Britta Velten
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/graper |
| Branch: RELEASE_3_11 |
| Last Commit: aa82f86 |
| Last Changed Date: 2020-04-27 15:22:20 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:54:54 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE graper PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 770/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| graper 1.4.0 Britta Velten
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: graper |
| Version: 1.4.0 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings graper_1.4.0.tar.gz |
| StartedAt: 2020-10-17 01:59:12 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 02:00:12 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 60.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings graper_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/graper.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.4.0’
* 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
* checking installed package size ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
libs 5.3Mb
* 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 R 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 ... OK
* 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 in ‘inst/doc’ ... 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
‘/home/biocbuild/bbs-3.11-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’ * installing *source* package ‘graper’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c fit_graper.cpp -o fit_graper.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.11-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.11-bioc/R/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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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=-908.964
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-576.326
ELB improved by 332.638
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-516.78
ELB improved by 59.5462
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-481.243
ELB improved by 35.5366
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.807
ELB improved by 15.4356
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.703
ELB improved by 7.10427
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.74
ELB improved by 4.96341
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.171
ELB improved by 4.56878
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.547
ELB improved by 4.62418
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.697
ELB improved by 4.84959
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.578
ELB improved by 5.11891
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.282
ELB improved by 5.29606
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.076
ELB improved by 5.20629
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.389
ELB improved by 4.68722
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.599
ELB improved by 3.78997
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.757
ELB improved by 2.84175
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.664
ELB improved by 2.09331
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.103
ELB improved by 1.56107
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.916
ELB improved by 1.18661
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.989
ELB improved by 0.926863
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.242
ELB improved by 0.746834
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.624
ELB improved by 0.618744
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.096
ELB improved by 0.527131
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.63
ELB improved by 0.466108
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.2
ELB improved by 0.429907
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.797
ELB improved by 0.403159
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.432
ELB improved by 0.365176
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.121
ELB improved by 0.311382
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.866
ELB improved by 0.254889
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.66
ELB improved by 0.206153
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.492
ELB improved by 0.167357
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.355
ELB improved by 0.137405
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.24
ELB improved by 0.114583
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.143
ELB improved by 0.0971658
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.059
ELB improved by 0.0836694
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.986
ELB improved by 0.0729673
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.922
ELB improved by 0.064272
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.865
ELB improved by 0.0570528
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.814
ELB improved by 0.0509535
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.768
ELB improved by 0.0457305
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.727
ELB improved by 0.041212
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.69
ELB improved by 0.0372726
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.656
ELB improved by 0.0338172
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.625
ELB improved by 0.0307716
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.597
ELB improved by 0.0280764
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.572
ELB improved by 0.0256829
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.548
ELB improved by 0.023551
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.526
ELB improved by 0.0216469
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.507
ELB improved by 0.0199417
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.488
ELB improved by 0.0184113
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.471
ELB improved by 0.0170346
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.455
ELB improved by 0.0157937
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.441
ELB improved by 0.0146728
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.427
ELB improved by 0.0136586
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.414
ELB improved by 0.0127391
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.402
ELB improved by 0.011904
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.391
ELB improved by 0.0111444
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.381
ELB improved by 0.0104523
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.371
ELB improved by 0.00982068
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-857.074
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-598.951
ELB improved by 258.123
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-538.945
ELB improved by 60.0062
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-488.147
ELB improved by 50.798
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.137
ELB improved by 30.0101
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.229
ELB improved by 11.9086
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.231
ELB improved by 4.99735
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.316
ELB improved by 2.91512
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.237
ELB improved by 2.07891
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.496
ELB improved by 1.74155
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.865
ELB improved by 1.63025
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.23
ELB improved by 1.6355
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.513
ELB improved by 1.71635
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.656
ELB improved by 1.85785
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.613
ELB improved by 2.04219
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.391
