Britta Velten
| Snapshot Date: 2026-01-23 13:40 -0500 (Fri, 23 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 2026-01-24 11:35 -0500 (Sat, 24 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4811 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4545 |
| 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 921/2345 | 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: 2026-01-23 20:19:41 -0500 (Fri, 23 Jan 2026) |
| EndedAt: 2026-01-23 20:20:15 -0500 (Fri, 23 Jan 2026) |
| EllapsedTime: 33.4 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) (2026-01-15 r89304)
* 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) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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=-864.804
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-564.115
ELB improved by 300.69
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-512.125
ELB improved by 51.9894
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-478.84
ELB improved by 33.2856
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.748
ELB improved by 15.0918
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.608
ELB improved by 7.1397
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.951
ELB improved by 5.65713
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.536
ELB improved by 6.415
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.833
ELB improved by 7.70336
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.572
ELB improved by 8.26111
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.451
ELB improved by 7.12067
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.51
ELB improved by 4.94063
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.368
ELB improved by 3.14288
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.206
ELB improved by 2.16128
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.526
ELB improved by 1.68
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.149
ELB improved by 1.37767
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.952
ELB improved by 1.19691
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.807
ELB improved by 1.14437
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.611
ELB improved by 1.19585
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.323
ELB improved by 1.28834
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.056
ELB improved by 1.26716
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.914
ELB improved by 1.14168
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.892
ELB improved by 1.02214
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.973
ELB improved by 0.919221
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.149
ELB improved by 0.824366
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.411
ELB improved by 0.737422
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.75
ELB improved by 0.661
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.153
ELB improved by 0.597013
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.607
ELB improved by 0.545979
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.1
ELB improved by 0.507131
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.621
ELB improved by 0.478577
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.164
ELB improved by 0.45746
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.724
ELB improved by 0.440235
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.301
ELB improved by 0.423141
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.898
ELB improved by 0.402901
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.52
ELB improved by 0.377553
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.173
ELB improved by 0.347143
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.859
ELB improved by 0.313756
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.579
ELB improved by 0.28062
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.328
ELB improved by 0.250728
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.102
ELB improved by 0.225784
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.896
ELB improved by 0.205921
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.706
ELB improved by 0.19002
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.53
ELB improved by 0.176226
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.368
ELB improved by 0.162332
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.221
ELB improved by 0.146224
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.095
ELB improved by 0.12687
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.989
ELB improved by 0.105265
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.905
ELB improved by 0.0839119
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.84
ELB improved by 0.0650846
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.79
ELB improved by 0.0497869
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.753
ELB improved by 0.037957
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.723
ELB improved by 0.0290547
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.701
ELB improved by 0.0224487
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.683
ELB improved by 0.0175766
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.669
ELB improved by 0.0139872
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.658
ELB improved by 0.0113363
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.649
ELB improved by 0.00936844
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-854.357
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-584.222
ELB improved by 270.135
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-524.613
ELB improved by 59.6086
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-482.825
ELB improved by 41.7889
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.199
ELB improved by 19.6254
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.957
ELB improved by 8.24232
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.88
ELB improved by 4.07665
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.026
ELB improved by 2.85443
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.529
ELB improved by 2.49723
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.109
ELB improved by 2.41984
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.658
ELB improved by 2.45038
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.15
ELB improved by 2.50801
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.631
ELB improved by 2.51979
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.225
ELB improved by 2.40546
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.106
ELB improved by 2.11942
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.403
ELB improved by 1.70224
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.143
ELB improved by 1.26084
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.253
ELB improved by 0.88947
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.63
ELB improved by 0.622671
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.184
ELB improved by 0.446772
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.85
ELB improved by 0.333376
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.591
ELB improved by 0.259528
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.38
ELB improved by 0.210699
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.202
ELB improved by 0.177945
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.047
ELB improved by 0.155587
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.907
ELB improved by 0.140007
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.778
ELB improved by 0.128955
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.657
ELB improved by 0.121059
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.541
ELB improved by 0.115487
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.429
ELB improved by 0.111733
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.32
ELB improved by 0.109478
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.211
ELB improved by 0.108525
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.103
ELB improved by 0.108753
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.992
