Britta Velten
| Snapshot Date: 2025-10-29 19:52 -0400 (Wed, 29 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: RELEASE_3_22 |
| git_last_commit: 76fc31b |
| git_last_commit_date: 2025-10-29 10:49:21 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-30 12:37 -0400 (Thu, 30 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| 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 922/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.26.0 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: graper |
| Version: 1.26.0 |
| 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_1.26.0.tar.gz |
| StartedAt: 2025-10-30 02:30:40 -0400 (Thu, 30 Oct 2025) |
| EndedAt: 2025-10-30 02:31:08 -0400 (Thu, 30 Oct 2025) |
| EllapsedTime: 28.3 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_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.26.0’
* 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.26.0’ ** 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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-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 version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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=-875.653
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-586.752
ELB improved by 288.901
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-528.425
ELB improved by 58.3274
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-488.523
ELB improved by 39.9023
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.484
ELB improved by 18.0386
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.625
ELB improved by 7.85888
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.754
ELB improved by 4.87057
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.691
ELB improved by 4.06349
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.821
ELB improved by 3.86981
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.89
ELB improved by 3.93092
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.744
ELB improved by 4.14633
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.36
ELB improved by 4.38385
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.952
ELB improved by 4.40785
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.959
ELB improved by 3.99347
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.785
ELB improved by 3.17388
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.52
ELB improved by 2.26522
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.964
ELB improved by 1.55546
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.859
ELB improved by 1.10472
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.03
ELB improved by 0.829691
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.389
ELB improved by 0.640726
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.892
ELB improved by 0.496849
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.503
ELB improved by 0.38908
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.192
ELB improved by 0.311498
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.936
ELB improved by 0.255563
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.722
ELB improved by 0.213939
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.54
ELB improved by 0.181809
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.384
ELB improved by 0.156252
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.249
ELB improved by 0.135468
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.13
ELB improved by 0.118288
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.026
ELB improved by 0.103913
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.935
ELB improved by 0.0917693
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.853
ELB improved by 0.0814323
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.781
ELB improved by 0.0725767
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.716
ELB improved by 0.0649483
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.657
ELB improved by 0.0583449
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.605
ELB improved by 0.0526026
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.557
ELB improved by 0.0475878
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.514
ELB improved by 0.0431897
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.475
ELB improved by 0.0393168
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.439
ELB improved by 0.0358926
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.406
ELB improved by 0.0328533
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.376
ELB improved by 0.0301454
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.348
ELB improved by 0.0277242
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.322
ELB improved by 0.0255519
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.299
ELB improved by 0.0235968
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.277
ELB improved by 0.0218319
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.257
ELB improved by 0.0202345
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.238
ELB improved by 0.018785
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.221
ELB improved by 0.0174666
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.204
ELB improved by 0.0162651
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.189
ELB improved by 0.0151679
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.175
ELB improved by 0.0141641
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.162
ELB improved by 0.0132443
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.149
ELB improved by 0.0124002
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.138
ELB improved by 0.0116243
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.127
ELB improved by 0.0109103
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.116
ELB improved by 0.0102524
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.107
ELB improved by 0.00964533
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-905.473
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-571.964
ELB improved by 333.509
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-515.376
ELB improved by 56.5876
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-481.04
ELB improved by 34.3362
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.698
ELB improved by 14.3419
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.764
ELB improved by 5.9341
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.814
ELB improved by 3.94964
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.354
ELB improved by 3.46029
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.017
ELB improved by 3.33661
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.666
ELB improved by 3.35174
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.3
ELB improved by 3.36517
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.06
ELB improved by 3.24028
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.175
ELB improved by 2.88503
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.833
ELB improved by 2.34246
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.073
ELB improved by 1.75929
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.805
ELB improved by 1.26817
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.873
ELB improved by 0.932469
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.131
ELB improved by 0.741555
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.48
ELB improved by 0.650958
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.857
ELB improved by 0.623275
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.221
ELB improved by 0.636048
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.549
ELB improved by 0.671415
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.839
ELB improved by 0.710265
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.092
ELB improved by 0.746853
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.303
ELB improved by 0.789424
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.47
ELB improved by 0.833117
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.598
ELB improved by 0.871833
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.682
ELB improved by 0.916111
