Britta Velten
| Snapshot Date: 2026-01-05 13:40 -0500 (Mon, 05 Jan 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 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-06 11:35 -0500 (Tue, 06 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" | 4815 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4593 |
| 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 915/2332 | 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: 2026-01-05 20:13:45 -0500 (Mon, 05 Jan 2026) |
| EndedAt: 2026-01-05 20:14:18 -0500 (Mon, 05 Jan 2026) |
| EllapsedTime: 32.4 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 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=-884.366
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-573.597
ELB improved by 310.768
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-514.212
ELB improved by 59.3856
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-477.428
ELB improved by 36.7836
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.491
ELB improved by 15.9368
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.116
ELB improved by 7.37547
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.771
ELB improved by 5.34527
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.786
ELB improved by 4.98515
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.74
ELB improved by 5.04531
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.6
ELB improved by 5.14067
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.591
ELB improved by 5.00889
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.135
ELB improved by 4.45561
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.611
ELB improved by 3.52363
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.119
ELB improved by 2.4929
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.481
ELB improved by 1.63718
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.43
ELB improved by 1.05176
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.735
ELB improved by 0.694118
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.249
ELB improved by 0.486103
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.885
ELB improved by 0.364195
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.597
ELB improved by 0.288239
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.36
ELB improved by 0.236536
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.162
ELB improved by 0.198631
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.992
ELB improved by 0.169616
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.845
ELB improved by 0.146893
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.716
ELB improved by 0.128793
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.602
ELB improved by 0.114131
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.5
ELB improved by 0.102048
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.408
ELB improved by 0.0919294
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.325
ELB improved by 0.0833321
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.249
ELB improved by 0.0759333
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.18
ELB improved by 0.069491
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.116
ELB improved by 0.0638205
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.057
ELB improved by 0.0587777
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.003
ELB improved by 0.0542503
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.953
ELB improved by 0.0501505
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.906
ELB improved by 0.046411
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.863
ELB improved by 0.042981
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.823
ELB improved by 0.0398224
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.786
ELB improved by 0.0369075
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.752
ELB improved by 0.0342152
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.721
ELB improved by 0.0317291
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.691
ELB improved by 0.0294353
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.664
ELB improved by 0.0273215
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.638
ELB improved by 0.0253758
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.615
ELB improved by 0.0235868
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.593
ELB improved by 0.021943
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.572
ELB improved by 0.0204334
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.553
ELB improved by 0.0190473
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.536
ELB improved by 0.0177744
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.519
ELB improved by 0.0166051
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.504
ELB improved by 0.0155301
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.489
ELB improved by 0.0145413
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.475
ELB improved by 0.0136308
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.463
ELB improved by 0.0127917
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.451
ELB improved by 0.0120175
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.439
ELB improved by 0.0113025
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.429
ELB improved by 0.0106414
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.419
ELB improved by 0.0100294
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.409
ELB improved by 0.00946242
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-885.466
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-564.821
ELB improved by 320.645
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-507.927
ELB improved by 56.8942
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-477.402
ELB improved by 30.5248
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.643
ELB improved by 13.7592
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.992
ELB improved by 7.65095
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.05
ELB improved by 6.94208
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.259
ELB improved by 7.7909
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.449
ELB improved by 8.8094
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.778
ELB improved by 8.671
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.865
ELB improved by 6.91343
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.148
ELB improved by 4.71741
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.929
ELB improved by 3.21847
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.457
ELB improved by 2.47243
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.573
ELB improved by 1.88362
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.264
ELB improved by 1.30917
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.313
ELB improved by 0.950739
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.552
ELB improved by 0.761401
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.889
ELB improved by 0.662719
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.271
ELB improved by 0.617793
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.656
ELB improved by 0.614862
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.004
ELB improved by 0.652584
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.292
ELB improved by 0.712161
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.554
ELB improved by 0.737755
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.84
ELB improved by 0.713977
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.159
ELB improved by 0.680794
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.506
ELB improved by 0.652748
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.879
ELB improved by 0.627002
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.277
ELB improved by 0.602713
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.694
ELB improved by 0.582329
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.124
ELB improved by 0.570308
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.551
ELB improved by 0.573026
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.951
ELB improved by 0.600189
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.285
