Britta Velten
| Snapshot Date: 2025-07-31 13:40 -0400 (Thu, 31 Jul 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: RELEASE_3_21 |
| git_last_commit: fb5f237 |
| git_last_commit_date: 2025-06-24 03:18:49 -0400 (Tue, 24 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-08-04 11:44 -0400 (Mon, 04 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 915/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.24.2 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: graper |
| Version: 1.24.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.24.2.tar.gz |
| StartedAt: 2025-08-01 04:25:38 -0400 (Fri, 01 Aug 2025) |
| EndedAt: 2025-08-01 04:27:39 -0400 (Fri, 01 Aug 2025) |
| EllapsedTime: 120.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.24.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/graper.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.24.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) predict.graper.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:23-24: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.24.2’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fit_graper.cpp -o fit_graper.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o graper.so RcppExports.o fit_graper.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-graper/00new/graper/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (graper)
graper.Rcheck/tests/testthat.Rout
R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(graper)
>
> test_check("graper")
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-847.3
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-583.907
ELB improved by 263.393
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-527.93
ELB improved by 55.9765
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-484.856
ELB improved by 43.0746
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.838
ELB improved by 24.0175
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.732
ELB improved by 10.106
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.305
ELB improved by 5.42705
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.621
ELB improved by 4.6843
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.705
ELB improved by 4.91612
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.266
ELB improved by 5.43831
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.524
ELB improved by 5.74205
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.196
ELB improved by 5.32811
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.069
ELB improved by 4.12768
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.375
ELB improved by 2.69328
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.758
ELB improved by 1.61718
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.763
ELB improved by 0.995121
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.099
ELB improved by 0.664388
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.613
ELB improved by 0.4855
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.23
ELB improved by 0.383533
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.907
ELB improved by 0.322298
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.623
ELB improved by 0.284323
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.362
ELB improved by 0.260859
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.115
ELB improved by 0.247322
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.874
ELB improved by 0.241232
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.632
ELB improved by 0.241245
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.386
ELB improved by 0.246686
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.128
ELB improved by 0.257301
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.855
ELB improved by 0.273115
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.561
ELB improved by 0.294329
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.24
ELB improved by 0.32122
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.886
ELB improved by 0.35404
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.493
ELB improved by 0.392881
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.055
ELB improved by 0.437557
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.568
ELB improved by 0.487505
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.026
ELB improved by 0.541746
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.427
ELB improved by 0.598923
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.77
ELB improved by 0.657488
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.053
ELB improved by 0.716125
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.28
ELB improved by 0.773652
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.456
ELB improved by 0.824059
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.614
ELB improved by 0.841323
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.83
ELB improved by 0.784647
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.169
ELB improved by 0.661043
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.644
ELB improved by 0.524406
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.236
ELB improved by 0.407889
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.918
ELB improved by 0.318149
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.665
ELB improved by 0.253105
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.456
ELB improved by 0.209535
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.27
ELB improved by 0.1856
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.088
ELB improved by 0.181606
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.891
ELB improved by 0.197252
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.669
ELB improved by 0.22186
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.435
ELB improved by 0.233791
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.205
ELB improved by 0.230558
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.983
ELB improved by 0.222035
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.789
ELB improved by 0.194172
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.645
ELB improved by 0.14366
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.548
ELB improved by 0.096786
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.481
ELB improved by 0.0674646
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.429
ELB improved by 0.0514581
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.387
ELB improved by 0.0424925
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.35
ELB improved by 0.0370023
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.317
ELB improved by 0.0332819
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.286
ELB improved by 0.0304963
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.258
ELB improved by 0.0282112
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.232
ELB improved by 0.0261978
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.207
ELB improved by 0.0243469
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.185
ELB improved by 0.0226216
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.164
ELB improved by 0.021023
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.144
ELB improved by 0.019566
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.126
ELB improved by 0.0182635
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.109
ELB improved by 0.017121
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.093
ELB improved by 0.0161359
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.077
ELB improved by 0.0153014
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.063
ELB improved by 0.0146093
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.049
ELB improved by 0.0140529
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.035
ELB improved by 0.0136281
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.022
ELB improved by 0.0133347
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.008
ELB improved by 0.0131766
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.995
ELB improved by 0.0131617
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.982
ELB improved by 0.0133019
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.968
ELB improved by 0.0136125
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.954
ELB improved by 0.0141099
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.939
ELB improved by 0.0148086
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.924
ELB improved by 0.0157135
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.907
ELB improved by 0.0168098
