Britta Velten
| Snapshot Date: 2026-05-21 13:45 -0400 (Thu, 21 May 2026) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: ba611e2 |
| git_last_commit_date: 2026-04-28 08:49:19 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-22 11:37 -0400 (Fri, 22 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4936 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There" | 4621 |
| 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 933/2378 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.29.0 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | | |||||||||
| See other builds for graper in R Universe. | ||||||||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: graper |
| Version: 1.29.0 |
| 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_1.29.0.tar.gz |
| StartedAt: 2026-05-21 19:52:07 -0400 (Thu, 21 May 2026) |
| EndedAt: 2026-05-21 19:52:37 -0400 (Thu, 21 May 2026) |
| EllapsedTime: 29.5 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_1.29.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.24-bioc/meat/graper.Rcheck’
* using R version 4.6.0 Patched (2026-05-01 r89994)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-21 23:52:08 UTC
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.29.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) predict.graper.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:23-24: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.24-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.29.0’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’ using SDK: ‘MacOSX26.2.sdk’ clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fit_graper.cpp -o fit_graper.o clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o graper.so RcppExports.o fit_graper.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-graper/00new/graper/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (graper)
graper.Rcheck/tests/testthat.Rout
R version 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(graper)
>
> test_check("graper")
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-852.856
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-572.245
ELB improved by 280.611
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-512.152
ELB improved by 60.0925
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.397
ELB improved by 39.7553
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.448
ELB improved by 14.9495
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.186
ELB improved by 5.26119
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.122
ELB improved by 3.06485
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.88
ELB improved by 2.24118
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.986
ELB improved by 1.89391
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.252
ELB improved by 1.7345
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.607
ELB improved by 1.64512
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.028
ELB improved by 1.57874
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.518
ELB improved by 1.51007
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.095
ELB improved by 1.42302
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.784
ELB improved by 1.31136
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.603
ELB improved by 1.18068
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.556
ELB improved by 1.04674
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.627
ELB improved by 0.929238
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.783
ELB improved by 0.843717
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.987
ELB improved by 0.795822
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.207
ELB improved by 0.780441
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.422
ELB improved by 0.785122
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.626
ELB improved by 0.796149
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.823
ELB improved by 0.803234
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.023
ELB improved by 0.799335
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.244
ELB improved by 0.77934
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.503
ELB improved by 0.741335
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.815
ELB improved by 0.688018
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.189
ELB improved by 0.625592
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.628
ELB improved by 0.560978
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.128
ELB improved by 0.499615
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.683
ELB improved by 0.444832
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.285
ELB improved by 0.398295
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.924
ELB improved by 0.360753
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.592
ELB improved by 0.33267
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.277
ELB improved by 0.314547
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.971
ELB improved by 0.306539
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.664
ELB improved by 0.306554
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.357
ELB improved by 0.307488
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.057
ELB improved by 0.300107
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.772
ELB improved by 0.284467
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.502
ELB improved by 0.270041
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.24
ELB improved by 0.262112
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.981
ELB improved by 0.259226
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.722
ELB improved by 0.258471
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.464
ELB improved by 0.257813
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.208
ELB improved by 0.256314
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.954
ELB improved by 0.254307
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.7
ELB improved by 0.254025
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.439
ELB improved by 0.26102
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.152
ELB improved by 0.286436
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.808
ELB improved by 0.343892
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.397
ELB improved by 0.411665
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.001
ELB improved by 0.395663
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.715
ELB improved by 0.286384
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.533
ELB improved by 0.182137
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.415
ELB improved by 0.117441
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.334
ELB improved by 0.0813074
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.273
ELB improved by 0.061115
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.223
ELB improved by 0.0494808
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.181
ELB improved by 0.0425899
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.142
ELB improved by 0.0385322
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.106
ELB improved by 0.0363777
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.07
ELB improved by 0.0357258
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.033
ELB improved by 0.0365115
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.995
ELB improved by 0.038954
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.951
ELB improved by 0.0436063
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.899
ELB improved by 0.0515072
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.835
ELB improved by 0.0644592
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.75
ELB improved by 0.0853894
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.631
ELB improved by 0.118325
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.465
ELB improved by 0.16593
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.245
ELB improved by 0.220168
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.994
ELB improved by 0.251242
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.762
ELB improved by 0.231566
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.583
ELB improved by 0.179716
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.451
ELB improved by 0.13136
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.353
ELB improved by 0.0984372
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.275
ELB improved by 0.0774554
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.212
ELB improved by 0.0630294
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.161
ELB improved by 0.0516821
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.119
ELB improved by 0.0419464
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.085
ELB improved by 0.0335814
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.058
ELB improved by 0.0267031
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.037
ELB improved by 0.0213052
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.02
ELB improved by 0.0171977
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.006
ELB improved by 0.0141136
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.994
ELB improved by 0.0117989
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.984
ELB improved by 0.0100488
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.975
ELB improved by 0.0087097