ELB improved by 0.66592
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.508
ELB improved by 0.77717
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.613
ELB improved by 0.894693
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.658
ELB improved by 0.954604
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.69
ELB improved by 0.96807
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.724
ELB improved by 0.966376
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.774
ELB improved by 0.949984
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.861
ELB improved by 0.912505
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.005
ELB improved by 0.856351
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.212
ELB improved by 0.792873
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.484
ELB improved by 0.728304
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.837
ELB improved by 0.647257
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.312
ELB improved by 0.524477
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.935
ELB improved by 0.377079
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.684
ELB improved by 0.251499
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.519
ELB improved by 0.164535
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.41
ELB improved by 0.108808
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.337
ELB improved by 0.0737392
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.285
ELB improved by 0.0515688
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.248
ELB improved by 0.0373478
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.22
ELB improved by 0.0280424
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.198
ELB improved by 0.0218086
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.18
ELB improved by 0.0175215
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.166
ELB improved by 0.0144888
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.153
ELB improved by 0.0122798
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.143
ELB improved by 0.0106231
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.133
ELB improved by 0.00934528
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-869.577
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-594.16
ELB improved by 275.418
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-534.844
ELB improved by 59.316
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-490.602
ELB improved by 44.2419
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.943
ELB improved by 23.6583
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.61
ELB improved by 9.33378
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.038
ELB improved by 4.57193
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.654
ELB improved by 3.38358
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.685
ELB improved by 2.96868
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.852
ELB improved by 2.83297
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.118
ELB improved by 2.73485
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.571
ELB improved by 2.54617
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.332
ELB improved by 2.23939
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.462
ELB improved by 1.87049
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.941
ELB improved by 1.52088
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.714
ELB improved by 1.22634
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.747
ELB improved by 0.966879
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.019
ELB improved by 0.728614
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.487
ELB improved by 0.531502
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.098
ELB improved by 0.389674
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.802
ELB improved by 0.295315
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.569
ELB improved by 0.233355
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.377
ELB improved by 0.191656
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.215
ELB improved by 0.162503
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.074
ELB improved by 0.141322
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.948
ELB improved by 0.125413
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.835
ELB improved by 0.113134
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.732
ELB improved by 0.103459
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.636
ELB improved by 0.0957211
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.546
ELB improved by 0.0894732
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.462
ELB improved by 0.0844077
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.382
ELB improved by 0.080306
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.305
ELB improved by 0.0770098
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.23
ELB improved by 0.0744015
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.158
ELB improved by 0.0723925
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.087
ELB improved by 0.0709156
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.017
ELB improved by 0.0699193
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.948
ELB improved by 0.0693647
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.878
ELB improved by 0.0692227
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.809
ELB improved by 0.0694727
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.739
ELB improved by 0.0701011
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.668
ELB improved by 0.0711007
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.595
ELB improved by 0.0724701
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.521
ELB improved by 0.0742134
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.445
ELB improved by 0.0763395
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.366
ELB improved by 0.0788619
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.284
ELB improved by 0.0817982
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.199
ELB improved by 0.0851688
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.11
ELB improved by 0.0889962
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.017
ELB improved by 0.0933034
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.918
ELB improved by 0.0981127
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.815
ELB improved by 0.103445
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.706
ELB improved by 0.109319
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.59
ELB improved by 0.115754
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.467
ELB improved by 0.122772
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.337
ELB improved by 0.130405
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.198
ELB improved by 0.138699
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.05
ELB improved by 0.147722
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.893
ELB improved by 0.15757
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.724
ELB improved by 0.168371
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.544
ELB improved by 0.180283
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.351
ELB improved by 0.193484
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.142
ELB improved by 0.208165
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.918
ELB improved by 0.224502
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.675
ELB improved by 0.24264
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.413
ELB improved by 0.26266
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.128
ELB improved by 0.284535
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.82
ELB improved by 0.307997
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.488
ELB improved by 0.332135
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.133
ELB improved by 0.354543
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.763
ELB improved by 0.370259
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.391
ELB improved by 0.372263
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.035
ELB improved by 0.355506