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.889
ELB improved by 0.0180472
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.87
ELB improved by 0.0193245
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.849
ELB improved by 0.0204798
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.828
ELB improved by 0.0213008
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.806
ELB improved by 0.0215651
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.785
ELB improved by 0.0211088
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.765
ELB improved by 0.0198982
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.747
ELB improved by 0.0180606
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.731
ELB improved by 0.0158496
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.718
ELB improved by 0.0135584
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.706
ELB improved by 0.0114299
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.697
ELB improved by 0.00960763
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-836.19
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-571.258
ELB improved by 264.932
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-509.413
ELB improved by 61.8451
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.986
ELB improved by 43.4273
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.446
ELB improved by 20.5396
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.467
ELB improved by 8.97927
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.25
ELB improved by 5.21671
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.733
ELB improved by 4.51683
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.127
ELB improved by 4.60636
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.289
ELB improved by 4.83826
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.342
ELB improved by 4.94691
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.518
ELB improved by 4.82376
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.063
ELB improved by 4.45492
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.415
ELB improved by 3.64837
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.801
ELB improved by 2.61375
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.014
ELB improved by 1.78723
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.796
ELB improved by 1.2179
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.918
ELB improved by 0.87774
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.216
ELB improved by 0.701988
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.61
ELB improved by 0.60651
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.069
ELB improved by 0.540362
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.572
ELB improved by 0.497664
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.089
ELB improved by 0.482347
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.602
ELB improved by 0.487364
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.099
ELB improved by 0.503307
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.575
ELB improved by 0.523848
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.03
ELB improved by 0.545195
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.465
ELB improved by 0.565024
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.883
ELB improved by 0.581902
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.288
ELB improved by 0.594779
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.685
ELB improved by 0.602445
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.082
ELB improved by 0.603169
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.487
ELB improved by 0.594892
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.911
ELB improved by 0.576206
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.363
ELB improved by 0.547983
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.848
ELB improved by 0.515398
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.357
ELB improved by 0.490454
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.864
ELB improved by 0.493876
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.327
ELB improved by 0.536967
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.772
ELB improved by 0.554868
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.302
ELB improved by 0.469169
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.957
ELB improved by 0.345883
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.706
ELB improved by 0.250159
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.523
ELB improved by 0.183664
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.386
ELB improved by 0.136726
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.283
ELB improved by 0.103253
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.203
ELB improved by 0.0793749
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.141
ELB improved by 0.0622404
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.091
ELB improved by 0.049771
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.051
ELB improved by 0.0405322
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.017
ELB improved by 0.0335614
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.989
ELB improved by 0.0282123
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.965
ELB improved by 0.0240437
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.944
ELB improved by 0.0207484
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.926
ELB improved by 0.0181081
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.91
ELB improved by 0.0159654
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.896
ELB improved by 0.0142051
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.883
ELB improved by 0.0127418
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.872
ELB improved by 0.0115119
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.861
ELB improved by 0.0104671
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.852
ELB improved by 0.0095709
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-821.587
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-547.607
ELB improved by 273.98
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-485.397
ELB improved by 62.2092
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.733
ELB improved by 38.6642
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.06
ELB improved by 15.6734
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.856
ELB improved by 6.20405
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.237
ELB improved by 3.61892
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.438
ELB improved by 2.79931
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.944
ELB improved by 2.49337
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.56
ELB improved by 2.38463
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.208
ELB improved by 2.352
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.86
ELB improved by 2.34774
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.51
ELB improved by 2.34985
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.173
ELB improved by 2.3368
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.897
ELB improved by 2.2763
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.762
ELB improved by 2.13477
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.852
ELB improved by 1.91053
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.203
ELB improved by 1.6484
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.804
ELB improved by 1.39954
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.611
ELB improved by 1.19246
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.567
ELB improved by 1.04413
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.61
ELB improved by 0.957072
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.692
ELB improved by 0.918205
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.784
ELB improved by 0.908027
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.873
ELB improved by 0.910367
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.956
ELB improved by 0.917094
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.03
ELB improved by 0.926802
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.091
ELB improved by 0.938877
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.143
ELB improved by 0.947893
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.192
ELB improved by 0.950447
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.233
ELB improved by 0.959432
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.228
