Britta Velten
| Snapshot Date: 2025-11-18 13:40 -0500 (Tue, 18 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: 95474d7 |
| git_last_commit_date: 2025-10-29 10:49:21 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-19 10:13 -0500 (Wed, 19 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4827 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4600 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4564 |
| 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 911/2325 | 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 | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: graper |
| Version: 1.27.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.27.0.tar.gz |
| StartedAt: 2025-11-18 21:29:32 -0500 (Tue, 18 Nov 2025) |
| EndedAt: 2025-11-18 21:30:57 -0500 (Tue, 18 Nov 2025) |
| EllapsedTime: 85.2 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) (2025-10-21 r88958)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
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 14.0.3 (clang-1403.0.22.14.1)’
* 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-x86_64/Resources/library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.27.0’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’ using SDK: ‘MacOSX11.3.1.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fit_graper.cpp -o fit_graper.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/x86_64-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-x86_64/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) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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=-863.83
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-575.85
ELB improved by 287.98
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-515.544
ELB improved by 60.3067
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-474.114
ELB improved by 41.4296
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.251
ELB improved by 20.8634
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.075
ELB improved by 9.17605
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.534
ELB improved by 5.5404
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.155
ELB improved by 4.37949
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.042
ELB improved by 4.1122
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.86
ELB improved by 4.18218
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.534
ELB improved by 4.32628
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.186
ELB improved by 4.34829
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.158
ELB improved by 4.02783
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.866
ELB improved by 3.29192
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.468
ELB improved by 2.39755
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.798
ELB improved by 1.67068
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.62
ELB improved by 1.1774
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.769
ELB improved by 0.851495
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.121
ELB improved by 0.647858
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.593
ELB improved by 0.527791
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.135
ELB improved by 0.458295
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.717
ELB improved by 0.418318
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.32
ELB improved by 0.396111
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.935
ELB improved by 0.385377
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.552
ELB improved by 0.382834
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.165
ELB improved by 0.386981
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.768
ELB improved by 0.397588
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.352
ELB improved by 0.415654
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.908
ELB improved by 0.443783
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.421
ELB improved by 0.487186
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.865
ELB improved by 0.555822
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.197
ELB improved by 0.668279
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.342
ELB improved by 0.855241
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.194
ELB improved by 1.14728
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.672
ELB improved by 1.52287
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.803
ELB improved by 1.86819
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.725
ELB improved by 2.07813
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.596
ELB improved by 2.12889
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.591
ELB improved by 2.00499
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.835
ELB improved by 1.75682
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.373
ELB improved by 1.46106
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.212
ELB improved by 1.16129
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.273
ELB improved by 0.939145
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.417
ELB improved by 0.856176
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.553
ELB improved by 0.863629
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.829
ELB improved by 0.724093
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.348
ELB improved by 0.481064
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.002
ELB improved by 0.345756
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.702
ELB improved by 0.299892
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.448
ELB improved by 0.254776
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.269
ELB improved by 0.178839
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.159
ELB improved by 0.1094
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.092
ELB improved by 0.0674509
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.046
ELB improved by 0.0458844
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.011
ELB improved by 0.0346519
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.983
ELB improved by 0.0280803
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.96
ELB improved by 0.0236471
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.939
ELB improved by 0.0203118
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.922
ELB improved by 0.0176387
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.906
ELB improved by 0.0154269
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.893
ELB improved by 0.013568
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.881
ELB improved by 0.0119929
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.87
ELB improved by 0.0106517
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.861
ELB improved by 0.00950555
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-905.085
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-580.226
ELB improved by 324.859
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-520.59
ELB improved by 59.6358
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-486.772
ELB improved by 33.8187
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.383
ELB improved by 13.3886
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.468
ELB improved by 5.91522
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.118
ELB improved by 4.34973
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.805
ELB improved by 4.31304
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.07
ELB improved by 4.73475
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.626
ELB improved by 5.44428
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.386
ELB improved by 6.2397
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.773
ELB improved by 6.61309
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.687
ELB improved by 6.08616
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.781
ELB improved by 4.9057
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.179
ELB improved by 3.60225
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.62
ELB improved by 2.55861
