| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:38 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the graper package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 804/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.8.0 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: 1.8.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings graper_1.8.0.tar.gz |
| StartedAt: 2021-10-14 19:45:30 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 19:46:48 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 77.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings graper_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/graper.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (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 ‘1.8.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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 ... 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 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 ‘/Users/biocbuild/bbs-3.13-bioc/meat/graper.Rcheck/00check.log’ for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘graper’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c fit_graper.cpp -o fit_graper.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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=-892.34
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-574.099
ELB improved by 318.241
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-509.682
ELB improved by 64.4169
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.011
ELB improved by 42.6706
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.881
ELB improved by 18.1305
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.202
ELB improved by 7.67881
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.582
ELB improved by 4.62002
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.251
ELB improved by 3.33074
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.543
ELB improved by 2.7078
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.085
ELB improved by 2.45799
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.654
ELB improved by 2.43144
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.101
ELB improved by 2.55283
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.315
ELB improved by 2.78661
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.217
ELB improved by 3.09739
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.827
ELB improved by 3.38997
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.344
ELB improved by 3.4832
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.098
ELB improved by 3.24574
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.341
ELB improved by 2.75687
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.125
ELB improved by 2.21625
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.39
ELB improved by 1.73485
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.085
ELB improved by 1.30486
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.149
ELB improved by 0.935917
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.493
ELB improved by 0.65646
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.027
ELB improved by 0.466235
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.68
ELB improved by 0.346561
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.406
ELB improved by 0.273988
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.177
ELB improved by 0.229658
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.975
ELB improved by 0.20175
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.791
ELB improved by 0.183665
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.619
ELB improved by 0.171846
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.455
ELB improved by 0.164369
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.295
ELB improved by 0.160174
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.136
ELB improved by 0.15867
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.977
ELB improved by 0.159538
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.814
ELB improved by 0.162632
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.646
ELB improved by 0.167927
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.47
ELB improved by 0.175503
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.285
ELB improved by 0.185539
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.087
ELB improved by 0.198307
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.872
ELB improved by 0.214178
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.639
ELB improved by 0.233579
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.382
ELB improved by 0.256891
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.098
ELB improved by 0.284233
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.783
ELB improved by 0.315188
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.434
ELB improved by 0.348747
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.05
ELB improved by 0.383891
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.629
ELB improved by 0.420641
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.169
ELB improved by 0.460235
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.666
ELB improved by 0.503021
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.121
ELB improved by 0.544595
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.547
ELB improved by 0.574404
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.965
ELB improved by 0.581648
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.402
ELB improved by 0.56321
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.878
ELB improved by 0.524434
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.402
ELB improved by 0.47573
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.972
ELB improved by 0.430068
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.57
ELB improved by 0.401847
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.163
ELB improved by 0.407438
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.704
ELB improved by 0.458351
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.19
ELB improved by 0.514075
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.723
ELB improved by 0.467486
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.387
ELB improved by 0.335351
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.167
ELB improved by 0.220658
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.019
ELB improved by 0.147555
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.916
ELB improved by 0.103192
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.841
ELB improved by 0.0753701
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.784
ELB improved by 0.0569088
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.74
ELB improved by 0.0439965
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.705
ELB improved by 0.034625
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.677
ELB improved by 0.0276745
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.655
ELB improved by 0.0224569
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.636
ELB improved by 0.0185085
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.621
ELB improved by 0.0154981
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.608
ELB improved by 0.013184
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.596
ELB improved by 0.0113882
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.586
ELB improved by 0.00998015
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-831.637
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-579.575
ELB improved by 252.062
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-514.618
ELB improved by 64.9572
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.402
ELB improved by 49.2163
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.256
ELB improved by 25.1454
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.886
ELB improved by 10.3709
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.639
ELB improved by 5.24677
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.579
ELB improved by 3.05995
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.45
ELB improved by 2.12832
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.736
ELB improved by 1.71476
