Britta Velten
| Snapshot Date: 2025-11-30 13:40 -0500 (Sun, 30 Nov 2025) |
| 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 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-01 11:35 -0500 (Mon, 01 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4866 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4572 |
| 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 913/2328 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.27.0 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 1.27.0 |
| 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: 2025-11-30 20:18:41 -0500 (Sun, 30 Nov 2025) |
| EndedAt: 2025-11-30 20:19:13 -0500 (Sun, 30 Nov 2025) |
| EllapsedTime: 31.5 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 Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.27.0’
* 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 15.0.0 (clang-1500.1.0.2.5)’
* 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 ... 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-arm64/Resources/library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.27.0’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.1.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fit_graper.cpp -o fit_graper.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o graper.so RcppExports.o fit_graper.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-graper/00new/graper/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (graper)
graper.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(graper)
>
> test_check("graper")
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-888.57
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-580.501
ELB improved by 308.069
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-525.945
ELB improved by 54.5566
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-491.906
ELB improved by 34.0391
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-476.497
ELB improved by 15.4083
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.239
ELB improved by 7.25868
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.198
ELB improved by 5.04023
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.318
ELB improved by 4.88027
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.023
ELB improved by 5.29515
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.428
ELB improved by 5.5954
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.217
ELB improved by 5.21007
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.153
ELB improved by 4.06492
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.439
ELB improved by 2.71327
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.755
ELB improved by 1.68394
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.676
ELB improved by 1.07929
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.905
ELB improved by 0.771163
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.278
ELB improved by 0.626696
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.712
ELB improved by 0.565938
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.165
ELB improved by 0.546942
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.617
ELB improved by 0.548087
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.057
ELB improved by 0.560068
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.477
ELB improved by 0.580303
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.869
ELB improved by 0.607493
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.23
ELB improved by 0.639625
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.555
ELB improved by 0.674516
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.845
ELB improved by 0.710496
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.098
ELB improved by 0.746663
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.315
ELB improved by 0.782893
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.496
ELB improved by 0.819615
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.638
ELB improved by 0.857107
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.744
ELB improved by 0.894122
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.818
ELB improved by 0.926239
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.873
ELB improved by 0.945291
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.932
ELB improved by 0.940918
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.028
ELB improved by 0.90376
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.199
ELB improved by 0.829617
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.475
ELB improved by 0.72372
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.874
ELB improved by 0.600955
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.394
ELB improved by 0.47941
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.022
ELB improved by 0.372813
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.734
ELB improved by 0.287518
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.51
ELB improved by 0.223587
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.333
ELB improved by 0.1774
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.189
ELB improved by 0.14414
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.069
ELB improved by 0.119463
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.969
ELB improved by 0.100271
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.884
ELB improved by 0.0847477
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.812
ELB improved by 0.0719832
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.751
ELB improved by 0.0615
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.698
ELB improved by 0.0529452
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.652
ELB improved by 0.0459806
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.612
ELB improved by 0.0402853
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.576
ELB improved by 0.0355814
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.545
ELB improved by 0.0316477
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.516
ELB improved by 0.0283165
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.491
ELB improved by 0.0254637
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.468
ELB improved by 0.0229979
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.447
ELB improved by 0.0208505
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.428
ELB improved by 0.0189693
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.411
ELB improved by 0.0173136
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.395
ELB improved by 0.0158508
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.38
ELB improved by 0.0145543
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.367
ELB improved by 0.0134021
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.354
ELB improved by 0.0123757
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.343
ELB improved by 0.0114593
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.332
ELB improved by 0.0106395
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.322
ELB improved by 0.0099047
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-867.3
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-564.788
ELB improved by 302.512
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-507.057
ELB improved by 57.7317
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.551
ELB improved by 36.5055
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.654
