Britta Velten
| Snapshot Date: 2025-11-12 13:40 -0500 (Wed, 12 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: 95474d7 |
| git_last_commit_date: 2025-10-29 10:49:21 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-13 11:32 -0500 (Thu, 13 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4013 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 911/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.27.0 (landing page) Britta Velten
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: graper |
| Version: 1.27.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.27.0.tar.gz |
| StartedAt: 2025-11-12 19:03:33 -0500 (Wed, 12 Nov 2025) |
| EndedAt: 2025-11-12 19:04:04 -0500 (Wed, 12 Nov 2025) |
| EllapsedTime: 31.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.27.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) predict.graper.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:23-24: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.27.0’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.1.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fit_graper.cpp -o fit_graper.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o graper.so RcppExports.o fit_graper.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-graper/00new/graper/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (graper)
graper.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(graper)
>
> test_check("graper")
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-858.997
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-549.516
ELB improved by 309.481
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-495.138
ELB improved by 54.3777
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.734
ELB improved by 27.4044
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.111
ELB improved by 11.6228
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.65
ELB improved by 5.46138
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.019
ELB improved by 3.63077
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.017
ELB improved by 3.00244
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.25
ELB improved by 2.76656
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.527
ELB improved by 2.72312
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.715
ELB improved by 2.81198
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.721
ELB improved by 2.99349
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.547
ELB improved by 3.17407
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.375
ELB improved by 3.17253
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.552
ELB improved by 2.82298
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.387
ELB improved by 2.165
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.937
ELB improved by 1.45015
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.028
ELB improved by 0.908652
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.445
ELB improved by 0.583203
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.039
ELB improved by 0.405931
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.73
ELB improved by 0.308775
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.478
ELB improved by 0.252197
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.261
ELB improved by 0.216789
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.068
ELB improved by 0.193191
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.891
ELB improved by 0.176571
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.727
ELB improved by 0.164097
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.573
ELB improved by 0.153915
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.429
ELB improved by 0.144857
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.292
ELB improved by 0.136428
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.163
ELB improved by 0.12868
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.042
ELB improved by 0.121887
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.925
ELB improved by 0.116231
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.814
ELB improved by 0.111686
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.706
ELB improved by 0.108085
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.6
ELB improved by 0.105212
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.497
ELB improved by 0.102868
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.397
ELB improved by 0.100891
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.297
ELB improved by 0.0991566
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.2
ELB improved by 0.0975736
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.104
ELB improved by 0.0960775
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.009
ELB improved by 0.0946257
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.916
ELB improved by 0.0931937
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.824
ELB improved by 0.0917721
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.734
ELB improved by 0.0903643
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.645
ELB improved by 0.0889838
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.557
ELB improved by 0.0876522
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.471
ELB improved by 0.0863962
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.386
ELB improved by 0.0852455
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.301
ELB improved by 0.0842302
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.218
ELB improved by 0.0833784
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.135
ELB improved by 0.0827148
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.053
ELB improved by 0.0822581
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.971
ELB improved by 0.0820205
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.889
ELB improved by 0.082006
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.807
ELB improved by 0.0822099
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.724
ELB improved by 0.0826184
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.641
ELB improved by 0.083209
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.557
ELB improved by 0.0839504
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.472
ELB improved by 0.0848036
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.386
ELB improved by 0.0857229
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.3
ELB improved by 0.0866567
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.212
ELB improved by 0.0875487
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.124
ELB improved by 0.0883389
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.035
ELB improved by 0.0889645
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.946
ELB improved by 0.0893614
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.856
ELB improved by 0.089466
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.767
ELB improved by 0.0892176
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.678
ELB improved by 0.0885615
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.591
ELB improved by 0.0874525
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.505
ELB improved by 0.0858584
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.421
ELB improved by 0.0837634
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.34
ELB improved by 0.0811708
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.262
ELB improved by 0.0781041
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.187
ELB improved by 0.0746069
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.117
ELB improved by 0.070741
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.05
ELB improved by 0.0665826
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.988
ELB improved by 0.0622174
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.93
ELB improved by 0.0577355
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.877
ELB improved by 0.0532253
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.828
ELB improved by 0.048769
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.784
ELB improved by 0.0444384
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.743
ELB improved by 0.0402922
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.707
ELB improved by 0.0363752
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.674
ELB improved by 0.0327184
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.645
ELB improved by 0.0293397
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.619
ELB improved by 0.0262462
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.595
ELB improved by 0.0234356
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.574
ELB improved by 0.0208989
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.556
ELB improved by 0.0186222
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.539
ELB improved by 0.0165881
