588
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-495.049
ELB improved by 44.4584
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.447
ELB improved by 24.6026
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.624
ELB improved by 11.8226
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.21
ELB improved by 7.41398
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.591
ELB improved by 6.61889
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.958
ELB improved by 6.63314
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.674
ELB improved by 6.284
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.479
ELB improved by 5.19519
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.638
ELB improved by 3.84066
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.849
ELB improved by 2.78933
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.748
ELB improved by 2.10146
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.151
ELB improved by 1.59636
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.975
ELB improved by 1.17578
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.098
ELB improved by 0.877046
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.41
ELB improved by 0.688476
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.855
ELB improved by 0.555266
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.404
ELB improved by 0.451054
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.029
ELB improved by 0.374089
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.708
ELB improved by 0.321296
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.423
ELB improved by 0.285393
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.163
ELB improved by 0.260099
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.921
ELB improved by 0.241463
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.694
ELB improved by 0.227194
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.478
ELB improved by 0.215962
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.271
ELB improved by 0.206986
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.071
ELB improved by 0.199849
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.877
ELB improved by 0.194434
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.686
ELB improved by 0.190943
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.496
ELB improved by 0.189988
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.303
ELB improved by 0.192805
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.101
ELB improved by 0.20167
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.881
ELB improved by 0.220648
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.624
ELB improved by 0.256412
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.308
ELB improved by 0.316767
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.907
ELB improved by 0.400134
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.426
ELB improved by 0.481922
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.883
ELB improved by 0.543013
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.273
ELB improved by 0.609496
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.589
ELB improved by 0.683835
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.901
ELB improved by 0.688634
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.284
ELB improved by 0.616187
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.75
ELB improved by 0.534629
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.28
ELB improved by 0.469739
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.86
ELB improved by 0.420256
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.478
ELB improved by 0.382103
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.125
ELB improved by 0.352296
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.797
ELB improved by 0.328587
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.488
ELB improved by 0.308933
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.197
ELB improved by 0.291268
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.923
ELB improved by 0.273559
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.669
ELB improved by 0.25407
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.437
ELB improved by 0.231747
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.231
ELB improved by 0.206548
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.051
ELB improved by 0.179456
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.899
ELB improved by 0.152087
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.773
ELB improved by 0.126111
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.67
ELB improved by 0.102805
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.587
ELB improved by 0.0828654
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.521
ELB improved by 0.0664387
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.468
ELB improved by 0.0532832
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.425
ELB improved by 0.042949
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.39
ELB improved by 0.034923
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.361
ELB improved by 0.0287187
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.337
ELB improved by 0.0239186
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.317
ELB improved by 0.0201865
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.3
ELB improved by 0.0172614
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.285
ELB improved by 0.014946
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.272
ELB improved by 0.0130933
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.26
ELB improved by 0.0115941
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.25
ELB improved by 0.0103676
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.24
ELB improved by 0.00935373
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.790 0.277 3.084
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.052 | 0.016 | 0.069 | |
| getPIPs | 0.045 | 0.015 | 0.060 | |
| graper | 0.088 | 0.026 | 0.114 | |
| makeExampleData | 0.009 | 0.001 | 0.010 | |
| makeExampleDataWithUnequalGroups | 0.013 | 0.000 | 0.014 | |
| plotELBO | 0.340 | 0.021 | 0.363 | |
| plotGroupPenalties | 1.334 | 0.053 | 1.396 | |
| plotPosterior | 0.741 | 0.022 | 0.765 | |
| predict.graper | 1.923 | 0.092 | 2.032 | |
| print.graper | 0.051 | 0.014 | 0.066 | |