Britta Velten
| Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: 82b0592 |
| git_last_commit_date: 2025-06-24 03:15:40 -0400 (Tue, 24 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-30 12:06 -0400 (Sat, 30 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
| 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 907/2320 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.25.2 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.25.2 |
| 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_1.25.2.tar.gz |
| StartedAt: 2025-08-29 21:15:26 -0400 (Fri, 29 Aug 2025) |
| EndedAt: 2025-08-29 21:16:43 -0400 (Fri, 29 Aug 2025) |
| EllapsedTime: 76.7 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_1.25.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.25.2’
* 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 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.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 ... NOTE
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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.22-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/4.5-x86_64/Resources/library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.25.2’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-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 version 4.5.1 (2025-06-13) -- "Great Square Root"
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=-915.589
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-611.935
ELB improved by 303.654
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-548.026
ELB improved by 63.9092
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-504.043
ELB improved by 43.9823
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-480.061
ELB improved by 23.9825
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.43
ELB improved by 12.6313
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.693
ELB improved by 7.73645
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.326
ELB improved by 6.36753
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.954
ELB improved by 6.37136
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.177
ELB improved by 6.77691
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.213
ELB improved by 6.96413
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.742
ELB improved by 6.47146
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.41
ELB improved by 5.3317
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.405
ELB improved by 4.00547
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.52
ELB improved by 2.88456
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.446
ELB improved by 2.07375
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.932
ELB improved by 1.51421
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.813
ELB improved by 1.1188
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.978
ELB improved by 0.834909
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.341
ELB improved by 0.637478
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.838
ELB improved by 0.503209
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.427
ELB improved by 0.410847
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.081
ELB improved by 0.345412
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.784
ELB improved by 0.297587
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.522
ELB improved by 0.261756
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.288
ELB improved by 0.234478
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.074
ELB improved by 0.213578
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.876
ELB improved by 0.197628
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.691
ELB improved by 0.185656
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.514
ELB improved by 0.176931
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.343
ELB improved by 0.170784
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.177
ELB improved by 0.166443
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.014
ELB improved by 0.162959
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.854
ELB improved by 0.159353
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.699
ELB improved by 0.15498
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.549
ELB improved by 0.149836
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.405
ELB improved by 0.144437
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.266
ELB improved by 0.139403
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.13
ELB improved by 0.135138
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.999
ELB improved by 0.131785
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.869
ELB improved by 0.129334
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.742
ELB improved by 0.127717
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.615
ELB improved by 0.126851
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.488
ELB improved by 0.126657
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.361
ELB improved by 0.12705
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.233
ELB improved by 0.127939
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.104
ELB improved by 0.129217
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.973
ELB improved by 0.13076
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.841
ELB improved by 0.132424
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.707
ELB improved by 0.134048
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.571
ELB improved by 0.135467
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.435
ELB improved by 0.136518
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.298
ELB improved by 0.137069
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.161
ELB improved by 0.137039
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.024
ELB improved by 0.136438
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.889
ELB improved by 0.135399
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.754
ELB improved by 0.134224
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.621
ELB improved by 0.133451
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.487
ELB improved by 0.133956
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.35
ELB improved by 0.137148
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.205
ELB improved by 0.145258
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.043
ELB improved by 0.161571
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.854
ELB improved by 0.189595
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.625
ELB improved by 0.228755
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.357
ELB improved by 0.26728
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.074
ELB improved by 0.28392
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.812
ELB improved by 0.26107
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.611
ELB improved by 0.201988
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.474
ELB improved by 0.136488
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.386
ELB improved by 0.087975
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.328
ELB improved by 0.057951
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.288
ELB improved by 0.0401414
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.259
ELB improved by 0.0293725
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.236
ELB improved by 0.0225915
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.218
ELB improved by 0.018125
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.203
ELB improved by 0.0150558
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.19
ELB improved by 0.012867
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.179
ELB improved by 0.0112562
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.169
ELB improved by 0.0100387
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.16
ELB improved by 0.00909668
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-887.411
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-572.358
ELB improved by 315.053
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-512.295
ELB improved by 60.0631
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-478.403
ELB improved by 33.8922
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.561
ELB improved by 13.8418
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.494
ELB improved by 6.06717
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.483
ELB improved by 4.01098
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.05
ELB improved by 3.43246
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.79
ELB improved by 3.2598
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.578
ELB improved by 3.21291
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.397
ELB improved by 3.18079
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.289
ELB improved by 3.10781
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.3
ELB improved by 2.98864
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.471
ELB improved by 2.82941
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.912
