Britta Velten
| Snapshot Date: 2024-06-23 14:00 -0400 (Sun, 23 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: RELEASE_3_19 |
| git_last_commit: a4dfa52 |
| git_last_commit_date: 2024-04-30 11:11:42 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-25 17:43 -0400 (Tue, 25 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
| 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 908/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.20.0 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | 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: 1.20.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.20.0.tar.gz |
| StartedAt: 2024-06-24 21:52:49 -0400 (Mon, 24 Jun 2024) |
| EndedAt: 2024-06-24 21:54:01 -0400 (Mon, 24 Jun 2024) |
| EllapsedTime: 71.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: graper.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### 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_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/graper.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.20.0’
* 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 ... WARNING
Found the following significant warnings:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
# warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
See ‘/Users/biocbuild/bbs-3.19-bioc/meat/graper.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* 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: 1 WARNING, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.19-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/4.4-arm64/Resources/library’
* installing *source* package ‘graper’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fit_graper.cpp -o fit_graper.o
In file included from fit_graper.cpp:4:
In file included from ./graper_linear_dense_ff.h:2:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/digamma.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/math_fwd.hpp:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
# warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o graper.so RcppExports.o fit_graper.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-graper/00new/graper/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (graper)
graper.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(graper)
>
> test_check("graper")
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-868.489
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-558.432
ELB improved by 310.056
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-496.939
ELB improved by 61.4938
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.489
ELB improved by 34.4496
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.897
ELB improved by 15.5919
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.619
ELB improved by 8.27762
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.542
ELB improved by 6.07743
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.731
ELB improved by 5.8113
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.421
ELB improved by 6.3101
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.263
ELB improved by 7.1579
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.396
ELB improved by 7.86699
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.666
ELB improved by 7.73005
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.251
ELB improved by 6.41492
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.691
ELB improved by 4.55987
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.726
ELB improved by 2.96478
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.846
ELB improved by 1.87987
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.625
ELB improved by 1.22174
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.787
ELB improved by 0.837958
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.177
ELB improved by 0.609981
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.71
ELB improved by 0.467014
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.338
ELB improved by 0.37126
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.035
ELB improved by 0.303186
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.783
ELB improved by 0.252487
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.569
ELB improved by 0.213431
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.387
ELB improved by 0.182599
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.229
ELB improved by 0.157817
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.091
ELB improved by 0.137621
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.97
ELB improved by 0.120984
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.863
ELB improved by 0.107158
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.767
ELB improved by 0.0955862
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.682
ELB improved by 0.0858459
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.604
ELB improved by 0.0776101
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.533
ELB improved by 0.0706234
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.469
ELB improved by 0.0646842
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.409
ELB improved by 0.0596324
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.354
ELB improved by 0.05534
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.302
ELB improved by 0.0517051
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.253
ELB improved by 0.0486465
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.207
ELB improved by 0.0461002
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.163
ELB improved by 0.0440168
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.121
ELB improved by 0.0423596
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.08
ELB improved by 0.041103
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.04
ELB improved by 0.0402321
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376
ELB improved by 0.0397421
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.96
ELB improved by 0.0396382
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.92
ELB improved by 0.0399364
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.88
ELB improved by 0.0406648
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.838
ELB improved by 0.0418648
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.794
ELB improved by 0.0435941
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.748
ELB improved by 0.0459303
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.699
ELB improved by 0.0489763
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.646
ELB improved by 0.0528671
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.589
ELB improved by 0.0577808
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.525
ELB improved by 0.0639518
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.453
ELB improved by 0.0716906
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.372
ELB improved by 0.0814092
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.278
ELB improved by 0.0936536
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.169
ELB improved by 0.109141
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.04
ELB improved by 0.128793
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.886
ELB improved by 0.15372
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.701
ELB improved by 0.1851
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.477
ELB improved by 0.223793
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.208
ELB improved by 0.269654
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.887
ELB improved by 0.320823
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.513
ELB improved by 0.373751
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.089
ELB improved by 0.424036
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.622
ELB improved by 0.466778
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.126
ELB improved by 0.496237
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.619
ELB improved by 0.506535
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.126
ELB improved by 0.49388
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.667
ELB improved by 0.458805