ELB improved by 1.00455
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.131
ELB improved by 1.09779
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.99
ELB improved by 1.14064
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.94
ELB improved by 1.04981
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.027
ELB improved by 0.912811
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.253
ELB improved by 0.774312
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.615
ELB improved by 0.63834
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.1
ELB improved by 0.514917
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.687
ELB improved by 0.412799
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.353
ELB improved by 0.333754
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.079
ELB improved by 0.274412
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.849
ELB improved by 0.22952
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.655
ELB improved by 0.194239
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.49
ELB improved by 0.165153
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.35
ELB improved by 0.140253
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.231
ELB improved by 0.118493
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.132
ELB improved by 0.099389
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.049
ELB improved by 0.0827518
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.98
ELB improved by 0.0685093
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.924
ELB improved by 0.0565807
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.877
ELB improved by 0.0468048
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.838
ELB improved by 0.0389313
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.805
ELB improved by 0.0326563
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.778
ELB improved by 0.0276703
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.754
ELB improved by 0.023695
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.734
ELB improved by 0.0204997
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.716
ELB improved by 0.0179035
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.7
ELB improved by 0.0157693
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.686
ELB improved by 0.0139949
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.673
ELB improved by 0.0125043
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.662
ELB improved by 0.0112409
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.652
ELB improved by 0.0101618
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.643
ELB improved by 0.00923434
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-882.867
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-598.825
ELB improved by 284.042
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-539.916
ELB improved by 58.9085
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-495.207
ELB improved by 44.7093
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.465
ELB improved by 23.7414
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.179
ELB improved by 9.28588
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.921
ELB improved by 4.25831
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.684
ELB improved by 3.23749
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.628
ELB improved by 3.05565
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.499
ELB improved by 3.12893
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.195
ELB improved by 3.30378
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.732
ELB improved by 3.46342
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.27
ELB improved by 3.46234
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.103
ELB improved by 3.16653
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.512
ELB improved by 2.59149
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.57
ELB improved by 1.94201
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.15
ELB improved by 1.41982
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.087
ELB improved by 1.06234
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.273
ELB improved by 0.814401
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.633
ELB improved by 0.640224
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.106
ELB improved by 0.527001
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.644
ELB improved by 0.461366
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.215
ELB improved by 0.429624
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.792
ELB improved by 0.42234
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.357
ELB improved by 0.435154
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.889
ELB improved by 0.468364
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.362
ELB improved by 0.527334
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.738
ELB improved by 0.623953
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.963
ELB improved by 0.775068
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.976
ELB improved by 0.986455
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.737
ELB improved by 1.23928
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.192
ELB improved by 1.54437
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.223
ELB improved by 1.96977
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.678
ELB improved by 2.54464
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.523
ELB improved by 3.15546
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.991
ELB improved by 3.53113
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.574
ELB improved by 3.41743
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.731
ELB improved by 2.84296
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.618
ELB improved by 2.11292
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.087
ELB improved by 1.53067
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.866
ELB improved by 1.22117
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.757
ELB improved by 1.1096
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.862
ELB improved by 0.894777
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.301
ELB improved by 0.560456
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.967
ELB improved by 0.334129
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.751
ELB improved by 0.216295
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.599
ELB improved by 0.152131
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.485
ELB improved by 0.113455
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.397
ELB improved by 0.0880744
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.327
ELB improved by 0.0703397
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.27
ELB improved by 0.0573635
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.222
ELB improved by 0.0475412
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.182
ELB improved by 0.0399156
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.148
ELB improved by 0.0338804
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.119
ELB improved by 0.0290319
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.094
ELB improved by 0.0250899
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.072
ELB improved by 0.0218536
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.053
ELB improved by 0.0191747
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.036
ELB improved by 0.0169418
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.021
ELB improved by 0.0150693
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.008
ELB improved by 0.0134908
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.996
ELB improved by 0.0121537
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.984
ELB improved by 0.0110161
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.974
ELB improved by 0.0100445
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.965
ELB improved by 0.00921155
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
4.540 0.448 5.131
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.081 | 0.042 | 0.125 | |
| getPIPs | 0.074 | 0.034 | 0.107 | |
| graper | 0.123 | 0.047 | 0.190 | |
| makeExampleData | 0.018 | 0.001 | 0.025 | |
| makeExampleDataWithUnequalGroups | 0.022 | 0.003 | 0.033 | |
| plotELBO | 0.450 | 0.045 | 0.505 | |
| plotGroupPenalties | 1.585 | 0.039 | 1.635 | |
| plotPosterior | 1.110 | 0.042 | 1.156 | |
| predict.graper | 2.812 | 0.177 | 3.077 | |
| print.graper | 0.065 | 0.027 | 0.093 | |