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.524
ELB improved by 0.0147778
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.511
ELB improved by 0.0131715
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.499
ELB improved by 0.0117499
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.489
ELB improved by 0.0104942
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.48
ELB improved by 0.00938668
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-878.8
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-598.521
ELB improved by 280.278
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-539.016
ELB improved by 59.5052
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-494.115
ELB improved by 44.9009
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.923
ELB improved by 24.1919
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.43
ELB improved by 11.4934
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.31
ELB improved by 7.12024
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.007
ELB improved by 6.3027
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.339
ELB improved by 6.66757
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.304
ELB improved by 7.03503
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.903
ELB improved by 6.40176
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.249
ELB improved by 4.65402
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.396
ELB improved by 2.85294
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.674
ELB improved by 1.72149
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.532
ELB improved by 1.1422
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.69
ELB improved by 0.841839
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.013
ELB improved by 0.677114
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.418
ELB improved by 0.595229
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.838
ELB improved by 0.579471
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.219
ELB improved by 0.619473
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.527
ELB improved by 0.691977
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.761
ELB improved by 0.765685
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.972
ELB improved by 0.789325
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.219
ELB improved by 0.752382
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.492
ELB improved by 0.727859
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.752
ELB improved by 0.739141
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.983
ELB improved by 0.769459
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.175
ELB improved by 0.808228
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.317
ELB improved by 0.857366
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.388
ELB improved by 0.929625
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.347
ELB improved by 1.04082
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.174
ELB improved by 1.17302
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.936
ELB improved by 1.23823
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.747
ELB improved by 1.18844
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.671
ELB improved by 1.07655
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.731
ELB improved by 0.939343
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.946
ELB improved by 0.7852
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.32
ELB improved by 0.625936
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.841
ELB improved by 0.479315
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.482
ELB improved by 0.359021
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.213
ELB improved by 0.269021
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.007
ELB improved by 0.20615
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.841
ELB improved by 0.165488
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.697
ELB improved by 0.144331
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.551
ELB improved by 0.145868
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.363
ELB improved by 0.187839
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.039
ELB improved by 0.3243
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.394
ELB improved by 0.644811
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.373
ELB improved by 1.02095
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.364
ELB improved by 1.00948
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.605
ELB improved by 0.758535
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.038
ELB improved by 0.567016
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.575
ELB improved by 0.462623
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.215
ELB improved by 0.360625
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.966
ELB improved by 0.248732
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.801
ELB improved by 0.164828
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.687
ELB improved by 0.114747
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.6
ELB improved by 0.0869941
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.528
ELB improved by 0.0719682
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.464
ELB improved by 0.0632672
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.408
ELB improved by 0.0561764
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.36
ELB improved by 0.0477008
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.323
ELB improved by 0.0374888
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.296
ELB improved by 0.0273716
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.276
ELB improved by 0.0192217
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.263
ELB improved by 0.0135809
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.253
ELB improved by 0.0099905
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-846.954
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-588.37
ELB improved by 258.585
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-528.768
ELB improved by 59.602
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-487.032
ELB improved by 41.7352
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.787
ELB improved by 24.2453
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.427
ELB improved by 12.3605
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.419
ELB improved by 7.00759
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.917
ELB improved by 5.50228
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.634
ELB improved by 5.28319
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.51
ELB improved by 5.12339
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.029
ELB improved by 4.48128
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.653
ELB improved by 3.37628
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.432
ELB improved by 2.22014
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.994
ELB improved by 1.43885
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.967
ELB improved by 1.02699
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.15
ELB improved by 0.816775
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.43
ELB improved by 0.720249
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.742
ELB improved by 0.687217
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.069
ELB improved by 0.673183
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.42
ELB improved by 0.64871
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.811
ELB improved by 0.60912
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.251
ELB improved by 0.560635
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.744
ELB improved by 0.507105
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.292
ELB improved by 0.451569
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.894
ELB improved by 0.397566
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.547
ELB improved by 0.347928
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.242
ELB improved by 0.30412
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.976
ELB improved by 0.266427
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.742
ELB improved by 0.234416
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.534
ELB improved by 0.207345
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.35
ELB improved by 0.18441
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.185
ELB improved by 0.164877
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.037
ELB improved by 0.148122
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.903
ELB improved by 0.13364
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.782
ELB improved by 0.121027
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.672
ELB improved by 0.109964
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.572
ELB improved by 0.100199