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.26
ELB improved by 0.406718
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.914
ELB improved by 0.346165
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.628
ELB improved by 0.285744
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.397
ELB improved by 0.231516
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.21
ELB improved by 0.1862
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.061
ELB improved by 0.149941
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.939
ELB improved by 0.121594
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.839
ELB improved by 0.0996831
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.756
ELB improved by 0.0827818
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.687
ELB improved by 0.0695075
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.628
ELB improved by 0.058474
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.58
ELB improved by 0.048475
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.541
ELB improved by 0.0388914
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.511
ELB improved by 0.0299036
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.489
ELB improved by 0.0221405
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.473
ELB improved by 0.0160634
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.461
ELB improved by 0.011677
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.453
ELB improved by 0.00866155
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-934.301
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-601.103
ELB improved by 333.197
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-540.684
ELB improved by 60.4197
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-501.183
ELB improved by 39.5011
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-483.2
ELB improved by 17.9826
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-476.149
ELB improved by 7.05099
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.416
ELB improved by 3.73263
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.443
ELB improved by 2.97301
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.608
ELB improved by 2.83565
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.702
ELB improved by 2.9055
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.642
ELB improved by 3.06059
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.47
ELB improved by 3.17178
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.396
ELB improved by 3.07378
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.709
ELB improved by 2.68714
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.577
ELB improved by 2.13206
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.958
ELB improved by 1.6191
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.699
ELB improved by 1.25923
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.652
ELB improved by 1.04616
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.719
ELB improved by 0.933809
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.841
ELB improved by 0.878039
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.992
ELB improved by 0.848702
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.16
ELB improved by 0.831728
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.335
ELB improved by 0.824842
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.502
ELB improved by 0.833137
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.633
ELB improved by 0.86901
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.677
ELB improved by 0.955997
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.556
ELB improved by 1.12145
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.224
ELB improved by 1.33188
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.736
ELB improved by 1.48828
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.132
ELB improved by 1.60389
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.407
ELB improved by 1.72446
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.569
ELB improved by 1.83788
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.639
ELB improved by 1.92999
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.598
ELB improved by 2.04171
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.336
ELB improved by 2.26165
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.87
ELB improved by 2.46548
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.703
ELB improved by 2.16697
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.27
ELB improved by 1.43387
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.398
ELB improved by 0.871413
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.845
ELB improved by 0.553516
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.468
ELB improved by 0.3765
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.196
ELB improved by 0.272458
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.989
ELB improved by 0.20669
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.827
ELB improved by 0.161814
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.698
ELB improved by 0.128982
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.595
ELB improved by 0.103693
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.511
ELB improved by 0.0837045
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.443
ELB improved by 0.0678701
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.388
ELB improved by 0.0554519
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.342
ELB improved by 0.0458125
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.303
ELB improved by 0.0383532
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.271
ELB improved by 0.0325481
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.243
ELB improved by 0.0279749
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.219
ELB improved by 0.0243172
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.197
ELB improved by 0.0213472
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.178
ELB improved by 0.0189026
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.161
ELB improved by 0.0168677
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.146
ELB improved by 0.0151581
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.133
ELB improved by 0.0137111
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.12
ELB improved by 0.012479
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.109
ELB improved by 0.0114243
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.098
ELB improved by 0.0105176
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.088
ELB improved by 0.00973486
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-873.908
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-581.745
ELB improved by 292.164
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-518.679
ELB improved by 63.066
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-477.006
ELB improved by 41.6727
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.604
ELB improved by 17.4024
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.306
ELB improved by 7.29714
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.23
ELB improved by 5.07659
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.374
ELB improved by 4.8559
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.294
ELB improved by 5.08002
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.057
ELB improved by 5.23648
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.092
ELB improved by 4.96546
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.94
ELB improved by 4.15155
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.878
ELB improved by 3.06268
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.785
ELB improved by 2.0927
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.34
ELB improved by 1.44544
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.239
ELB improved by 1.10113
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.273
ELB improved by 0.966
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.317
ELB improved by 0.955608
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.326
