Britta Velten
| Snapshot Date: 2026-04-21 13:40 -0400 (Tue, 21 Apr 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 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-22 11:35 -0400 (Wed, 22 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4738 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4701 |
| 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 938/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.27.0 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| See other builds for graper in R Universe. | ||||||||||||||
|
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: 2026-04-21 20:08:08 -0400 (Tue, 21 Apr 2026) |
| EndedAt: 2026-04-21 20:08:40 -0400 (Tue, 21 Apr 2026) |
| EllapsedTime: 32.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck’
* using R version 4.6.0 alpha (2026-04-08 r89818)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-22 00:08:08 UTC
* 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 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.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/Resources/library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.27.0’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’ using SDK: ‘MacOSX26.2.sdk’ clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -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/Resources/library/00LOCK-graper/00new/graper/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (graper)
graper.Rcheck/tests/testthat.Rout
R version 4.6.0 alpha (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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=-880.264
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-588.841
ELB improved by 291.423
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-529.081
ELB improved by 59.7603
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-489.191
ELB improved by 39.8897
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.504
ELB improved by 17.6875
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.678
ELB improved by 7.82565
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.593
ELB improved by 5.08479
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.959
ELB improved by 4.63387
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.088
ELB improved by 4.87139
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.683
ELB improved by 5.40497
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.637
ELB improved by 6.04633
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.184
ELB improved by 6.45262
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.005
ELB improved by 6.17879
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.856
ELB improved by 5.1491
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.022
ELB improved by 3.8344
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.308
ELB improved by 2.71406
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.379
ELB improved by 1.92834
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.97
ELB improved by 1.409
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.915
ELB improved by 1.05497
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.128
ELB improved by 0.786902
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.562
ELB improved by 0.566233
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.161
ELB improved by 0.401511
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.865
ELB improved by 0.295667
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.634
ELB improved by 0.230855
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.445
ELB improved by 0.18891
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.286
ELB improved by 0.159206
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.149
ELB improved by 0.136576
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.031
ELB improved by 0.118544
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.927
ELB improved by 0.103812
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.835
ELB improved by 0.0915997
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.754
ELB improved by 0.0813809
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.681
ELB improved by 0.0727688
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.616
ELB improved by 0.065468
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.557
ELB improved by 0.0592477
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.503
ELB improved by 0.053925
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.453
ELB improved by 0.0493536
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.408
ELB improved by 0.0454149
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.366
ELB improved by 0.0420115
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.327
ELB improved by 0.0390621
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.29
ELB improved by 0.0364967
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.256
ELB improved by 0.0342538
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.224
ELB improved by 0.0322772
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.193
ELB improved by 0.0305151
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.164
ELB improved by 0.0289188
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.137
ELB improved by 0.027443
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.111
ELB improved by 0.0260476
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.086
ELB improved by 0.024699
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.063
ELB improved by 0.0233717
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.041
ELB improved by 0.02205
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.02
ELB improved by 0.0207274
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.001
ELB improved by 0.019406
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.983
ELB improved by 0.0180949
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.966
ELB improved by 0.0168075
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.95
ELB improved by 0.01556
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.936
ELB improved by 0.0143686
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.923
ELB improved by 0.0132478
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.91
ELB improved by 0.0122088
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.899
ELB improved by 0.0112586
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.889
ELB improved by 0.0103996
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.879
ELB improved by 0.00963025
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-917.755
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-584.302
ELB improved by 333.453
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-526.825
ELB improved by 57.477
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-496.863
ELB improved by 29.9621
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-484.556
ELB improved by 12.307
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-478.4
ELB improved by 6.15565
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.668
ELB improved by 4.73165
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.037
ELB improved by 4.63161
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.048
ELB improved by 4.9888
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.675
ELB improved by 5.37259
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.301
ELB improved by 5.37454
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.555
ELB improved by 4.74555
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.931
ELB improved by 3.62472
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.482
ELB improved by 2.44857
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.926
ELB improved by 1.55626
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.934
ELB improved by 0.991706
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.269
ELB improved by 0.665012
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.786
ELB improved by 0.482785
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.406
ELB improved by 0.379819
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.088
ELB improved by 0.318652
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.808
ELB improved by 0.279953
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.554
ELB improved by 0.25407
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.318
ELB improved by 0.236101
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.094
ELB improved by 0.223443
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.88
ELB improved by 0.214634
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.671
ELB improved by 0.208802
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.465
ELB improved by 0.205413
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.261
ELB improved by 0.204134
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.056