ELB improved by 2.55861
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.804
ELB improved by 2.10782
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.18
ELB improved by 1.62411
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.938
ELB improved by 1.24212
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.968
ELB improved by 0.969798
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.178
ELB improved by 0.790762
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.493
ELB improved by 0.684352
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.865
ELB improved by 0.62786
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.263
ELB improved by 0.602651
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.666
ELB improved by 0.59703
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.06
ELB improved by 0.605776
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.433
ELB improved by 0.627024
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.778
ELB improved by 0.654664
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.109
ELB improved by 0.66933
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.459
ELB improved by 0.649487
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.86
ELB improved by 0.599258
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.319
ELB improved by 0.540938
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.83
ELB improved by 0.489038
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.383
ELB improved by 0.447064
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.969
ELB improved by 0.414184
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.58
ELB improved by 0.388824
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.211
ELB improved by 0.369586
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.855
ELB improved by 0.35534
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.51
ELB improved by 0.34515
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.172
ELB improved by 0.3382
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.838
ELB improved by 0.333758
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.507
ELB improved by 0.33123
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.176
ELB improved by 0.330402
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.844
ELB improved by 0.332085
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.505
ELB improved by 0.33958
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.143
ELB improved by 0.361475
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.729
ELB improved by 0.413992
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.219
ELB improved by 0.510242
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.579
ELB improved by 0.63982
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.763
ELB improved by 0.815865
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.782
ELB improved by 0.981539
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.905
ELB improved by 0.876614
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.302
ELB improved by 0.603531
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.899
ELB improved by 0.403215
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.614
ELB improved by 0.284038
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.402
ELB improved by 0.212359
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.234
ELB improved by 0.168306
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.093
ELB improved by 0.140683
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.971
ELB improved by 0.121921
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.865
ELB improved by 0.106637
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.772
ELB improved by 0.0921752
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.694
ELB improved by 0.0784871
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.627
ELB improved by 0.0665482
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.57
ELB improved by 0.0569454
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.521
ELB improved by 0.0496463
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.476
ELB improved by 0.0443527
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.436
ELB improved by 0.0407695
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.397
ELB improved by 0.0386777
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.359
ELB improved by 0.0379087
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.321
ELB improved by 0.0382827
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.281
ELB improved by 0.0395175
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.24
ELB improved by 0.0410991
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.198
ELB improved by 0.0421709
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.156
ELB improved by 0.0416266
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.118
ELB improved by 0.0386114
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.085
ELB improved by 0.0332138
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.058
ELB improved by 0.0266004
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.038
ELB improved by 0.0202757
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.022
ELB improved by 0.0152149
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.011
ELB improved by 0.0116343
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.002
ELB improved by 0.00928237
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-848.484
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-583.991
ELB improved by 264.492
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-523.186
ELB improved by 60.805
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-478.107
ELB improved by 45.0792
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.236
ELB improved by 22.8707
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.631
ELB improved by 9.60536
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.48
ELB improved by 5.15061
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.34
ELB improved by 4.14048
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.256
ELB improved by 4.08427
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.887
ELB improved by 4.3684
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.02
ELB improved by 4.86755
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.603
ELB improved by 5.41666
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.997
ELB improved by 5.60572
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.009
ELB improved by 4.98809
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.312
ELB improved by 3.69735
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.917
ELB improved by 2.39463
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.422
ELB improved by 1.49547
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.447
ELB improved by 0.975255
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.76
ELB improved by 0.686422
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.236
ELB improved by 0.523872
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.813
ELB improved by 0.42359
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.467
ELB improved by 0.346057
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.186
ELB improved by 0.280272
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.955
ELB improved by 0.231582
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.755
ELB improved by 0.19977
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.576
ELB improved by 0.178818
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.412
ELB improved by 0.163704
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.261
ELB improved by 0.151778
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.119
ELB improved by 0.141798
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.986
ELB improved by 0.133156
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.86
ELB improved by 0.125524
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.742
ELB improved by 0.118714
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.629
ELB improved by 0.112619
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.522
ELB improved by 0.107187
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.419
ELB improved by 0.102407
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.321
ELB improved by 0.0983067
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.226
ELB improved by 0.0949477
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.134
ELB improved by 0.0924404
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.043
ELB improved by 0.0909641
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.952
ELB improved by 0.090812
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.859
ELB improved by 0.0924777
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.763
ELB improved by 0.0968247
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.657
ELB improved by 0.105422
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.536
ELB improved by 0.121182
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.387
ELB improved by 0.149338