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-907.944
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-570.694
ELB improved by 337.25
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-514.209
ELB improved by 56.4853
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-483.401
ELB improved by 30.8075
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.841
ELB improved by 11.5599
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.099
ELB improved by 4.7427
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.484
ELB improved by 2.61496
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.704
ELB improved by 1.7792
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.27
ELB improved by 1.43406
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.01
ELB improved by 1.26066
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.855
ELB improved by 1.15436
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.775
ELB improved by 1.0805
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.749
ELB improved by 1.02594
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.764
ELB improved by 0.985269
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.808
ELB improved by 0.955475
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.874
ELB improved by 0.933674
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.958
ELB improved by 0.916297
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.059
ELB improved by 0.899322
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.18
ELB improved by 0.879054
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.327
ELB improved by 0.852712
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.509
ELB improved by 0.818139
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.736
ELB improved by 0.773172
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.019
ELB improved by 0.716415
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.37
ELB improved by 0.649694
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.79
ELB improved by 0.579545
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.275
ELB improved by 0.515273
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.81
ELB improved by 0.464732
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.379
ELB improved by 0.431468
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.964
ELB improved by 0.414928
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.551
ELB improved by 0.41233
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.131
ELB improved by 0.420353
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.695
ELB improved by 0.435954
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.239
ELB improved by 0.45641
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.76
ELB improved by 0.478904
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.26
ELB improved by 0.50013
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.743
ELB improved by 0.516567
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.218
ELB improved by 0.525531
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.691
ELB improved by 0.526146
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.172
ELB improved by 0.519395
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.665
ELB improved by 0.507451
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.172
ELB improved by 0.492889
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.694
ELB improved by 0.478029
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.229
ELB improved by 0.464553
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.776
ELB improved by 0.453369
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.331
ELB improved by 0.444669
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.893
ELB improved by 0.438066
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.46
ELB improved by 0.432725
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.033
ELB improved by 0.427464
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.612
ELB improved by 0.420828
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.201
ELB improved by 0.411149
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.804
ELB improved by 0.396703
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.428
ELB improved by 0.376061
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.079
ELB improved by 0.348638
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.764
ELB improved by 0.315152
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.487
ELB improved by 0.277575
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.248
ELB improved by 0.238483
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.048
ELB improved by 0.200267
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.883
ELB improved by 0.164772
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.75
ELB improved by 0.133311
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.643
ELB improved by 0.10669
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.558
ELB improved by 0.0851317
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.49
ELB improved by 0.0683008
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.434
ELB improved by 0.0554964
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.388
ELB improved by 0.045899
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.35
ELB improved by 0.038747
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.316
ELB improved by 0.0334181
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.287
ELB improved by 0.0294417
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.26
ELB improved by 0.0264768
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.236
ELB improved by 0.0242795
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.213
ELB improved by 0.0226701
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.192
ELB improved by 0.0215055
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.171
ELB improved by 0.0206579
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.151
ELB improved by 0.0199997
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.132
ELB improved by 0.0193982
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.113
ELB improved by 0.0187212
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.095
ELB improved by 0.0178574
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.078
ELB improved by 0.0167432
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.063
ELB improved by 0.0153839
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.049
ELB improved by 0.0138533
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.037
ELB improved by 0.0122671
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.026
ELB improved by 0.0107433
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.017
ELB improved by 0.00937033
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-868.27
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-592.49
ELB improved by 275.781
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-533.242
ELB improved by 59.2474
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-491.988
ELB improved by 41.2547
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.475
ELB improved by 20.5129
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.993
ELB improved by 9.48153
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.779
ELB improved by 7.21464
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.24
ELB improved by 7.53845
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.027
ELB improved by 8.21315
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.717
ELB improved by 8.30975
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.594
ELB improved by 7.12281
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.503
ELB improved by 5.09157
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.161
ELB improved by 3.34231
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.939
ELB improved by 2.2213
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.315
ELB improved by 1.62451
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.962
ELB improved by 1.35306
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.694
ELB improved by 1.26738
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.415
ELB improved by 1.27932
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.26
ELB improved by 1.15514
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.451
ELB improved by 0.808578
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.961
ELB improved by 0.489981
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.657
ELB improved by 0.304821
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.445
ELB improved by 0.211304
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.284
ELB improved by 0.16138
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.153
ELB improved by 0.130624
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.044
ELB improved by 0.109112
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.951
ELB improved by 0.0928501
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.871
ELB improved by 0.080025
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.802
ELB improved by 0.0696616
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.74
ELB improved by 0.0611547
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.686
ELB improved by 0.0540933
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.638
ELB improved by 0.0481833
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.595