ELB improved by 2.22209
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.075
ELB improved by 2.31638
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.818
ELB improved by 2.25716
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.78
ELB improved by 2.03763
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.061
ELB improved by 1.71894
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.672
ELB improved by 1.38934
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.557
ELB improved by 1.11452
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.637
ELB improved by 0.92081
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.84
ELB improved by 0.796449
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.124
ELB improved by 0.716536
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.462
ELB improved by 0.661941
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.84
ELB improved by 0.622134
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.247
ELB improved by 0.592338
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.677
ELB improved by 0.57055
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.121
ELB improved by 0.555583
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.575
ELB improved by 0.546023
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.035
ELB improved by 0.539779
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.501
ELB improved by 0.534011
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.976
ELB improved by 0.525349
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.465
ELB improved by 0.510425
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.979
ELB improved by 0.486627
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.526
ELB improved by 0.452801
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.116
ELB improved by 0.409607
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.757
ELB improved by 0.359406
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.451
ELB improved by 0.305789
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.198
ELB improved by 0.252827
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.994
ELB improved by 0.204142
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.832
ELB improved by 0.162113
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.705
ELB improved by 0.127624
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.604
ELB improved by 0.100361
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.525
ELB improved by 0.0793482
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.461
ELB improved by 0.0633996
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.41
ELB improved by 0.0513961
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.368
ELB improved by 0.0423975
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.332
ELB improved by 0.0356624
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.301
ELB improved by 0.0306257
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.274
ELB improved by 0.0268627
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.25
ELB improved by 0.024055
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.228
ELB improved by 0.0219616
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.208
ELB improved by 0.0203967
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.189
ELB improved by 0.0192123
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.171
ELB improved by 0.0182872
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.153
ELB improved by 0.017519
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.136
ELB improved by 0.0168212
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.12
ELB improved by 0.0161235
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.105
ELB improved by 0.0153742
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.09
ELB improved by 0.0145437
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.077
ELB improved by 0.0136258
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.064
ELB improved by 0.0126362
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.052
ELB improved by 0.0116065
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.042
ELB improved by 0.010576
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.032
ELB improved by 0.00958325
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-821.488
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-548.317
ELB improved by 273.171
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-485.145
ELB improved by 63.1722
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.555
ELB improved by 37.5904
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.126
ELB improved by 16.4283
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.782
ELB improved by 7.34465
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.97
ELB improved by 4.81137
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.717
ELB improved by 4.25315
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.47
ELB improved by 4.24764
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.03
ELB improved by 4.43924
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.406
ELB improved by 4.62468
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.817
ELB improved by 4.58912
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.68
ELB improved by 4.137
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.411
ELB improved by 3.26808
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.136
ELB improved by 2.27505
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.647
ELB improved by 1.48968
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.646
ELB improved by 1.00093
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.92
ELB improved by 0.726191
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.348
ELB improved by 0.571537
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.867
ELB improved by 0.48069
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.442
ELB improved by 0.425337
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.051
ELB improved by 0.391271
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.68
ELB improved by 0.370751
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.321
ELB improved by 0.358898
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.969
ELB improved by 0.352051
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.622
ELB improved by 0.347267
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.279
ELB improved by 0.342596
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.942
ELB improved by 0.337495
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.609
ELB improved by 0.332768
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.279
ELB improved by 0.330161
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.947
ELB improved by 0.33228
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.603
ELB improved by 0.343426
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.232
ELB improved by 0.371572
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.801
ELB improved by 0.430923
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.263
ELB improved by 0.537654
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.585
ELB improved by 0.678255
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.797
ELB improved by 0.787398
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.967
ELB improved by 0.830481
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.142
ELB improved by 0.825011
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.349
ELB improved by 0.793053
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.601
ELB improved by 0.747629
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.91
ELB improved by 0.690995
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.286
ELB improved by 0.624471
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.733
ELB improved by 0.553084