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.714
ELB improved by 0.321386
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.437
ELB improved by 0.276809
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.208
ELB improved by 0.229562
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.022
ELB improved by 0.185356
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.875
ELB improved by 0.147245
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.759
ELB improved by 0.116117
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.667
ELB improved by 0.0915076
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.595
ELB improved by 0.0723606
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.538
ELB improved by 0.0575215
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.492
ELB improved by 0.045983
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.455
ELB improved by 0.0369604
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.425
ELB improved by 0.0298767
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.4
ELB improved by 0.0243124
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.38
ELB improved by 0.0199538
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.364
ELB improved by 0.0165549
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.35
ELB improved by 0.0139153
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.338
ELB improved by 0.0118694
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.328
ELB improved by 0.0102819
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.319
ELB improved by 0.00904417
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-870.501
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-581.42
ELB improved by 289.081
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-522.336
ELB improved by 59.0842
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-485.765
ELB improved by 36.5705
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.018
ELB improved by 14.7475
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.658
ELB improved by 6.36017
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.167
ELB improved by 4.49022
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.217
ELB improved by 3.95007
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.421
ELB improved by 3.79585
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.704
ELB improved by 3.71772
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.181
ELB improved by 3.52321
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.06
ELB improved by 3.1209
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.502
ELB improved by 2.55754
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.537
ELB improved by 1.96463
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.094
ELB improved by 1.44386
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.059
ELB improved by 1.03477
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.317
ELB improved by 0.741632
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.771
ELB improved by 0.54589
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.353
ELB improved by 0.418782
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.018
ELB improved by 0.334978
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.74
ELB improved by 0.277313
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.505
ELB improved by 0.235535
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.301
ELB improved by 0.203798
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.122
ELB improved by 0.178757
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.964
ELB improved by 0.15843
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.822
ELB improved by 0.141585
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.695
ELB improved by 0.12741
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.579
ELB improved by 0.115342
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.474
ELB improved by 0.104974
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.378
ELB improved by 0.0959957
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.29
ELB improved by 0.0881695
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.209
ELB improved by 0.0813063
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.134
ELB improved by 0.0752542
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.064
ELB improved by 0.0698895
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.999
ELB improved by 0.0651105
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.938
ELB improved by 0.0608332
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.881
ELB improved by 0.0569871
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.827
ELB improved by 0.0535134
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.777
ELB improved by 0.0503623
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.729
ELB improved by 0.0474915
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.685
ELB improved by 0.0448654
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.642
ELB improved by 0.0424533
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.602
ELB improved by 0.0402291
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.564
ELB improved by 0.0381705
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.527
ELB improved by 0.0362583
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.493
ELB improved by 0.034476
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.46
ELB improved by 0.0328096
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.429
ELB improved by 0.0312468
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.399
ELB improved by 0.0297773
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.371
ELB improved by 0.0283921
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.344
ELB improved by 0.0270836
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.318
ELB improved by 0.0258451
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.293
ELB improved by 0.0246709
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.27
ELB improved by 0.0235562
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.247
ELB improved by 0.0224966
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.226
ELB improved by 0.0214885
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.205
ELB improved by 0.0205286
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.186
ELB improved by 0.0196141
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.167
ELB improved by 0.0187424
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.149
ELB improved by 0.0179114
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.132
ELB improved by 0.017119
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.115
ELB improved by 0.0163632
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.1
ELB improved by 0.0156424
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.085
ELB improved by 0.0149551
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.07
ELB improved by 0.0142996
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.057
ELB improved by 0.0136746
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.044
ELB improved by 0.0130789
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.031
ELB improved by 0.012511
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.019
ELB improved by 0.0119698
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.008
ELB improved by 0.0114541
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.997
ELB improved by 0.0109629
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.986
ELB improved by 0.0104949
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.976
ELB improved by 0.0100493
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.967
ELB improved by 0.00962492
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
1.131 0.098 1.253
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.013 | 0.006 | 0.021 | |
| getPIPs | 0.012 | 0.005 | 0.017 | |
| graper | 0.018 | 0.009 | 0.028 | |
| makeExampleData | 0.001 | 0.000 | 0.002 | |
| makeExampleDataWithUnequalGroups | 0.002 | 0.001 | 0.002 | |
| plotELBO | 0.121 | 0.008 | 0.130 | |
| plotGroupPenalties | 0.356 | 0.008 | 0.394 | |
| plotPosterior | 0.309 | 0.014 | 0.342 | |
| predict.graper | 0.218 | 0.031 | 0.262 | |
| print.graper | 0.011 | 0.005 | 0.016 | |