Britta Velten
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: RELEASE_3_21 |
| git_last_commit: fb5f237 |
| git_last_commit_date: 2025-06-24 03:18:49 -0400 (Tue, 24 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:39 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 915/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.24.2 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | 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: 1.24.2 |
| 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_1.24.2.tar.gz |
| StartedAt: 2025-10-14 04:46:26 -0400 (Tue, 14 Oct 2025) |
| EndedAt: 2025-10-14 04:48:46 -0400 (Tue, 14 Oct 2025) |
| EllapsedTime: 140.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.24.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/graper.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘1.24.2’
* 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-3.21-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 ‘1.24.2’ ** 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 RC (2025-06-05 r88288) -- "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=-873.986
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-573.958
ELB improved by 300.028
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-516.792
ELB improved by 57.1657
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-483.018
ELB improved by 33.7746
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.26
ELB improved by 16.7578
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.705
ELB improved by 7.55478
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.169
ELB improved by 4.53615
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.253
ELB improved by 3.91619
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.352
ELB improved by 3.90029
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.332
ELB improved by 4.02009
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.354
ELB improved by 3.97862
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.807
ELB improved by 3.5463
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.028
ELB improved by 2.77919
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.047
ELB improved by 1.9814
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.674
ELB improved by 1.37293
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.696
ELB improved by 0.977569
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.956
ELB improved by 0.740207
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.351
ELB improved by 0.604844
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.821
ELB improved by 0.530089
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.33
ELB improved by 0.491112
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.855
ELB improved by 0.475308
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.378
ELB improved by 0.47667
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.884
ELB improved by 0.49394
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.355
ELB improved by 0.529142
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.77
ELB improved by 0.585388
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.103
ELB improved by 0.666426
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.326
ELB improved by 0.77738
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.401
ELB improved by 0.924936
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.285
ELB improved by 1.11596
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.931
ELB improved by 1.35354
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.303
ELB improved by 1.62866
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.396
ELB improved by 1.90675
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.279
ELB improved by 2.11721
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.106
ELB improved by 2.17217
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.076
ELB improved by 2.03013
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.328
ELB improved by 1.7485
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.877
ELB improved by 1.45086
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.627
ELB improved by 1.25031
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.419
ELB improved by 1.20753
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.182
ELB improved by 1.23725
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.084
ELB improved by 1.09797
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.257
ELB improved by 0.827206
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.69
ELB improved by 0.566572
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.326
ELB improved by 0.364228
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.077
ELB improved by 0.248658
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.879
ELB improved by 0.198231
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.695
ELB improved by 0.184519
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.506
ELB improved by 0.188926
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.319
ELB improved by 0.186878
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.157
ELB improved by 0.16135
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.028
ELB improved by 0.129049
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.916
ELB improved by 0.112829
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.795
ELB improved by 0.120766
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.634
ELB improved by 0.160958
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.388
ELB improved by 0.245781
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.035
ELB improved by 0.353009
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.648
ELB improved by 0.386518
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.36
ELB improved by 0.288981
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.203
ELB improved by 0.156194
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.126
ELB improved by 0.0772855
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.083
ELB improved by 0.0434259
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.053
ELB improved by 0.0294657
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.03
ELB improved by 0.0230405
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.011
ELB improved by 0.0194688
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.994
ELB improved by 0.0170646
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.978
ELB improved by 0.0152171
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.965
ELB improved by 0.0136939
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.952
ELB improved by 0.0123963
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.941
ELB improved by 0.0112738
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.931
ELB improved by 0.010295
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.921
ELB improved by 0.0094374
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-852.534
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-571.785
ELB improved by 280.749
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-511.982
ELB improved by 59.8033
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.112
ELB improved by 39.87
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.436
ELB improved by 19.6761
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.743
ELB improved by 8.69245
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.111
ELB improved by 4.63209
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.835
ELB improved by 3.27634
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.96
ELB improved by 2.87488
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.076
ELB improved by 2.88456
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.05
ELB improved by 3.02552
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.957
ELB improved by 3.09299
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.031
ELB improved by 2.92578
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.54
ELB improved by 2.4912
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.609
ELB improved by 1.93068
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.185
ELB improved by 1.42484
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.134
ELB improved by 1.05102
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.337
ELB improved by 0.797064
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.705
ELB improved by 0.631289
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.178
ELB improved by 0.52675
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.718