ELB improved by 0.204779
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.849
ELB improved by 0.207278
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.637
ELB improved by 0.211675
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.419
ELB improved by 0.218142
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.192
ELB improved by 0.226992
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.954
ELB improved by 0.238691
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.7
ELB improved by 0.253787
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.427
ELB improved by 0.272635
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.132
ELB improved by 0.29476
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.814
ELB improved by 0.318193
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.474
ELB improved by 0.340118
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.115
ELB improved by 0.359541
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.736
ELB improved by 0.37907
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.332
ELB improved by 0.403308
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.895
ELB improved by 0.436912
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.411
ELB improved by 0.484639
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.858
ELB improved by 0.552316
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.209
ELB improved by 0.649388
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.418
ELB improved by 0.791182
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.46
ELB improved by 0.957866
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.448
ELB improved by 1.01224
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.539
ELB improved by 0.908897
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.774
ELB improved by 0.765194
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.145
ELB improved by 0.62908
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.632
ELB improved by 0.512287
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.203
ELB improved by 0.429343
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.802
ELB improved by 0.400464
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.34
ELB improved by 0.462345
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.68
ELB improved by 0.659694
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.816
ELB improved by 0.864041
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.058
ELB improved by 0.757907
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.571
ELB improved by 0.487516
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.268
ELB improved by 0.303307
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.048
ELB improved by 0.219386
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.855
ELB improved by 0.193552
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.662
ELB improved by 0.19297
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.469
ELB improved by 0.192567
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.29
ELB improved by 0.178763
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.139
ELB improved by 0.151379
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.023
ELB improved by 0.116087
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.941
ELB improved by 0.0821975
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.884
ELB improved by 0.0571558
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.842
ELB improved by 0.0415963
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.81
ELB improved by 0.0324684
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.783
ELB improved by 0.0268916
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.759
ELB improved by 0.0231574
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.739
ELB improved by 0.0204126
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.721
ELB improved by 0.0182497
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.704
ELB improved by 0.0164682
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.689
ELB improved by 0.014961
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.676
ELB improved by 0.0136648
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.663
ELB improved by 0.0125382
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.652
ELB improved by 0.0115519
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.641
ELB improved by 0.0106836
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.631
ELB improved by 0.00991584
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-824.093
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-562.737
ELB improved by 261.356
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-502.303
ELB improved by 60.4347
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.82
ELB improved by 41.4823
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.919
ELB improved by 17.9011
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.149
ELB improved by 6.76999
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.116
ELB improved by 4.03376
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.808
ELB improved by 3.30725
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.607
ELB improved by 3.20124
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.237
ELB improved by 3.3701
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.641
ELB improved by 3.59567
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.981
ELB improved by 3.65994
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.617
ELB improved by 3.36392
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.909
ELB improved by 2.70891
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.963
ELB improved by 1.94561
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.632
ELB improved by 1.3312
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.702
ELB improved by 0.929404
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.037
ELB improved by 0.665129
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.563
ELB improved by 0.474585
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.214
ELB improved by 0.348629
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.939
ELB improved by 0.275261
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.705
ELB improved by 0.233304
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.497
ELB improved by 0.20854
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.303
ELB improved by 0.193693
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.118
ELB improved by 0.184993
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.938
ELB improved by 0.18033
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.759
ELB improved by 0.178435
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.581
ELB improved by 0.178526
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.401
ELB improved by 0.18013
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.218
ELB improved by 0.183017
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.031
ELB improved by 0.187176
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.838
ELB improved by 0.19282
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.637
ELB improved by 0.200428
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.426
ELB improved by 0.210819
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.201
ELB improved by 0.225237
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.956
ELB improved by 0.245355
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.683
ELB improved by 0.272827
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.375
ELB improved by 0.307742
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.029
ELB improved by 0.346182
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.649
ELB improved by 0.380399
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.244
ELB improved by 0.404536
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.826
ELB improved by 0.418177
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.403
ELB improved by 0.422761
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.984
ELB improved by 0.419379
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.574
ELB improved by 0.409624
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.179
ELB improved by 0.395036
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.804
ELB improved by 0.375711
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.452
ELB improved by 0.351037
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.131
ELB improved by 0.321901
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.839
ELB improved by 0.291394
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.576
ELB improved by 0.263561
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.334
ELB improved by 0.241993
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.104
ELB improved by 0.229141
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.879