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.707
ELB improved by 0.974995
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.658
ELB improved by 1.04874
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.527
ELB improved by 1.13145
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.318
ELB improved by 1.20895
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.058
ELB improved by 1.25933
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.784
ELB improved by 1.27486
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.498
ELB improved by 1.28539
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.228
ELB improved by 1.26998
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.132
ELB improved by 1.09598
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.311
ELB improved by 0.821382
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.726
ELB improved by 0.584757
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.317
ELB improved by 0.409512
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.03
ELB improved by 0.286117
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.827
ELB improved by 0.203508
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.677
ELB improved by 0.149682
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.563
ELB improved by 0.114245
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.473
ELB improved by 0.0900641
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.4
ELB improved by 0.0728582
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.34
ELB improved by 0.0601629
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.289
ELB improved by 0.0505275
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.246
ELB improved by 0.04305
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.209
ELB improved by 0.0371384
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.177
ELB improved by 0.0323871
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.148
ELB improved by 0.028511
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.123
ELB improved by 0.0253057
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.1
ELB improved by 0.0226222
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.08
ELB improved by 0.0203504
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.062
ELB improved by 0.018408
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.045
ELB improved by 0.0167325
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.03
ELB improved by 0.0152758
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.016
ELB improved by 0.0140007
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.003
ELB improved by 0.0128777
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.991
ELB improved by 0.0118832
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.98
ELB improved by 0.0109985
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.97
ELB improved by 0.0102081
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.96
ELB improved by 0.00949921
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-882.454
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-571.425
ELB improved by 311.03
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-514.751
ELB improved by 56.6738
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-480.595
ELB improved by 34.1559
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.824
ELB improved by 14.7712
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.177
ELB improved by 6.64647
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.907
ELB improved by 4.27044
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.232
ELB improved by 3.67448
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.57
ELB improved by 3.66275
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.656
ELB improved by 3.91372
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.412
ELB improved by 4.24382
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.895
ELB improved by 4.51726
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.32
ELB improved by 4.5745
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.232
ELB improved by 4.08791
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.142
ELB improved by 3.09013
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.016
ELB improved by 2.12673
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.564
ELB improved by 1.45194
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.506
ELB improved by 1.05802
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.645
ELB improved by 0.86029
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.866
ELB improved by 0.779019
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.104
ELB improved by 0.762553
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.322
ELB improved by 0.782144
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.499
ELB improved by 0.822298
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.625
ELB improved by 0.874019
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.694
ELB improved by 0.931282
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.704
ELB improved by 0.989926
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.656
ELB improved by 1.04843
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.546
ELB improved by 1.10931
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.368
ELB improved by 1.17886
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.104
ELB improved by 1.26383
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.738
ELB improved by 1.36541
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.268
ELB improved by 1.47059
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.724
ELB improved by 1.54414
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.189
ELB improved by 1.5342
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.785
ELB improved by 1.40458
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.613
ELB improved by 1.17152
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.715
ELB improved by 0.898413
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.065
ELB improved by 0.650234
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.606
ELB improved by 0.458443
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.284
ELB improved by 0.322211
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.056
ELB improved by 0.227975
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.893
ELB improved by 0.163287
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.773
ELB improved by 0.119503
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.683
ELB improved by 0.0902355
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.612
ELB improved by 0.0705837
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.555
ELB improved by 0.0570632
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.508
ELB improved by 0.0474135
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.468
ELB improved by 0.0402455
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.433
ELB improved by 0.0347199
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.403
ELB improved by 0.0303244
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.376
ELB improved by 0.0267381
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.352
ELB improved by 0.0237537
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.331
ELB improved by 0.0212319
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.312
ELB improved by 0.019076
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.295
ELB improved by 0.0172164
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.279
ELB improved by 0.0156011
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.265
ELB improved by 0.0141904
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.252
ELB improved by 0.0129528
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.24
ELB improved by 0.0118632
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.229
ELB improved by 0.0109009
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.219
ELB improved by 0.0100487
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.21
ELB improved by 0.00929218
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-851.471
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-578.474
ELB improved by 272.997