ELB improved by 0.460501
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.302
ELB improved by 0.416029
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.916
ELB improved by 0.385451
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.55
ELB improved by 0.366052
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.195
ELB improved by 0.355571
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.844
ELB improved by 0.351197
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.493
ELB improved by 0.350498
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.141
ELB improved by 0.351845
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.787
ELB improved by 0.354258
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.43
ELB improved by 0.35717
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.07
ELB improved by 0.360299
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.706
ELB improved by 0.363651
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.338
ELB improved by 0.367576
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.966
ELB improved by 0.372791
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.585
ELB improved by 0.380292
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.194
ELB improved by 0.391211
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.787
ELB improved by 0.406622
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.36
ELB improved by 0.426996
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.91
ELB improved by 0.450455
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.44
ELB improved by 0.469536
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.969
ELB improved by 0.471302
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.521
ELB improved by 0.448394
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.112
ELB improved by 0.408844
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.745
ELB improved by 0.366959
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.413
ELB improved by 0.332004
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.106
ELB improved by 0.307227
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.816
ELB improved by 0.290237
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.544
ELB improved by 0.271897
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.301
ELB improved by 0.242846
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.095
ELB improved by 0.205329
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.926
ELB improved by 0.169136
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.787
ELB improved by 0.139561
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.67
ELB improved by 0.116255
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.573
ELB improved by 0.0973228
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.492
ELB improved by 0.0815085
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.423
ELB improved by 0.0683097
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.366
ELB improved by 0.0575113
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.317
ELB improved by 0.0489017
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.275
ELB improved by 0.0422362
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.237
ELB improved by 0.0372914
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.203
ELB improved by 0.0339178
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.171
ELB improved by 0.0320769
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.14
ELB improved by 0.0318801
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.106
ELB improved by 0.0336454
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.068
ELB improved by 0.0379735
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.022
ELB improved by 0.0457884
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.964
ELB improved by 0.0581558
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.888
ELB improved by 0.075566
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.792
ELB improved by 0.0968245
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.672
ELB improved by 0.119072
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.533
ELB improved by 0.139677
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.376
ELB improved by 0.156838
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.206
ELB improved by 0.16976
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.023
ELB improved by 0.182973
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.819
ELB improved by 0.203914
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.596
ELB improved by 0.223456
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.384
ELB improved by 0.211809
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.219
ELB improved by 0.165413
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.101
ELB improved by 0.117458
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.013
ELB improved by 0.0883558
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.935
ELB improved by 0.0782961
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.85
ELB improved by 0.084059
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.746
ELB improved by 0.10443
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.612
ELB improved by 0.134041
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.461
ELB improved by 0.151392
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.326
ELB improved by 0.135102
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.224
ELB improved by 0.101832
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.149
ELB improved by 0.0751595
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.092
ELB improved by 0.0567403
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.049
ELB improved by 0.0424573
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.019
ELB improved by 0.0306445
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.997
ELB improved by 0.021275
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.983
ELB improved by 0.0144337
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.973
ELB improved by 0.00979717
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-886.409
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-602.971
ELB improved by 283.438
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-540.931
ELB improved by 62.0397
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-494.035
ELB improved by 46.8961
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.275
ELB improved by 24.7602
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.829
ELB improved by 12.4464
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.89
ELB improved by 8.9389
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.026
ELB improved by 8.86351
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.955
ELB improved by 9.07081
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.027
ELB improved by 7.92856
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.328
ELB improved by 5.69924
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.672
ELB improved by 3.65525
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.313
ELB improved by 2.35967
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.664
ELB improved by 1.6491
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.443
ELB improved by 1.22048
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.556
ELB improved by 0.886957
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.919
ELB improved by 0.637094
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.441
ELB improved by 0.477758
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.061
ELB improved by 0.379901
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.744
ELB improved by 0.317318
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.469
ELB improved by 0.275483
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.222
ELB improved by 0.246981
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.994
ELB improved by 0.227871
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.778
ELB improved by 0.215949
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.568
ELB improved by 0.210002
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.358
ELB improved by 0.209486
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.144
ELB improved by 0.214407
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.919
ELB improved by 0.225261
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.676
ELB improved by 0.242909
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.408
ELB improved by 0.268095