ELB improved by 0.225986
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.646
ELB improved by 0.232364
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.395
ELB improved by 0.250673
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.099
ELB improved by 0.296369
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.697
ELB improved by 0.40198
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.175
ELB improved by 0.522431
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.728
ELB improved by 0.446305
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.469
ELB improved by 0.259841
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.317
ELB improved by 0.151451
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.213
ELB improved by 0.104512
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.131
ELB improved by 0.0814049
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.064
ELB improved by 0.067012
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.008
ELB improved by 0.0563569
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.96
ELB improved by 0.0478127
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.919
ELB improved by 0.0408029
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.884
ELB improved by 0.0350529
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.854
ELB improved by 0.0303556
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.827
ELB improved by 0.026518
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.804
ELB improved by 0.0233645
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.783
ELB improved by 0.0207464
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.765
ELB improved by 0.0185463
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.748
ELB improved by 0.0166751
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.733
ELB improved by 0.0150664
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.719
ELB improved by 0.013671
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.707
ELB improved by 0.012452
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.695
ELB improved by 0.0113808
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.685
ELB improved by 0.0104354
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.675
ELB improved by 0.00959787
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-873.435
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-579.187
ELB improved by 294.248
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-522.049
ELB improved by 57.1383
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-483.799
ELB improved by 38.2497
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.111
ELB improved by 18.6879
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.261
ELB improved by 7.85065
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.422
ELB improved by 3.8391
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.809
ELB improved by 2.61226
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.543
ELB improved by 2.26629
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.304
ELB improved by 2.23879
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.007
ELB improved by 2.29788
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.696
ELB improved by 2.31088
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.51
ELB improved by 2.18607
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.606
ELB improved by 1.90318
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.075
ELB improved by 1.53144
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.901
ELB improved by 1.17368
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.011
ELB improved by 0.889889
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.33
ELB improved by 0.681078
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.803
ELB improved by 0.527078
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.387
ELB improved by 0.416204
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.045
ELB improved by 0.341795
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.751
ELB improved by 0.294577
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.485
ELB improved by 0.265165
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.239
ELB improved by 0.246825
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.003
ELB improved by 0.235321
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.775
ELB improved by 0.227993
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.552
ELB improved by 0.223109
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.333
ELB improved by 0.219518
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.116
ELB improved by 0.216461
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.903
ELB improved by 0.21348
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.692
ELB improved by 0.210347
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.485
ELB improved by 0.207014
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.282
ELB improved by 0.203562
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.082
ELB improved by 0.200149
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.885
ELB improved by 0.196961
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.691
ELB improved by 0.194167
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.499
ELB improved by 0.191884
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.309
ELB improved by 0.190158
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.12
ELB improved by 0.188947
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.931
ELB improved by 0.188126
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.744
ELB improved by 0.187489
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.557
ELB improved by 0.186773
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.372
ELB improved by 0.185672
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.188
ELB improved by 0.183868
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.007
ELB improved by 0.181056
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.83
ELB improved by 0.176981
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.658
ELB improved by 0.171457
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.494
ELB improved by 0.164403
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.338
ELB improved by 0.155856
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.192
ELB improved by 0.145974
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.057
ELB improved by 0.135026
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.934
ELB improved by 0.123362
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.822
ELB improved by 0.111377
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.723
ELB improved by 0.0994602
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.635
ELB improved by 0.0879629
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.558
ELB improved by 0.0771643
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.49
ELB improved by 0.0672596
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.432
ELB improved by 0.058359
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.381
ELB improved by 0.0504979
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.338
ELB improved by 0.043653
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.3
ELB improved by 0.03776
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.267
ELB improved by 0.0327304
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.239
ELB improved by 0.0284644
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.214
ELB improved by 0.0248609
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.192
ELB improved by 0.0218238
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.173
ELB improved by 0.0192656
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.156
ELB improved by 0.0171091
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.141
ELB improved by 0.0152876
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.127
ELB improved by 0.0137443
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.114
ELB improved by 0.0124317
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.103
ELB improved by 0.0113102
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.093
ELB improved by 0.0103472
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.083
ELB improved by 0.00951564
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
1.037 0.085 1.120
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.029 | 0.007 | 0.036 | |
| getPIPs | 0.027 | 0.007 | 0.033 | |
| graper | 0.044 | 0.010 | 0.054 | |
| makeExampleData | 0.004 | 0.000 | 0.004 | |
| makeExampleDataWithUnequalGroups | 0.004 | 0.001 | 0.004 | |
| plotELBO | 0.124 | 0.007 | 0.131 | |
| plotGroupPenalties | 0.442 | 0.013 | 0.468 | |
| plotPosterior | 0.233 | 0.011 | 0.248 | |
| predict.graper | 1.025 | 0.047 | 1.076 | |
| print.graper | 0.027 | 0.007 | 0.034 | |