Britta Velten
| Snapshot Date: 2026-01-04 13:40 -0500 (Sun, 04 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 2026-01-05 11:35 -0500 (Mon, 05 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: 2026-01-04 20:12:01 -0500 (Sun, 04 Jan 2026) |
| EndedAt: 2026-01-04 20:12:33 -0500 (Sun, 04 Jan 2026) |
| EllapsedTime: 31.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck’
* using R 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=-860.011
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-567.542
ELB improved by 292.468
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-506.634
ELB improved by 60.9084
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.559
ELB improved by 38.0751
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.393
ELB improved by 16.1664
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.298
ELB improved by 7.09425
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.17
ELB improved by 5.12874
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.255
ELB improved by 4.91489
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.818
ELB improved by 5.4371
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.407
ELB improved by 6.4103
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.007
ELB improved by 7.40032
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.369
ELB improved by 7.63809
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.647
ELB improved by 6.7222
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.534
ELB improved by 5.11267
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.096
ELB improved by 3.4384
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.94
ELB improved by 2.15569
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.582
ELB improved by 1.3575
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.675
ELB improved by 0.907827
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.013
ELB improved by 0.661334
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.488
ELB improved by 0.525203
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.039
ELB improved by 0.449071
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.634
ELB improved by 0.404698
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.263
ELB improved by 0.371553
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.929
ELB improved by 0.333692
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.641
ELB improved by 0.287643
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.398
ELB improved by 0.243243
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.189
ELB improved by 0.209413
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.002
ELB improved by 0.186866
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.829
ELB improved by 0.172563
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.666
ELB improved by 0.163763
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.507
ELB improved by 0.158749
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.35
ELB improved by 0.156423
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.195
ELB improved by 0.155932
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.038
ELB improved by 0.156515
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.88
ELB improved by 0.157534
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.722
ELB improved by 0.158579
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.562
ELB improved by 0.159512
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.402
ELB improved by 0.160375
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.241
ELB improved by 0.161264
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.078
ELB improved by 0.162259
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.915
ELB improved by 0.163435
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.75
ELB improved by 0.164878
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.583
ELB improved by 0.166706
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.414
ELB improved by 0.169056
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.242
ELB improved by 0.17207
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.066
ELB improved by 0.175871
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.886
ELB improved by 0.180535
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.7
ELB improved by 0.186062
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.508
ELB improved by 0.192348
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.308
ELB improved by 0.19916
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.102
ELB improved by 0.206109
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.89
ELB improved by 0.212639
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.672
ELB improved by 0.21804
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.45
ELB improved by 0.221481
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.228
ELB improved by 0.222105
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.009
ELB improved by 0.21916
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.797
ELB improved by 0.212162
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.596
ELB improved by 0.201049
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.409
ELB improved by 0.18625
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.241
ELB improved by 0.168641
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.091
ELB improved by 0.149383
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.962
ELB improved by 0.1297
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.851
ELB improved by 0.110673
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.758
ELB improved by 0.0931028
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.68
ELB improved by 0.0774695
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.616
ELB improved by 0.0639663
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.564
ELB improved by 0.05257
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.521
ELB improved by 0.0431203
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.485
ELB improved by 0.0353864
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.456
ELB improved by 0.0291157
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.432
ELB improved by 0.0240635
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.412
ELB improved by 0.0200086
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.395
ELB improved by 0.0167604
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.381
ELB improved by 0.0141592
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.369
ELB improved by 0.0120739
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.359
ELB improved by 0.0103984
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.35
ELB improved by 0.00904794
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-919.195
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-581.042
ELB improved by 338.153
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-524.851
ELB improved by 56.191
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-490.653
ELB improved by 34.1972
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.616
ELB improved by 18.0375
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.549
ELB improved by 9.06678
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.487
ELB improved by 6.06183
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.937
ELB improved by 5.55068
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.201
ELB improved by 5.73582
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.278
ELB improved by 5.92257
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.707
ELB improved by 5.57083
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.167
ELB improved by 4.54048
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.838
ELB improved by 3.32862
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.368
ELB improved by 2.46975
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.464
ELB improved by 1.90418
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.139
ELB improved by 1.32519
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.308
ELB improved by 0.83092
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.78
ELB improved by 0.52851
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.415
ELB improved by 0.364762
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.142
ELB improved by 0.273103
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.925
ELB improved by 0.216662
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.747
ELB improved by 0.178402
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.596
ELB improved by 0.150485
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.467
ELB improved by 0.12905
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.355