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-515.731
ELB improved by 62.7435
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.15
ELB improved by 47.5804
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.25
ELB improved by 23.9004
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.843
ELB improved by 9.40719
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.361
ELB improved by 4.48136
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.584
ELB improved by 2.7767
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.572
ELB improved by 2.01269
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.907
ELB improved by 1.66478
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.37
ELB improved by 1.53707
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.844
ELB improved by 1.52603
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.268
ELB improved by 1.5762
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.613
ELB improved by 1.65453
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.88
ELB improved by 1.73347
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.1
ELB improved by 1.77998
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.346
ELB improved by 1.75414
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.721
ELB improved by 1.62452
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.327
ELB improved by 1.39445
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.216
ELB improved by 1.11069
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.379
ELB improved by 0.836449
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.765
ELB improved by 0.614235
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.311
ELB improved by 0.453773
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.967
ELB improved by 0.344583
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.696
ELB improved by 0.271397
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.474
ELB improved by 0.221678
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.287
ELB improved by 0.186975
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.125
ELB improved by 0.162037
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.981
ELB improved by 0.143681
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.851
ELB improved by 0.129972
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.731
ELB improved by 0.119723
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.619
ELB improved by 0.112199
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.512
ELB improved by 0.106956
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.409
ELB improved by 0.103727
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.306
ELB improved by 0.102334
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.204
ELB improved by 0.102587
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.099
ELB improved by 0.104173
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.993
ELB improved by 0.106563
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.884
ELB improved by 0.109033
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.773
ELB improved by 0.110888
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.661
ELB improved by 0.111793
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.549
ELB improved by 0.111925
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.437
ELB improved by 0.111792
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.326
ELB improved by 0.111873
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.213
ELB improved by 0.112386
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.1
ELB improved by 0.11329
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.986
ELB improved by 0.114397
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.87
ELB improved by 0.115483
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.754
ELB improved by 0.116354
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.637
ELB improved by 0.116866
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.52
ELB improved by 0.116937
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.403
ELB improved by 0.116548
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.288
ELB improved by 0.11574
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.173
ELB improved by 0.114614
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.06
ELB improved by 0.113319
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.948
ELB improved by 0.112048
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.837
ELB improved by 0.111027
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.726
ELB improved by 0.110513
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.615
ELB improved by 0.110796
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.503
ELB improved by 0.112217
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.388
ELB improved by 0.115199
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.268
ELB improved by 0.120306
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.139
ELB improved by 0.128306
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.999
ELB improved by 0.140202
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.842
ELB improved by 0.157089
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.662
ELB improved by 0.179531
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.456
ELB improved by 0.206322
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.222
ELB improved by 0.233639
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.966
ELB improved by 0.256748
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.692
ELB improved by 0.273323
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.409
ELB improved by 0.28375
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.12
ELB improved by 0.288735
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.832
ELB improved by 0.288299
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.549
ELB improved by 0.282248
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.279
ELB improved by 0.270528
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.026
ELB improved by 0.253292
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.794
ELB improved by 0.231101
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.589
ELB improved by 0.20523
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.412
ELB improved by 0.177672
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.261
ELB improved by 0.150628
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.135
ELB improved by 0.125831
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.031
ELB improved by 0.104193
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.945
ELB improved by 0.0858912
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.874
ELB improved by 0.0706577
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.816
ELB improved by 0.058061
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.769
ELB improved by 0.0476718
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.729
ELB improved by 0.0391262
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.697
ELB improved by 0.0321297
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.671
ELB improved by 0.0264389
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.649
ELB improved by 0.0218443
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.631
ELB improved by 0.0181599
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.616
ELB improved by 0.0152213
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.603
ELB improved by 0.0128851
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.592
ELB improved by 0.0110298
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.582
ELB improved by 0.00955444
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
0.963 0.077 1.038
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.029 | 0.008 | 0.038 | |
| getPIPs | 0.027 | 0.007 | 0.034 | |
| graper | 0.051 | 0.011 | 0.064 | |
| makeExampleData | 0.003 | 0.001 | 0.004 | |
| makeExampleDataWithUnequalGroups | 0.004 | 0.000 | 0.006 | |
| plotELBO | 0.129 | 0.009 | 0.144 | |
| plotGroupPenalties | 0.464 | 0.011 | 0.488 | |
| plotPosterior | 0.216 | 0.009 | 0.226 | |
| predict.graper | 1.033 | 0.032 | 1.078 | |
| print.graper | 0.027 | 0.005 | 0.031 | |