ELB improved by 17.897
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.352
ELB improved by 8.30206
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.996
ELB improved by 5.35586
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.061
ELB improved by 4.93484
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.711
ELB improved by 5.35013
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.806
ELB improved by 5.90561
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.918
ELB improved by 5.88724
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.942
ELB improved by 4.97658
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.333
ELB improved by 3.60905
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.99
ELB improved by 2.34245
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.516
ELB improved by 1.47437
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.517
ELB improved by 0.998585
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.768
ELB improved by 0.749827
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.153
ELB improved by 0.614948
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.611
ELB improved by 0.541839
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.1
ELB improved by 0.510994
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.576
ELB improved by 0.524331
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.976
ELB improved by 0.599632
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.245
ELB improved by 0.731172
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.418
ELB improved by 0.82659
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.608
ELB improved by 0.810522
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.849
ELB improved by 0.758648
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.104
ELB improved by 0.74478
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.337
ELB improved by 0.767472
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.521
ELB improved by 0.81591
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.631
ELB improved by 0.889982
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.639
ELB improved by 0.991326
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.549
ELB improved by 1.09098
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.445
ELB improved by 1.10373
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.442
ELB improved by 1.00302
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.578
ELB improved by 0.863607
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.856
ELB improved by 0.72212
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.269
ELB improved by 0.58751
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.798
ELB improved by 0.470815
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.418
ELB improved by 0.379837
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.101
ELB improved by 0.316869
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.818
ELB improved by 0.283487
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.527
ELB improved by 0.290663
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.153
ELB improved by 0.373924
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.582
ELB improved by 0.570514
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.846
ELB improved by 0.73606
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.153
ELB improved by 0.693728
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.58
ELB improved by 0.572547
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.123
ELB improved by 0.456863
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.764
ELB improved by 0.359368
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.475
ELB improved by 0.288928
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.231
ELB improved by 0.244265
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.028
ELB improved by 0.202566
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.88
ELB improved by 0.148098
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.784
ELB improved by 0.0961255
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.722
ELB improved by 0.0616025
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.68
ELB improved by 0.0422962
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.648
ELB improved by 0.0314907
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.624
ELB improved by 0.0249056
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.603
ELB improved by 0.0205114
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.586
ELB improved by 0.0173782
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.571
ELB improved by 0.0150388
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.557
ELB improved by 0.0132295
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.546
ELB improved by 0.0117884
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.535
ELB improved by 0.0106113
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.525
ELB improved by 0.00962939
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-871.46
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-561.469
ELB improved by 309.992
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-503.844
ELB improved by 57.625
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.611
ELB improved by 35.2329
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.737
ELB improved by 15.874
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.504
ELB improved by 8.23281
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.643
ELB improved by 6.86097
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.989
ELB improved by 7.65389
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.788
ELB improved by 9.20125
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.753
ELB improved by 10.0351
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.156
ELB improved by 8.59651
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.536
ELB improved by 5.62057
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.356
ELB improved by 3.17943
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.538
ELB improved by 1.81855
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.412
ELB improved by 1.12587
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.655
ELB improved by 0.756935
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.111
ELB improved by 0.543411
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.702
ELB improved by 0.409104
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.384
ELB improved by 0.318755
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.129
ELB improved by 0.254953
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.92
ELB improved by 0.208285
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.747
ELB improved by 0.17319
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.601
ELB improved by 0.146161
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.476
ELB improved by 0.124891
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.368
ELB improved by 0.107831
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.274
ELB improved by 0.093916
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.192
ELB improved by 0.0824019
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.119
ELB improved by 0.0727574
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.055
ELB improved by 0.0645948
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.997
ELB improved by 0.0576245