ELB improved by 0.11202
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.257
ELB improved by 0.0981673
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.17
ELB improved by 0.0867086
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.093
ELB improved by 0.0771083
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.024
ELB improved by 0.0689824
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.962
ELB improved by 0.0620454
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.906
ELB improved by 0.0560799
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.855
ELB improved by 0.0509165
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.809
ELB improved by 0.0464216
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.766
ELB improved by 0.0424886
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.727
ELB improved by 0.039031
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.691
ELB improved by 0.0359786
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.658
ELB improved by 0.0332734
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.627
ELB improved by 0.0308676
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.598
ELB improved by 0.0287211
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.572
ELB improved by 0.0268003
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.547
ELB improved by 0.0250769
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.523
ELB improved by 0.0235267
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.501
ELB improved by 0.0221291
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.48
ELB improved by 0.0208665
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.46
ELB improved by 0.0197236
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.442
ELB improved by 0.0186873
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.424
ELB improved by 0.0177459
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.407
ELB improved by 0.0168897
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.391
ELB improved by 0.0161096
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.375
ELB improved by 0.0153981
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.361
ELB improved by 0.0147483
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.347
ELB improved by 0.0141543
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.333
ELB improved by 0.0136106
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.32
ELB improved by 0.0131125
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.307
ELB improved by 0.0126558
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.295
ELB improved by 0.0122366
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.283
ELB improved by 0.0118516
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.272
ELB improved by 0.0114977
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.26
ELB improved by 0.0111722
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.25
ELB improved by 0.0108725
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.239
ELB improved by 0.0105964
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.229
ELB improved by 0.0103418
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.218
ELB improved by 0.010107
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.209
ELB improved by 0.00989025
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-860.152
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-596.582
ELB improved by 263.57
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-538.002
ELB improved by 58.5801
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-491.773
ELB improved by 46.2291
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.054
ELB improved by 24.719
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.494
ELB improved by 10.5603
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.895
ELB improved by 5.59842
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.781
ELB improved by 4.1139
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.082
ELB improved by 3.69988
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.377
ELB improved by 3.70457
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.493
ELB improved by 3.88428
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.425
ELB improved by 4.06817
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.439
ELB improved by 3.9851
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.072
ELB improved by 3.36749
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.692
ELB improved by 2.38045
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.2
ELB improved by 1.49136
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.28
ELB improved by 0.920336
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.672
ELB improved by 0.607858
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.232
ELB improved by 0.439874
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.889
ELB improved by 0.343207
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.607
ELB improved by 0.281939
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.367
ELB improved by 0.239561
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.159
ELB improved by 0.20834
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.975
ELB improved by 0.18442
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.809
ELB improved by 0.165691
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.658
ELB improved by 0.150874
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.519
ELB improved by 0.139117
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.389
ELB improved by 0.129828
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.267
ELB improved by 0.122577
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.149
ELB improved by 0.117055
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.036
ELB improved by 0.113036
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.926
ELB improved by 0.110356
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.817
ELB improved by 0.1089
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.709
ELB improved by 0.108589
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.599
ELB improved by 0.109382
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.488
ELB improved by 0.111264
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.374
ELB improved by 0.114253
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.255
ELB improved by 0.11839
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.132
ELB improved by 0.123748
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.001
ELB improved by 0.130427
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.863
ELB improved by 0.13856
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.714
ELB improved by 0.148316
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.554
ELB improved by 0.15991
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.381
ELB improved by 0.173615
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.191
ELB improved by 0.18978
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.982
ELB improved by 0.208862
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.751
ELB improved by 0.231465
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.492
ELB improved by 0.258434
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.201
ELB improved by 0.291018
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.87
ELB improved by 0.331204
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.488
ELB improved by 0.382391
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.037
ELB improved by 0.450597
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.491
ELB improved by 0.546016
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.809
ELB improved by 0.681547
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.954
ELB improved by 0.855338
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.94
ELB improved by 1.01395
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.859
ELB improved by 1.08107
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.805
ELB improved by 1.05366
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.837
ELB improved by 0.968115
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.994
ELB improved by 0.843267
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.301
ELB improved by 0.692617
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.763
ELB improved by 0.537938
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.361
ELB improved by 0.402076
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.065
ELB improved by 0.296121
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.846
ELB improved by 0.219476
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.679
ELB improved by 0.166568