ELB improved by 0.0432072
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.556
ELB improved by 0.0390002
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.52
ELB improved by 0.0354361
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.488
ELB improved by 0.0324171
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.458
ELB improved by 0.0298683
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.43
ELB improved by 0.0277335
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.404
ELB improved by 0.025973
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.38
ELB improved by 0.0245637
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.356
ELB improved by 0.0234996
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.334
ELB improved by 0.0227952
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.311
ELB improved by 0.0224911
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.288
ELB improved by 0.0226628
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.265
ELB improved by 0.0234325
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.24
ELB improved by 0.0249817
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.213
ELB improved by 0.0275515
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.181
ELB improved by 0.0313985
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.144
ELB improved by 0.0366388
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.102
ELB improved by 0.0429106
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.053
ELB improved by 0.0489657
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403
ELB improved by 0.0527538
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.947
ELB improved by 0.0526102
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.899
ELB improved by 0.0487006
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.856
ELB improved by 0.0428193
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.819
ELB improved by 0.0368037
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.787
ELB improved by 0.0315759
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.76
ELB improved by 0.02729
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.736
ELB improved by 0.0237809
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.715
ELB improved by 0.0208398
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.697
ELB improved by 0.0183086
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.681
ELB improved by 0.0160912
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.667
ELB improved by 0.0141374
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.654
ELB improved by 0.0124233
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.644
ELB improved by 0.0109352
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.634
ELB improved by 0.00966009
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-855.488
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-561.006
ELB improved by 294.482
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-500.661
ELB improved by 60.3447
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.298
ELB improved by 34.363
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.625
ELB improved by 12.673
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.599
ELB improved by 5.02599
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.485
ELB improved by 3.11453
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.899
ELB improved by 2.58595
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.438
ELB improved by 2.46092
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.96
ELB improved by 2.47804
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.422
ELB improved by 2.53751
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.845
ELB improved by 2.57765
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.305
ELB improved by 2.53952
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.936
ELB improved by 2.36925
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.889
ELB improved by 2.04674
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.264
ELB improved by 1.62534
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.052
ELB improved by 1.21122
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.171
ELB improved by 0.88104
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.521
ELB improved by 0.650081
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.022
ELB improved by 0.499089
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.62
ELB improved by 0.40223
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.281
ELB improved by 0.339172
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.984
ELB improved by 0.297315
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.714
ELB improved by 0.269502
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.463
ELB improved by 0.251337
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.223
ELB improved by 0.239863
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.99
ELB improved by 0.233132
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.76
ELB improved by 0.229971
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.53
ELB improved by 0.229763
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.298
ELB improved by 0.232255
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.06
ELB improved by 0.237405
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.815
ELB improved by 0.245219
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.56
ELB improved by 0.255551
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.292
ELB improved by 0.267859
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.011
ELB improved by 0.280994
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.717
ELB improved by 0.293273
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.414
ELB improved by 0.303027
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.105
ELB improved by 0.309367
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.793
ELB improved by 0.312471
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.479
ELB improved by 0.313102
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.167
ELB improved by 0.311984
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.858
ELB improved by 0.309529
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.552
ELB improved by 0.305886
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.251
ELB improved by 0.301097
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.956
ELB improved by 0.295265
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.667
ELB improved by 0.288722
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.385
ELB improved by 0.282214
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.108
ELB improved by 0.277089
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.832
ELB improved by 0.275483
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.552
ELB improved by 0.280249
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.259
ELB improved by 0.29331
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.949
ELB improved by 0.309304
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.642
ELB improved by 0.30755
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.371
ELB improved by 0.27097
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.151
ELB improved by 0.220056
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.971
ELB improved by 0.179927
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.82
ELB improved by 0.151009
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.692
ELB improved by 0.127936
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.583
ELB improved by 0.108443
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.492
ELB improved by 0.0918091
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.414
ELB improved by 0.0776412
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.348
ELB improved by 0.0655887
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.293
ELB improved by 0.0553351
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.246
ELB improved by 0.0466178
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.207
ELB improved by 0.039229
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.174
ELB improved by 0.033001
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.146
ELB improved by 0.0277889
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.123
ELB improved by 0.0234595
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.103
ELB improved by 0.0198876
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.086
ELB improved by 0.0169568
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.072
ELB improved by 0.014562
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.059
ELB improved by 0.0126111
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.048
ELB improved by 0.0110256
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.038
ELB improved by 0.00974032
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
1.027 0.078 1.101
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.029 | 0.005 | 0.033 | |
| getPIPs | 0.027 | 0.006 | 0.032 | |
| graper | 0.043 | 0.005 | 0.049 | |
| makeExampleData | 0.004 | 0.000 | 0.004 | |
| makeExampleDataWithUnequalGroups | 0.004 | 0.000 | 0.005 | |
| plotELBO | 0.121 | 0.005 | 0.125 | |
| plotGroupPenalties | 0.432 | 0.007 | 0.439 | |
| plotPosterior | 0.213 | 0.007 | 0.221 | |
| predict.graper | 1.012 | 0.026 | 1.039 | |
| print.graper | 0.027 | 0.004 | 0.030 | |