ELB improved by 0.991311
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.271
ELB improved by 1.0547
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.09
ELB improved by 1.18133
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.759
ELB improved by 1.33083
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.326
ELB improved by 1.43264
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.811
ELB improved by 1.51534
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.172
ELB improved by 1.63849
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.31
ELB improved by 1.86189
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.095
ELB improved by 2.21558
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.428
ELB improved by 2.66711
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.323
ELB improved by 3.10495
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.938
ELB improved by 3.38449
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.578
ELB improved by 3.35988
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.576
ELB improved by 3.00245
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.151
ELB improved by 2.42467
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.409
ELB improved by 1.74197
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.227
ELB improved by 1.18181
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.399
ELB improved by 0.828405
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.815
ELB improved by 0.58425
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.419
ELB improved by 0.395333
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.154
ELB improved by 0.265792
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.967
ELB improved by 0.186341
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.83
ELB improved by 0.137112
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.726
ELB improved by 0.104547
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.644
ELB improved by 0.0816746
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.579
ELB improved by 0.064938
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.527
ELB improved by 0.0523588
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.484
ELB improved by 0.042726
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.449
ELB improved by 0.0352445
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.419
ELB improved by 0.0293668
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.395
ELB improved by 0.0247039
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.374
ELB improved by 0.0209729
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.356
ELB improved by 0.0179648
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.34
ELB improved by 0.0155226
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.327
ELB improved by 0.0135271
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.315
ELB improved by 0.0118868
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.304
ELB improved by 0.0105308
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.295
ELB improved by 0.00940372
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-862.235
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-587.859
ELB improved by 274.376
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-525.094
ELB improved by 62.7651
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-481.051
ELB improved by 44.0427
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.726
ELB improved by 20.325
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.056
ELB improved by 8.67068
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.476
ELB improved by 5.57997
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.59
ELB improved by 4.88582
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.777
ELB improved by 4.81272
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.982
ELB improved by 4.79553
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.459
ELB improved by 4.52215
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.578
ELB improved by 3.88131
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.562
ELB improved by 3.01564
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.386
ELB improved by 2.17697
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.86
ELB improved by 1.52588
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.775
ELB improved by 1.08456
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.972
ELB improved by 0.80339
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.347
ELB improved by 0.624272
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.843
ELB improved by 0.504488
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.426
ELB improved by 0.417384
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.078
ELB improved by 0.347648
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.79
ELB improved by 0.287981
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.553
ELB improved by 0.236609
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.359
ELB improved by 0.194079
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.199
ELB improved by 0.160462
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.064
ELB improved by 0.134577
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.95
ELB improved by 0.114651
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.85
ELB improved by 0.099041
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.764
ELB improved by 0.0865153
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.688
ELB improved by 0.0762353
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.62
ELB improved by 0.0676427
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.56
ELB improved by 0.0603595
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.506
ELB improved by 0.0541199
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.457
ELB improved by 0.0487296
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.413
ELB improved by 0.0440412
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.373
ELB improved by 0.0399399
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.337
ELB improved by 0.0363342
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.303
ELB improved by 0.0331503
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.273
ELB improved by 0.0303276
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.245
ELB improved by 0.0278162
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.22
ELB improved by 0.0255745
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.196
ELB improved by 0.0235674
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.174
ELB improved by 0.0217656
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.154
ELB improved by 0.0201438
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.136
ELB improved by 0.0186808
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.118
ELB improved by 0.0173582
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.102
ELB improved by 0.01616
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.087
ELB improved by 0.0150727
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.073
ELB improved by 0.0140843
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.06
ELB improved by 0.0131844
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.047
ELB improved by 0.012364
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.036
ELB improved by 0.011615
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.025
ELB improved by 0.0109305
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.014
ELB improved by 0.0103042
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.005
ELB improved by 0.00973067
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.769 0.223 3.015
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.091 | 0.016 | 0.106 | |
| getPIPs | 0.083 | 0.013 | 0.097 | |
| graper | 0.136 | 0.018 | 0.153 | |
| makeExampleData | 0.013 | 0.001 | 0.014 | |
| makeExampleDataWithUnequalGroups | 0.037 | 0.003 | 0.040 | |
| plotELBO | 0.268 | 0.018 | 0.287 | |
| plotGroupPenalties | 0.769 | 0.024 | 0.797 | |
| plotPosterior | 0.616 | 0.019 | 0.636 | |
| predict.graper | 3.096 | 0.082 | 3.187 | |
| print.graper | 0.082 | 0.011 | 0.093 | |