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.548
ELB improved by 0.131052
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.441
ELB improved by 0.10728
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.35
ELB improved by 0.0906679
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.272
ELB improved by 0.0777661
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.206
ELB improved by 0.0663999
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.15
ELB improved by 0.0557837
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.104
ELB improved by 0.0461848
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.066
ELB improved by 0.0381493
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.034
ELB improved by 0.0318935
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.007
ELB improved by 0.0272235
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.983
ELB improved by 0.0237593
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.962
ELB improved by 0.021136
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.943
ELB improved by 0.0190826
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.925
ELB improved by 0.0174206
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.909
ELB improved by 0.0160373
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.895
ELB improved by 0.0148617
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.881
ELB improved by 0.0138472
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.868
ELB improved by 0.0129621
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.856
ELB improved by 0.0121838
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.844
ELB improved by 0.011495
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.833
ELB improved by 0.0108828
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.823
ELB improved by 0.0103369
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.813
ELB improved by 0.00984884
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-885.917
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-604.413
ELB improved by 281.504
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-551.39
ELB improved by 53.0231
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-510.024
ELB improved by 41.3664
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-485.341
ELB improved by 24.6829
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-474.104
ELB improved by 11.2371
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.193
ELB improved by 5.91121
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.242
ELB improved by 4.95022
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.328
ELB improved by 4.91467
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.501
ELB improved by 4.82692
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.158
ELB improved by 4.34266
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.687
ELB improved by 3.47068
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.174
ELB improved by 2.51324
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.416
ELB improved by 1.75813
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.155
ELB improved by 1.26072
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.201
ELB improved by 0.954684
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.423
ELB improved by 0.777414
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.742
ELB improved by 0.680784
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.131
ELB improved by 0.611827
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.602
ELB improved by 0.52824
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.16
ELB improved by 0.442373
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.779
ELB improved by 0.380507
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.437
ELB improved by 0.34211
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.12
ELB improved by 0.317843
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.818
ELB improved by 0.301496
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.528
ELB improved by 0.289763
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.247
ELB improved by 0.28076
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.974
ELB improved by 0.273307
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.708
ELB improved by 0.266652
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.447
ELB improved by 0.260359
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.193
ELB improved by 0.254249
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.945
ELB improved by 0.248366
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.702
ELB improved by 0.242939
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.463
ELB improved by 0.238338
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.228
ELB improved by 0.235051
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.995
ELB improved by 0.23368
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.76
ELB improved by 0.234999
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.519
ELB improved by 0.240103
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.269
ELB improved by 0.250733
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.999
ELB improved by 0.269971
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.695
ELB improved by 0.303688
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.332
ELB improved by 0.363313
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.863
ELB improved by 0.468879
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.224
ELB improved by 0.638926
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.387
ELB improved by 0.836948
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.418
ELB improved by 0.969021
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.381
ELB improved by 1.0366
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.285
ELB improved by 1.09682
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.124
ELB improved by 1.16025
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.954
ELB improved by 1.16983
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.908
ELB improved by 1.04677
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.068
ELB improved by 0.839846
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.419
ELB improved by 0.648657
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.915
ELB improved by 0.504615
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.53
ELB improved by 0.38504
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.258
ELB improved by 0.271935
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.077
ELB improved by 0.180799
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.953
ELB improved by 0.123504
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.86
ELB improved by 0.092996
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.782
ELB improved by 0.0781271
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.711
ELB improved by 0.0709093
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.645
ELB improved by 0.0660659
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.585
ELB improved by 0.060158
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.533
ELB improved by 0.0520071
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.49
ELB improved by 0.0427242
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.456
ELB improved by 0.0341759
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.429
ELB improved by 0.0274283
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.406
ELB improved by 0.0225325
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.387
ELB improved by 0.019065
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.371
ELB improved by 0.016565
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.356
ELB improved by 0.0146896
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.343
ELB improved by 0.0132186
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.331
ELB improved by 0.0120192
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.32
ELB improved by 0.0110116
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.309
ELB improved by 0.0101472
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.3
ELB improved by 0.0093952
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
1.138 0.098 1.248
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.015 | 0.006 | 0.021 | |
| getPIPs | 0.012 | 0.005 | 0.019 | |
| graper | 0.019 | 0.006 | 0.027 | |
| makeExampleData | 0.002 | 0.001 | 0.002 | |
| makeExampleDataWithUnequalGroups | 0.002 | 0.000 | 0.003 | |
| plotELBO | 0.117 | 0.008 | 0.130 | |
| plotGroupPenalties | 0.367 | 0.007 | 0.395 | |
| plotPosterior | 0.317 | 0.016 | 0.347 | |
| predict.graper | 0.220 | 0.030 | 0.264 | |
| print.graper | 0.011 | 0.005 | 0.016 | |