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.107
ELB improved by 0.300211
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.772
ELB improved by 0.335724
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.403
ELB improved by 0.368834
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.007
ELB improved by 0.395969
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.589
ELB improved by 0.418464
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.149
ELB improved by 0.439297
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.689
ELB improved by 0.459871
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.209
ELB improved by 0.480057
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.71
ELB improved by 0.49915
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.194
ELB improved by 0.516564
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.661
ELB improved by 0.532346
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.114
ELB improved by 0.547307
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.551
ELB improved by 0.562824
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.968
ELB improved by 0.583126
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.345
ELB improved by 0.623439
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.636
ELB improved by 0.708237
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.829
ELB improved by 0.807018
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.053
ELB improved by 0.775823
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.455
ELB improved by 0.598703
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.037
ELB improved by 0.41824
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.746
ELB improved by 0.290389
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.539
ELB improved by 0.206722
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.388
ELB improved by 0.151499
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.274
ELB improved by 0.113813
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.187
ELB improved by 0.087196
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.119
ELB improved by 0.067856
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.066
ELB improved by 0.0534893
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.023
ELB improved by 0.0426321
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.989
ELB improved by 0.0343142
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.961
ELB improved by 0.0278696
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.938
ELB improved by 0.0228286
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.919
ELB improved by 0.0188526
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.903
ELB improved by 0.0156933
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.89
ELB improved by 0.0131662
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.879
ELB improved by 0.0111321
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.87
ELB improved by 0.0094855
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-874.64
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-586.805
ELB improved by 287.835
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-527.289
ELB improved by 59.5157
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-487.423
ELB improved by 39.8665
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.47
ELB improved by 19.953
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.433
ELB improved by 9.0364
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.143
ELB improved by 5.29058
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.628
ELB improved by 4.51439
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.032
ELB improved by 4.59641
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.22
ELB improved by 4.81253
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.523
ELB improved by 4.69697
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.529
ELB improved by 3.99386
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.583
ELB improved by 2.94565
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.533
ELB improved by 2.04975
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.012
ELB improved by 1.52161
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.755
ELB improved by 1.25668
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.661
ELB improved by 1.09433
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.686
ELB improved by 0.974813
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.781
ELB improved by 0.90487
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.903
ELB improved by 0.878381
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.026
ELB improved by 0.87684
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.14
ELB improved by 0.885653
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.241
ELB improved by 0.898623
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.324
ELB improved by 0.917294
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.374
ELB improved by 0.950302
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.359
ELB improved by 1.01485
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.228
ELB improved by 1.1308
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.956
ELB improved by 1.27266
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.598
ELB improved by 1.35737
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.204
ELB improved by 1.39376
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.736
ELB improved by 1.46827
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.083
ELB improved by 1.65271
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.165
ELB improved by 1.91884
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.832
ELB improved by 2.33302
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.384
ELB improved by 2.44801
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.05
ELB improved by 2.33347
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.866
ELB improved by 2.18418
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.327
ELB improved by 1.53897
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.373
ELB improved by 0.953618
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.77
ELB improved by 0.60346
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.315
ELB improved by 0.454691
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.918
ELB improved by 0.397457
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.598
ELB improved by 0.319632
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.381
ELB improved by 0.217376
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.241
ELB improved by 0.139286
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.147
ELB improved by 0.094515
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.077
ELB improved by 0.0700585
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.021
ELB improved by 0.0553699
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.976
ELB improved by 0.0453924
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.938
ELB improved by 0.0379895
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.906
ELB improved by 0.0322119
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.878
ELB improved by 0.0275767
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.855
ELB improved by 0.0237985
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.834
ELB improved by 0.020688
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.816
ELB improved by 0.0181094
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.8
ELB improved by 0.0159603
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.786
ELB improved by 0.0141612
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.773
ELB improved by 0.0126492
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.762
ELB improved by 0.0113739
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.751
ELB improved by 0.0102944
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.742
ELB improved by 0.0093775
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
5.352 0.493 6.317
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.082 | 0.044 | 0.135 | |
| getPIPs | 0.076 | 0.036 | 0.121 | |
| graper | 0.125 | 0.053 | 0.197 | |
| makeExampleData | 0.036 | 0.005 | 0.042 | |
| makeExampleDataWithUnequalGroups | 0.021 | 0.001 | 0.024 | |
| plotELBO | 0.619 | 0.045 | 0.819 | |
| plotGroupPenalties | 2.638 | 0.139 | 3.381 | |
| plotPosterior | 1.614 | 0.049 | 1.884 | |
| predict.graper | 2.946 | 0.191 | 3.385 | |
| print.graper | 0.074 | 0.031 | 0.115 | |