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.243
ELB improved by 1.49246
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.902
ELB improved by 1.34168
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.679
ELB improved by 1.22266
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.555
ELB improved by 1.12434
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.511
ELB improved by 1.04342
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.535
ELB improved by 0.976314
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.618
ELB improved by 0.916716
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.762
ELB improved by 0.855822
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.977
ELB improved by 0.78506
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.277
ELB improved by 0.700247
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.673
ELB improved by 0.604417
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.166
ELB improved by 0.506592
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.749
ELB improved by 0.417086
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.406
ELB improved by 0.343017
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.119
ELB improved by 0.286805
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.872
ELB improved by 0.247305
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.65
ELB improved by 0.221704
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.443
ELB improved by 0.206925
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.243
ELB improved by 0.20031
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.043
ELB improved by 0.199803
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.839
ELB improved by 0.203888
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.628
ELB improved by 0.211456
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.406
ELB improved by 0.221679
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.172
ELB improved by 0.233936
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.924
ELB improved by 0.247823
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.661
ELB improved by 0.263213
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.381
ELB improved by 0.280384
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.081
ELB improved by 0.300143
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.757
ELB improved by 0.323937
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.403
ELB improved by 0.353892
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.01
ELB improved by 0.392691
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.567
ELB improved by 0.4431
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.06
ELB improved by 0.506827
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.477
ELB improved by 0.582728
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.812
ELB improved by 0.665156
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.068
ELB improved by 0.744061
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.259
ELB improved by 0.809139
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.404
ELB improved by 0.854557
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.53
ELB improved by 0.874466
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.668
ELB improved by 0.861508
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.848
ELB improved by 0.820377
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.08
ELB improved by 0.767976
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.372
ELB improved by 0.708041
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.748
ELB improved by 0.6238
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.237
ELB improved by 0.511241
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.843
ELB improved by 0.394516
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.545
ELB improved by 0.297924
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.315
ELB improved by 0.229583
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.127
ELB improved by 0.188318
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.953
ELB improved by 0.173431
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.762
ELB improved by 0.191694
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.5
ELB improved by 0.261814
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.103
ELB improved by 0.396444
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.584
ELB improved by 0.519273
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.095
ELB improved by 0.489269
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.71
ELB improved by 0.384793
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.344
ELB improved by 0.365841
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.912
ELB improved by 0.432434
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.482
ELB improved by 0.429749
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.16
ELB improved by 0.322239
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.937
ELB improved by 0.222931
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.788
ELB improved by 0.14924
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.693
ELB improved by 0.0947073
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.633
ELB improved by 0.0595057
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.594
ELB improved by 0.039532
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.565
ELB improved by 0.0287437
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.542
ELB improved by 0.0227394
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.523
ELB improved by 0.0190951
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.507
ELB improved by 0.0166299
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.492
ELB improved by 0.0147932
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.478
ELB improved by 0.0133265
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.466
ELB improved by 0.012103
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.455
ELB improved by 0.0110554
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.445
ELB improved by 0.0101444
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.436
ELB improved by 0.00934434
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-896.968
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-581.205
ELB improved by 315.763
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-527.496
ELB improved by 53.7092
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-495.261
ELB improved by 32.2347
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-479.559
ELB improved by 15.7024
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.235
ELB improved by 7.32415
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.949
ELB improved by 4.2856
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.707
ELB improved by 3.24195
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.882
ELB improved by 2.82506
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.303
ELB improved by 2.57884
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.964
ELB improved by 2.33904
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.912
ELB improved by 2.05197
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.194
ELB improved by 1.71779
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.829
ELB improved by 1.36572
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.793
ELB improved by 1.03591
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.031
ELB improved by 0.761823
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.475
ELB improved by 0.556261
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.062
ELB improved by 0.412384
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.748
ELB improved by 0.314806
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.499
ELB improved by 0.24859
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.296
ELB improved by 0.202625
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.127
ELB improved by 0.169615
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.982
ELB improved by 0.145014
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.856
ELB improved by 0.126029
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.745
ELB improved by 0.110921
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.646