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.248
ELB improved by 0.485065
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.817
ELB improved by 0.430257
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.419
ELB improved by 0.398618
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.025
ELB improved by 0.393476
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.637
ELB improved by 0.388208
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.305
ELB improved by 0.331544
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.068
ELB improved by 0.237032
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.909
ELB improved by 0.159197
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.799
ELB improved by 0.110041
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.719
ELB improved by 0.0796402
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.66
ELB improved by 0.0598472
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.613
ELB improved by 0.0463018
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.577
ELB improved by 0.0366889
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.547
ELB improved by 0.0296826
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.523
ELB improved by 0.0244671
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.502
ELB improved by 0.0205132
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.485
ELB improved by 0.0174652
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.469
ELB improved by 0.0150776
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.456
ELB improved by 0.0131779
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.445
ELB improved by 0.0116434
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.434
ELB improved by 0.0103858
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.425
ELB improved by 0.00934112
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-822.617
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-551.075
ELB improved by 271.541
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-493.789
ELB improved by 57.286
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.125
ELB improved by 25.6644
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.371
ELB improved by 8.75437
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.984
ELB improved by 4.38667
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.781
ELB improved by 3.20337
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.927
ELB improved by 2.85348
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.145
ELB improved by 2.78228
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.359
ELB improved by 2.786
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.597
ELB improved by 2.76214
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.951
ELB improved by 2.64587
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.561
ELB improved by 2.39003
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.574
ELB improved by 1.98693
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.062
ELB improved by 1.51214
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.975
ELB improved by 1.08679
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.192
ELB improved by 0.782608
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.597
ELB improved by 0.59546
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.109
ELB improved by 0.488422
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.68
ELB improved by 0.428491
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.285
ELB improved by 0.395121
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.908
ELB improved by 0.376939
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.54
ELB improved by 0.367668
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.177
ELB improved by 0.363591
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.815
ELB improved by 0.362256
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.453
ELB improved by 0.361883
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.091
ELB improved by 0.361141
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.732
ELB improved by 0.359093
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.377
ELB improved by 0.355213
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.028
ELB improved by 0.34939
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.686
ELB improved by 0.341889
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.353
ELB improved by 0.333263
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.028
ELB improved by 0.324243
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.713
ELB improved by 0.315635
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.405
ELB improved by 0.308266
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.102
ELB improved by 0.303
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.801
ELB improved by 0.300844
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.497
ELB improved by 0.303205
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.185
ELB improved by 0.312428
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.852
ELB improved by 0.332886
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.479
ELB improved by 0.372798
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.035
ELB improved by 0.444479
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.485
ELB improved by 0.550018
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.84
ELB improved by 0.644932
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.169
ELB improved by 0.670762
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.528
ELB improved by 0.641103
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.944
ELB improved by 0.584433
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.437
ELB improved by 0.506675
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.023
ELB improved by 0.41421
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.703
ELB improved by 0.319564
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.468
ELB improved by 0.235062
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.301
ELB improved by 0.167602
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.182
ELB improved by 0.118075
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.099
ELB improved by 0.0837067
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.038
ELB improved by 0.0606009
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.993
ELB improved by 0.0452335
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.958
ELB improved by 0.03495
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.93
ELB improved by 0.0279361
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.907
ELB improved by 0.023017
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.888
ELB improved by 0.0194523
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.871
ELB improved by 0.0167801
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.856
ELB improved by 0.0147116
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.843
ELB improved by 0.0130638
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.831
ELB improved by 0.0117182
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.821
ELB improved by 0.0105968
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.811
ELB improved by 0.00964605
ELB converged
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 24 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
4.425 0.121 4.532
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.076 | 0.003 | 0.093 | |
| getPIPs | 0.067 | 0.005 | 0.073 | |
| graper | 0.110 | 0.009 | 0.118 | |
| makeExampleData | 0.023 | 0.003 | 0.027 | |
| makeExampleDataWithUnequalGroups | 0.017 | 0.000 | 0.017 | |
| plotELBO | 0.266 | 0.023 | 0.306 | |
| plotGroupPenalties | 0.884 | 0.020 | 0.905 | |
| plotPosterior | 0.607 | 0.008 | 0.615 | |
| predict.graper | 2.058 | 0.016 | 2.074 | |
| print.graper | 0.075 | 0.000 | 0.075 | |