ELB improved by 0.110095
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.88
ELB improved by 0.112525
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.764
ELB improved by 0.116057
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.643
ELB improved by 0.12074
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.516
ELB improved by 0.126657
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.383
ELB improved by 0.133932
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.24
ELB improved by 0.142729
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.087
ELB improved by 0.153251
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.921
ELB improved by 0.165732
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.74
ELB improved by 0.180428
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.543
ELB improved by 0.197586
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.325
ELB improved by 0.217411
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.085
ELB improved by 0.240031
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.82
ELB improved by 0.265483
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.526
ELB improved by 0.2937
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.202
ELB improved by 0.324505
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.844
ELB improved by 0.357522
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.452
ELB improved by 0.391959
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.026
ELB improved by 0.426162
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.569
ELB improved by 0.456946
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.09
ELB improved by 0.479131
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.603
ELB improved by 0.48655
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.128
ELB improved by 0.475307
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.681
ELB improved by 0.44675
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.275
ELB improved by 0.40657
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.914
ELB improved by 0.361274
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.598
ELB improved by 0.315851
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.324
ELB improved by 0.273351
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.089
ELB improved by 0.235151
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.888
ELB improved by 0.201345
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.716
ELB improved by 0.171333
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.572
ELB improved by 0.144563
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.451
ELB improved by 0.121019
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.35
ELB improved by 0.101107
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.265
ELB improved by 0.0852033
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.191
ELB improved by 0.0733747
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.126
ELB improved by 0.0654058
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.065
ELB improved by 0.0609429
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.005
ELB improved by 0.0595516
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.945
ELB improved by 0.0606517
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.881
ELB improved by 0.0634251
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.814
ELB improved by 0.0668669
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.744
ELB improved by 0.0700342
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.672
ELB improved by 0.0722063
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.599
ELB improved by 0.0726669
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.529
ELB improved by 0.0705327
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.464
ELB improved by 0.0653109
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.406
ELB improved by 0.057663
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.357
ELB improved by 0.0491376
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.316
ELB improved by 0.041113
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.281
ELB improved by 0.0342238
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.253
ELB improved by 0.0285315
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.229
ELB improved by 0.0238736
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.209
ELB improved by 0.0200609
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.192
ELB improved by 0.0169375
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.178
ELB improved by 0.0143837
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.165
ELB improved by 0.0123053
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.155
ELB improved by 0.0106246
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.145
ELB improved by 0.0092739
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-858.776
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-584.096
ELB improved by 274.68
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-523.223
ELB improved by 60.8731
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-480.872
ELB improved by 42.3515
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.56
ELB improved by 20.3119
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.122
ELB improved by 9.4375
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.141
ELB improved by 5.98128
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.861
ELB improved by 5.28007
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.507
ELB improved by 5.3537
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.198
ELB improved by 5.30884
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.453
ELB improved by 4.74565
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.741
ELB improved by 3.71131
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.167
ELB improved by 2.57427
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.492
ELB improved by 1.67564
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.396
ELB improved by 1.09563
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.645
ELB improved by 0.751043
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.1
ELB improved by 0.545194
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.684
ELB improved by 0.415858
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.354
ELB improved by 0.329527
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.086
ELB improved by 0.268721
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.862
ELB improved by 0.223995
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.672
ELB improved by 0.189945
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.508
ELB improved by 0.163296
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.366
ELB improved by 0.141966
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.242
ELB improved by 0.124575
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.132
ELB improved by 0.110177
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.033
ELB improved by 0.0981054
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.946
ELB improved by 0.0878734
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.866
ELB improved by 0.0791209
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.795
ELB improved by 0.0715743
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.73
ELB improved by 0.065022
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.671
ELB improved by 0.0592982
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.616
ELB improved by 0.0542707
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.566
ELB improved by 0.049833
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.521
ELB improved by 0.0458985
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.478
ELB improved by 0.0423961
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.439
ELB improved by 0.0392666
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.402
ELB improved by 0.0364608
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.369
ELB improved by 0.0339372
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.337
ELB improved by 0.0316609
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.307