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.734
ELB improved by 1.88672
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.236
ELB improved by 1.49761
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.959
ELB improved by 1.27693
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.818
ELB improved by 1.14101
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.778
ELB improved by 1.04044
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.826
ELB improved by 0.951742
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.958
ELB improved by 0.868056
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.166
ELB improved by 0.791504
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.438
ELB improved by 0.728478
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.749
ELB improved by 0.689143
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.056
ELB improved by 0.692495
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.284
ELB improved by 0.772522
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.356
ELB improved by 0.927914
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.362
ELB improved by 0.993916
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.452
ELB improved by 0.909903
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.633
ELB improved by 0.818733
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.879
ELB improved by 0.754377
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.184
ELB improved by 0.695299
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.561
ELB improved by 0.622577
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.03
ELB improved by 0.531499
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.598
ELB improved by 0.431527
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.262
ELB improved by 0.336248
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.007
ELB improved by 0.254882
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.816
ELB improved by 0.190554
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.674
ELB improved by 0.142226
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.567
ELB improved by 0.107019
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.485
ELB improved by 0.0817517
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.422
ELB improved by 0.0636698
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.371
ELB improved by 0.0506473
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.33
ELB improved by 0.041147
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.296
ELB improved by 0.0340965
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.267
ELB improved by 0.0287618
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.242
ELB improved by 0.0246432
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.221
ELB improved by 0.0214
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.202
ELB improved by 0.0187974
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.186
ELB improved by 0.016672
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.171
ELB improved by 0.0149081
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.157
ELB improved by 0.0134225
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.145
ELB improved by 0.0121544
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.134
ELB improved by 0.011059
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.124
ELB improved by 0.0101027
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.115
ELB improved by 0.0092604
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-858.823
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-578.737
ELB improved by 280.086
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-517.319
ELB improved by 61.4185
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-474.833
ELB improved by 42.4859
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.569
ELB improved by 19.2641
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.031
ELB improved by 7.53806
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.57
ELB improved by 4.46058
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.829
ELB improved by 3.74133
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.296
ELB improved by 3.53309
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.851
ELB improved by 3.44454
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.516
ELB improved by 3.33552
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.376
ELB improved by 3.14014
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.553
ELB improved by 2.82294
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.173
ELB improved by 2.37966
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.32
ELB improved by 1.8525
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.985
ELB improved by 1.3352
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.062
ELB improved by 0.923197
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.415
ELB improved by 0.646908
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.936
ELB improved by 0.479329
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.556
ELB improved by 0.380291
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.236
ELB improved by 0.319906
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.955
ELB improved by 0.280794
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.701
ELB improved by 0.253849
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.467
ELB improved by 0.234436
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.246
ELB improved by 0.220163
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.037
ELB improved by 0.20973
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.834
ELB improved by 0.202367
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.637
ELB improved by 0.197564
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.442
ELB improved by 0.194939
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.248
ELB improved by 0.194179
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.053
ELB improved by 0.195019
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.855
ELB improved by 0.19724
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.655
ELB improved by 0.200667
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.449
ELB improved by 0.205183
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.239
ELB improved by 0.210737
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.021
ELB improved by 0.217357
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.796
ELB improved by 0.225161
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.562
ELB improved by 0.234362
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.317
ELB improved by 0.245271
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.058
ELB improved by 0.258284
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.784
ELB improved by 0.273863
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.492
ELB improved by 0.292485
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.177
ELB improved by 0.314546
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.837
ELB improved by 0.340207
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.468
ELB improved by 0.369133
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.068
ELB improved by 0.400165
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.637
ELB improved by 0.430986
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.179
ELB improved by 0.45802
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.702
ELB improved by 0.476814
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.219
ELB improved by 0.483029
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.745
ELB improved by 0.473807
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.296
ELB improved by 0.448975
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.885
ELB improved by 0.411495
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.518
ELB improved by 0.366809
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.197
ELB improved by 0.321372
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.916
ELB improved by 0.28106
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.665