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.189
ELB improved by 0.197765
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.917
ELB improved by 0.272125
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.553
ELB improved by 0.363907
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.09
ELB improved by 0.462541
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.474
ELB improved by 0.615805
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.458
ELB improved by 1.01644
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.557
ELB improved by 1.9008
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.216
ELB improved by 2.34166
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.162
ELB improved by 2.05314
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.346
ELB improved by 1.81612
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.803
ELB improved by 1.54344
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.588
ELB improved by 1.21486
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.698
ELB improved by 0.889825
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.089
ELB improved by 0.608993
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.696
ELB improved by 0.393445
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.448
ELB improved by 0.247379
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.292
ELB improved by 0.156695
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.189
ELB improved by 0.102333
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.12
ELB improved by 0.0696917
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.07
ELB improved by 0.0496922
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.033
ELB improved by 0.0370858
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.004
ELB improved by 0.0288786
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.981
ELB improved by 0.0233453
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.961
ELB improved by 0.0194744
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.944
ELB improved by 0.0166626
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.93
ELB improved by 0.0145432
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.917
ELB improved by 0.01289
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.906
ELB improved by 0.0115605
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.895
ELB improved by 0.0104634
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.885
ELB improved by 0.00953897
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-833.3
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-580.659
ELB improved by 252.64
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-519.847
ELB improved by 60.8125
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.01
ELB improved by 49.8368
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.315
ELB improved by 28.6951
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.767
ELB improved by 11.5473
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.676
ELB improved by 5.09118
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.433
ELB improved by 3.24326
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.012
ELB improved by 2.42056
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.996
ELB improved by 2.01688
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.193
ELB improved by 1.80236
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.524
ELB improved by 1.66918
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.955
ELB improved by 1.56885
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.476
ELB improved by 1.47945
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.085
ELB improved by 1.39108
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.786
ELB improved by 1.299
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.585
ELB improved by 1.20099
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.488
ELB improved by 1.09679
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.5
ELB improved by 0.988189
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.621
ELB improved by 0.878525
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.849
ELB improved by 0.771767
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.178
ELB improved by 0.67149
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.598
ELB improved by 0.580331
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.098
ELB improved by 0.499962
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.666
ELB improved by 0.431309
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.292
ELB improved by 0.374735
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.961
ELB improved by 0.330106
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.665
ELB improved by 0.296829
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.391
ELB improved by 0.273946
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.13
ELB improved by 0.260318
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.876
ELB improved by 0.254819
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.619
ELB improved by 0.256497
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.354
ELB improved by 0.264654
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.076
ELB improved by 0.278885
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.776
ELB improved by 0.299083
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.451
ELB improved by 0.325456
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.092
ELB improved by 0.358601
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.693
ELB improved by 0.399692
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.242
ELB improved by 0.450843
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.726
ELB improved by 0.515505
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.128
ELB improved by 0.598043
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.428
ELB improved by 0.700161
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.614
ELB improved by 0.813832
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.691
ELB improved by 0.923334
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.666
ELB improved by 1.02495
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.535
ELB improved by 1.13131
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.283
ELB improved by 1.25181
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.905
ELB improved by 1.3775
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.438
ELB improved by 1.4679
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.984
ELB improved by 1.45388
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.682
ELB improved by 1.30138
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.619
ELB improved by 1.06313
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.804
ELB improved by 0.815245
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.205
ELB improved by 0.599091
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.774
ELB improved by 0.431171
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.458
ELB improved by 0.315704
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.211
ELB improved by 0.246904
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.998
ELB improved by 0.213417
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.796
ELB improved by 0.201446
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.602
ELB improved by 0.194346
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.425
ELB improved by 0.176542
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.281
ELB improved by 0.144495
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.173
ELB improved by 0.107644
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.097
ELB improved by 0.0758584
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.045
ELB improved by 0.0526346
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.007
ELB improved by 0.0371504
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.98
ELB improved by 0.0272894
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.959
ELB improved by 0.0210803
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.942
ELB improved by 0.0170972
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.928
ELB improved by 0.014431
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.915
ELB improved by 0.0125428
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.904
ELB improved by 0.0111259
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.894
ELB improved by 0.0100081
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.885
ELB improved by 0.00909204
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.464 0.246 2.718
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.050 | 0.017 | 0.067 | |
| getPIPs | 0.045 | 0.013 | 0.060 | |
| graper | 0.079 | 0.021 | 0.101 | |
| makeExampleData | 0.009 | 0.001 | 0.010 | |
| makeExampleDataWithUnequalGroups | 0.011 | 0.002 | 0.012 | |
| plotELBO | 0.258 | 0.022 | 0.282 | |
| plotGroupPenalties | 0.775 | 0.021 | 0.800 | |
| plotPosterior | 0.592 | 0.021 | 0.615 | |
| predict.graper | 1.915 | 0.088 | 2.012 | |
| print.graper | 0.046 | 0.013 | 0.060 | |