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.48
ELB improved by 0.091531
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.397
ELB improved by 0.0837976
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.32
ELB improved by 0.0768682
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.249
ELB improved by 0.0706355
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.184
ELB improved by 0.0650104
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.124
ELB improved by 0.0599185
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.069
ELB improved by 0.0552972
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.018
ELB improved by 0.0510929
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.971
ELB improved by 0.0472598
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.927
ELB improved by 0.0437584
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.886
ELB improved by 0.0405542
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.849
ELB improved by 0.0376173
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.814
ELB improved by 0.0349213
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.781
ELB improved by 0.0324429
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.751
ELB improved by 0.0301614
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.723
ELB improved by 0.0280585
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.697
ELB improved by 0.026118
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.673
ELB improved by 0.0243252
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.65
ELB improved by 0.0226671
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.629
ELB improved by 0.0211319
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.609
ELB improved by 0.0197091
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.591
ELB improved by 0.0183894
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.574
ELB improved by 0.017164
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.558
ELB improved by 0.0160256
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.543
ELB improved by 0.014967
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.529
ELB improved by 0.013982
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.516
ELB improved by 0.0130651
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.503
ELB improved by 0.012211
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.492
ELB improved by 0.0114152
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.481
ELB improved by 0.0106734
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.471
ELB improved by 0.00998183
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-856.759
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-569.077
ELB improved by 287.682
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-511.564
ELB improved by 57.5127
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-479.34
ELB improved by 32.2246
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.777
ELB improved by 12.5627
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.045
ELB improved by 5.7316
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.29
ELB improved by 3.7549
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.146
ELB improved by 3.14451
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.996
ELB improved by 3.15045
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.6
ELB improved by 3.39541
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.979
ELB improved by 3.62138
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.425
ELB improved by 3.55414
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.391
ELB improved by 3.03396
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.163
ELB improved by 2.22805
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.679
ELB improved by 1.48373
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.689
ELB improved by 0.989477
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.964
ELB improved by 0.724943
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.362
ELB improved by 0.602145
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.814
ELB improved by 0.548662
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.288
ELB improved by 0.52551
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.768
ELB improved by 0.520185
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.24
ELB improved by 0.527813
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.7
ELB improved by 0.540336
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.151
ELB improved by 0.549059
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.601
ELB improved by 0.550146
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.055
ELB improved by 0.545163
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.518
ELB improved by 0.537907
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.986
ELB improved by 0.531581
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.46
ELB improved by 0.526111
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.943
ELB improved by 0.516504
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.446
ELB improved by 0.497292
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.976
ELB improved by 0.469818
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.536
ELB improved by 0.440309
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.123
ELB improved by 0.413215
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.733
ELB improved by 0.389886
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.362
ELB improved by 0.370393
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.007
ELB improved by 0.354994
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.662
ELB improved by 0.345207
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.317
ELB improved by 0.345519
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.95
ELB improved by 0.366623
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.524
ELB improved by 0.42568
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.012
ELB improved by 0.512238
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.48
ELB improved by 0.532409
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.031
ELB improved by 0.449247
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.681
ELB improved by 0.349046
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.405
ELB improved by 0.275994
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.178
ELB improved by 0.227752
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.983
ELB improved by 0.194891
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.812
ELB improved by 0.170493
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.662
ELB improved by 0.150518
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.529
ELB improved by 0.133007
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.412
ELB improved by 0.117265
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.308
ELB improved by 0.103232
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.217
ELB improved by 0.0910548
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.136
ELB improved by 0.0808174
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.064
ELB improved by 0.0724076
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.999
ELB improved by 0.0655179
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.939
ELB improved by 0.0597331
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.884
ELB improved by 0.054634
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.834
ELB improved by 0.0498616
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.789
ELB improved by 0.0451376
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.749
ELB improved by 0.0402765
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.714
ELB improved by 0.0352258
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.684
ELB improved by 0.0301041
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.658
ELB improved by 0.0251726
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.638
ELB improved by 0.0207232
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.621
ELB improved by 0.0169573
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.607
ELB improved by 0.0139318
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.595
ELB improved by 0.0115851
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.585
ELB improved by 0.00979601
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
1.032 0.084 1.140
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.014 | 0.007 | 0.021 | |
| getPIPs | 0.012 | 0.006 | 0.018 | |
| graper | 0.020 | 0.010 | 0.035 | |
| makeExampleData | 0.003 | 0.000 | 0.003 | |
| makeExampleDataWithUnequalGroups | 0.002 | 0.001 | 0.002 | |
| plotELBO | 0.126 | 0.009 | 0.139 | |
| plotGroupPenalties | 0.445 | 0.008 | 0.479 | |
| plotPosterior | 0.214 | 0.011 | 0.228 | |
| predict.graper | 0.215 | 0.038 | 0.264 | |
| print.graper | 0.011 | 0.005 | 0.017 | |