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.945
ELB improved by 0.0516263
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.899
ELB improved by 0.0464295
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.857
ELB improved by 0.0419001
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.819
ELB improved by 0.0379309
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.785
ELB improved by 0.0344359
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.753
ELB improved by 0.0313448
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.725
ELB improved by 0.0286001
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.699
ELB improved by 0.0261539
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.675
ELB improved by 0.0239665
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.653
ELB improved by 0.0220044
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.632
ELB improved by 0.0202394
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.614
ELB improved by 0.0186475
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.596
ELB improved by 0.0172082
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.581
ELB improved by 0.0159039
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.566
ELB improved by 0.0147194
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.552
ELB improved by 0.0136415
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.54
ELB improved by 0.0126588
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.528
ELB improved by 0.0117614
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.517
ELB improved by 0.0109405
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.507
ELB improved by 0.0101883
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.497
ELB improved by 0.00949827
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-880.337
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-580.465
ELB improved by 299.872
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-517.323
ELB improved by 63.1421
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.434
ELB improved by 43.8887
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.651
ELB improved by 19.7828
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.648
ELB improved by 9.00302
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.216
ELB improved by 6.43245
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.083
ELB improved by 6.13289
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.072
ELB improved by 7.01103
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.382
ELB improved by 8.68966
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.096
ELB improved by 10.2859
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.96
ELB improved by 10.1365
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.09
ELB improved by 7.87018
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.659
ELB improved by 5.431
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.912
ELB improved by 3.74647
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.436
ELB improved by 2.47648
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.807
ELB improved by 1.62886
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.678
ELB improved by 1.12843
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.836
ELB improved by 0.842386
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.16
ELB improved by 0.675719
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.586
ELB improved by 0.574414
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.075
ELB improved by 0.510678
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.605
ELB improved by 0.470191
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.16
ELB improved by 0.445207
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.729
ELB improved by 0.43132
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.303
ELB improved by 0.425933
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.875
ELB improved by 0.427474
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.44
ELB improved by 0.434955
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.992
ELB improved by 0.447755
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.527
ELB improved by 0.465639
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.037
ELB improved by 0.489294
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-366.515
ELB improved by 0.521993
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.942
ELB improved by 0.573906
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-365.271
ELB improved by 0.670724
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-364.422
ELB improved by 0.848454
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-363.388
ELB improved by 1.03484
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-362.384
ELB improved by 1.00387
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-361.551
ELB improved by 0.833181
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-360.857
ELB improved by 0.69389
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-360.267
ELB improved by 0.589176
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-359.765
ELB improved by 0.502444
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-359.334
ELB improved by 0.431097
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-358.958
ELB improved by 0.375448
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-358.622
ELB improved by 0.336244
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-358.308
ELB improved by 0.313964
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-358.005
ELB improved by 0.30375
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-357.717
ELB improved by 0.287949
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-357.473
ELB improved by 0.244015
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-357.297
ELB improved by 0.175922
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-357.183
ELB improved by 0.113948
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-357.108
ELB improved by 0.0743264
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-357.056
ELB improved by 0.0522382
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-357.017
ELB improved by 0.0393908
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-356.986
ELB improved by 0.0310347
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-356.961
ELB improved by 0.0250771
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-356.94
ELB improved by 0.0206
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-356.923
ELB improved by 0.0171428
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-356.908
ELB improved by 0.0144325
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-356.896
ELB improved by 0.0122858
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-356.886
ELB improved by 0.0105705
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-356.876
ELB improved by 0.00918828
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
1.042 0.091 1.148
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.013 | 0.006 | 0.020 | |
| getPIPs | 0.011 | 0.006 | 0.018 | |
| graper | 0.024 | 0.008 | 0.033 | |
| makeExampleData | 0.001 | 0.001 | 0.002 | |
| makeExampleDataWithUnequalGroups | 0.002 | 0.000 | 0.002 | |
| plotELBO | 0.116 | 0.007 | 0.125 | |
| plotGroupPenalties | 0.445 | 0.010 | 0.464 | |
| plotPosterior | 0.219 | 0.010 | 0.231 | |
| predict.graper | 0.219 | 0.027 | 0.248 | |
| print.graper | 0.012 | 0.006 | 0.017 | |