ELB improved by 0.250101
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.435
ELB improved by 0.230451
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.214
ELB improved by 0.220895
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.998
ELB improved by 0.215611
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.794
ELB improved by 0.204863
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.612
ELB improved by 0.181959
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.461
ELB improved by 0.150721
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.34
ELB improved by 0.120965
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.241
ELB improved by 0.0986288
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.157
ELB improved by 0.0838593
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.083
ELB improved by 0.074189
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.017
ELB improved by 0.0667781
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.957
ELB improved by 0.0593253
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.906
ELB improved by 0.0507256
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.865
ELB improved by 0.0413705
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.833
ELB improved by 0.0325154
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.807
ELB improved by 0.0251812
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.788
ELB improved by 0.0196361
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.772
ELB improved by 0.0156139
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.759
ELB improved by 0.0127029
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.749
ELB improved by 0.0105559
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.74
ELB improved by 0.00893257
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-858.418
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-580.665
ELB improved by 277.753
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-518.942
ELB improved by 61.7235
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-477.416
ELB improved by 41.5261
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.949
ELB improved by 18.467
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.269
ELB improved by 7.67993
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.666
ELB improved by 4.60318
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.78
ELB improved by 3.88579
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.963
ELB improved by 3.81678
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.052
ELB improved by 3.91137
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.167
ELB improved by 3.88435
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.62
ELB improved by 3.54745
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.721
ELB improved by 2.89908
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.59
ELB improved by 2.1308
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.139
ELB improved by 1.45081
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.188
ELB improved by 0.950751
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.557
ELB improved by 0.631691
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.111
ELB improved by 0.445352
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.775
ELB improved by 0.336359
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.506
ELB improved by 0.268741
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.283
ELB improved by 0.223733
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.091
ELB improved by 0.19187
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.922
ELB improved by 0.168176
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.773
ELB improved by 0.149865
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.637
ELB improved by 0.135271
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.514
ELB improved by 0.12334
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.401
ELB improved by 0.113375
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.296
ELB improved by 0.104897
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.198
ELB improved by 0.0975637
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.107
ELB improved by 0.0911238
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.022
ELB improved by 0.0853901
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.941
ELB improved by 0.0802189
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.866
ELB improved by 0.0754987
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.795
ELB improved by 0.0711419
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.728
ELB improved by 0.0670798
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.664
ELB improved by 0.0632611
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.605
ELB improved by 0.0596517
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.549
ELB improved by 0.0562349
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.496
ELB improved by 0.0530094
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.446
ELB improved by 0.0499856
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.398
ELB improved by 0.0471799
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.354
ELB improved by 0.0446085
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.312
ELB improved by 0.0422846
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.271
ELB improved by 0.0402158
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.233
ELB improved by 0.0384057
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.196
ELB improved by 0.0368548
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.16
ELB improved by 0.0355617
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.126
ELB improved by 0.0345235
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.092
ELB improved by 0.0337341
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.059
ELB improved by 0.03318
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.026
ELB improved by 0.0328344
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.994
ELB improved by 0.0326474
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.961
ELB improved by 0.0325373
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.929
ELB improved by 0.032386
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.897
ELB improved by 0.0320473
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.865
ELB improved by 0.0313734
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.835
ELB improved by 0.030258
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.806
ELB improved by 0.0286772
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.78
ELB improved by 0.0267053
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.755
ELB improved by 0.0244909
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.733
ELB improved by 0.0222085
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.713
ELB improved by 0.0200095
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.695
ELB improved by 0.0179956
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.679
ELB improved by 0.0162154
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.664
ELB improved by 0.0146766
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.651
ELB improved by 0.0133614
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.638
ELB improved by 0.0122404
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.627
ELB improved by 0.0112817
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.617
ELB improved by 0.0104555
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.607
ELB improved by 0.00973656
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.689 0.285 3.009
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.053 | 0.018 | 0.071 | |
| getPIPs | 0.048 | 0.015 | 0.064 | |
| graper | 0.100 | 0.024 | 0.125 | |
| makeExampleData | 0.009 | 0.001 | 0.010 | |
| makeExampleDataWithUnequalGroups | 0.012 | 0.001 | 0.013 | |
| plotELBO | 0.323 | 0.021 | 0.347 | |
| plotGroupPenalties | 1.219 | 0.040 | 1.267 | |
| plotPosterior | 0.708 | 0.034 | 0.747 | |
| predict.graper | 1.765 | 0.064 | 1.834 | |
| print.graper | 0.045 | 0.010 | 0.055 | |