ELB improved by 0.0985835
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.558
ELB improved by 0.088289
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.478
ELB improved by 0.0795477
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.406
ELB improved by 0.0720202
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.341
ELB improved by 0.0654644
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.281
ELB improved by 0.0597034
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.227
ELB improved by 0.0546046
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.176
ELB improved by 0.0500657
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.13
ELB improved by 0.046006
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.088
ELB improved by 0.0423605
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.049
ELB improved by 0.0390761
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.013
ELB improved by 0.0361082
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.979
ELB improved by 0.0334193
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.949
ELB improved by 0.0309775
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.92
ELB improved by 0.0287554
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.893
ELB improved by 0.0267292
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.868
ELB improved by 0.0248782
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.845
ELB improved by 0.0231845
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.823
ELB improved by 0.0216321
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.803
ELB improved by 0.0202071
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.784
ELB improved by 0.0188972
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.767
ELB improved by 0.0176915
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.75
ELB improved by 0.0165803
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.734
ELB improved by 0.0155549
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.72
ELB improved by 0.0146076
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.706
ELB improved by 0.0137315
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.693
ELB improved by 0.0129203
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.681
ELB improved by 0.0121685
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.67
ELB improved by 0.0114711
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.659
ELB improved by 0.0108234
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.648
ELB improved by 0.0102215
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.639
ELB improved by 0.00966153
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-930.254
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-584.58
ELB improved by 345.675
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-525.336
ELB improved by 59.2436
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-490.052
ELB improved by 35.2836
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-474.2
ELB improved by 15.8523
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.45
ELB improved by 7.74993
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.723
ELB improved by 5.72702
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.26
ELB improved by 5.46348
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.501
ELB improved by 5.75832
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.624
ELB improved by 5.8777
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.376
ELB improved by 5.24778
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.451
ELB improved by 3.92531
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.897
ELB improved by 2.55395
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.305
ELB improved by 1.59203
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.272
ELB improved by 1.03264
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.556
ELB improved by 0.716056
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.028
ELB improved by 0.527984
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.619
ELB improved by 0.408981
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.29
ELB improved by 0.329164
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.017
ELB improved by 0.272935
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.785
ELB improved by 0.231727
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.585
ELB improved by 0.200585
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.408
ELB improved by 0.176504
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.25
ELB improved by 0.157596
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.108
ELB improved by 0.142645
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.977
ELB improved by 0.130862
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.855
ELB improved by 0.121745
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.74
ELB improved by 0.114984
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.63
ELB improved by 0.110401
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.522
ELB improved by 0.107869
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.415
ELB improved by 0.107206
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.307
ELB improved by 0.108023
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.197
ELB improved by 0.109558
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.086
ELB improved by 0.110653
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.976
ELB improved by 0.110008
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.87
ELB improved by 0.106698
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.769
ELB improved by 0.100651
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.676
ELB improved by 0.0927203
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.592
ELB improved by 0.0841702
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.516
ELB improved by 0.0759222
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.448
ELB improved by 0.0681733
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.388
ELB improved by 0.0606214
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.335
ELB improved by 0.0529824
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.289
ELB improved by 0.0453664
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.251
ELB improved by 0.0382611
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.219
ELB improved by 0.0321955
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.191
ELB improved by 0.0274229
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.167
ELB improved by 0.0238654
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.146
ELB improved by 0.0212589
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.127
ELB improved by 0.0193148
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.109
ELB improved by 0.0178036
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.092
ELB improved by 0.0165713
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.077
ELB improved by 0.015523
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.062
ELB improved by 0.0146032
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.049
ELB improved by 0.0137794
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.036
ELB improved by 0.0130319
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.023
ELB improved by 0.0123483
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.011
ELB improved by 0.0117199
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424
ELB improved by 0.0111403
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.99
ELB improved by 0.0106043
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.98
ELB improved by 0.0101077
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.97
ELB improved by 0.00964678
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
3.235 0.275 3.516
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.070 | 0.025 | 0.099 | |
| getPIPs | 0.051 | 0.016 | 0.066 | |
| graper | 0.112 | 0.035 | 0.147 | |
| makeExampleData | 0.016 | 0.001 | 0.018 | |
| makeExampleDataWithUnequalGroups | 0.017 | 0.002 | 0.020 | |
| plotELBO | 0.266 | 0.027 | 0.294 | |
| plotGroupPenalties | 0.895 | 0.024 | 0.919 | |
| plotPosterior | 0.920 | 0.061 | 1.015 | |
| predict.graper | 2.409 | 0.110 | 2.525 | |
| print.graper | 0.067 | 0.022 | 0.091 | |