ELB improved by 0.0296019
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.28
ELB improved by 0.0277347
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.253
ELB improved by 0.0260375
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.229
ELB improved by 0.0244912
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.206
ELB improved by 0.0230795
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.184
ELB improved by 0.0217879
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.164
ELB improved by 0.0206042
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.144
ELB improved by 0.0195172
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.125
ELB improved by 0.0185173
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.108
ELB improved by 0.0175961
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.091
ELB improved by 0.0167459
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.075
ELB improved by 0.0159601
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.06
ELB improved by 0.0152328
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.045
ELB improved by 0.0145585
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.031
ELB improved by 0.0139326
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.018
ELB improved by 0.0133509
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.005
ELB improved by 0.0128094
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.993
ELB improved by 0.0123048
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.981
ELB improved by 0.011834
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.97
ELB improved by 0.0113941
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.959
ELB improved by 0.0109827
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.948
ELB improved by 0.0105975
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.938
ELB improved by 0.0102363
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.928
ELB improved by 0.00989747
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-896.784
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-597.106
ELB improved by 299.677
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-534.592
ELB improved by 62.5148
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-491.993
ELB improved by 42.5989
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.394
ELB improved by 21.5985
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.307
ELB improved by 11.0874
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.025
ELB improved by 8.28154
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.549
ELB improved by 8.47671
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.764
ELB improved by 8.78432
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.998
ELB improved by 7.76587
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.328
ELB improved by 5.67066
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.678
ELB improved by 3.64972
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.364
ELB improved by 2.31422
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.833
ELB improved by 1.53093
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.776
ELB improved by 1.0566
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.986
ELB improved by 0.789938
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.336
ELB improved by 0.650208
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.768
ELB improved by 0.568427
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.273
ELB improved by 0.494421
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.864
ELB improved by 0.409012
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.535
ELB improved by 0.328877
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.264
ELB improved by 0.27193
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.026
ELB improved by 0.237837
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.806
ELB improved by 0.219271
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.595
ELB improved by 0.210932
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.385
ELB improved by 0.210515
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.167
ELB improved by 0.217606
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.934
ELB improved by 0.232879
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.677
ELB improved by 0.25753
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.385
ELB improved by 0.292423
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.048
ELB improved by 0.336669
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.661
ELB improved by 0.386786
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.222
ELB improved by 0.438772
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.731
ELB improved by 0.491663
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.183
ELB improved by 0.547188
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.577
ELB improved by 0.606492
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.908
ELB improved by 0.668696
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.177
ELB improved by 0.731275
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.386
ELB improved by 0.790907
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.541
ELB improved by 0.845082
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.646
ELB improved by 0.894739
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.702
ELB improved by 0.944676
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.713
ELB improved by 0.988498
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.736
ELB improved by 0.977097
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.863
ELB improved by 0.873466
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.104
ELB improved by 0.758609
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.354
ELB improved by 0.74992
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.452
ELB improved by 0.902292
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.376
ELB improved by 1.07585
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.326
ELB improved by 1.04961
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.53
ELB improved by 0.796408
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.052
ELB improved by 0.478102
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.79
ELB improved by 0.262167
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.634
ELB improved by 0.155884
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.526
ELB improved by 0.107546
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.442
ELB improved by 0.0837149
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.371
ELB improved by 0.0710305
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.307
ELB improved by 0.0647902
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.243
ELB improved by 0.0631542
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.179
ELB improved by 0.0646849
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.112
ELB improved by 0.0668016
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.047
ELB improved by 0.0653439
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.99
ELB improved by 0.0570954
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.946
ELB improved by 0.0436302
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.916
ELB improved by 0.0301611
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.895
ELB improved by 0.0203166
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.881
ELB improved by 0.0143509
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.87
ELB improved by 0.0109955
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.861
ELB improved by 0.00906738
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
1.100 0.110 1.275
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.013 | 0.011 | 0.025 | |
| getPIPs | 0.011 | 0.007 | 0.022 | |
| graper | 0.019 | 0.011 | 0.033 | |
| makeExampleData | 0.002 | 0.001 | 0.002 | |
| makeExampleDataWithUnequalGroups | 0.002 | 0.000 | 0.002 | |
| plotELBO | 0.115 | 0.009 | 0.142 | |
| plotGroupPenalties | 0.358 | 0.012 | 0.432 | |
| plotPosterior | 0.335 | 0.017 | 0.364 | |
| predict.graper | 0.216 | 0.040 | 0.288 | |
| print.graper | 0.011 | 0.009 | 0.034 | |