Britta Velten
| Snapshot Date: 2024-07-23 14:00 -0400 (Tue, 23 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: 7b45fcc |
| git_last_commit_date: 2024-04-30 11:11:42 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-24 11:40 -0400 (Wed, 24 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4688 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4284 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4455 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4404 |
| 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 886/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.21.0 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 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: 1.21.0 |
| 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_1.21.0.tar.gz |
| StartedAt: 2024-07-23 21:41:17 -0400 (Tue, 23 Jul 2024) |
| EndedAt: 2024-07-23 21:42:40 -0400 (Tue, 23 Jul 2024) |
| EllapsedTime: 82.1 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_1.21.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/graper.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.21.0’
* 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-x86_64/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-3.20-bioc/meat/graper.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* 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-3.20-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-x86_64/Resources/library’
* installing *source* package ‘graper’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fit_graper.cpp -o fit_graper.o
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-x86_64/Resources/library/BH/include/boost/math/special_functions/digamma.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/math_fwd.hpp:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/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 x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o graper.so RcppExports.o fit_graper.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-graper/00new/graper/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (graper)
graper.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(graper)
>
> test_check("graper")
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-841.317
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-590.973
ELB improved by 250.344
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-529.711
ELB improved by 61.2622
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-477.648
ELB improved by 52.063
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.396
ELB improved by 30.2513
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.71
ELB improved by 12.686
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.753
ELB improved by 5.95702
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.666
ELB improved by 4.08765
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.244
ELB improved by 3.42218
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.064
ELB improved by 3.17974
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.94
ELB improved by 3.12346
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.779
ELB improved by 3.16168
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.532
ELB improved by 3.24701
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.216
ELB improved by 3.31617
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.939
ELB improved by 3.2762
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.909
ELB improved by 3.03068
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.361
ELB improved by 2.54752
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.399
ELB improved by 1.96173
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.916
ELB improved by 1.48341
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.718
ELB improved by 1.19766
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.644
ELB improved by 1.07445
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.586
ELB improved by 1.05762
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.481
ELB improved by 1.10573
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.286
ELB improved by 1.19424
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.977
ELB improved by 1.30893
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.536
ELB improved by 1.44115
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.952
ELB improved by 1.58376
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.229
ELB improved by 1.72355
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.398
ELB improved by 1.83124
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.538
ELB improved by 1.85984
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.771
ELB improved by 1.76654
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.218
ELB improved by 1.55314
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.929
ELB improved by 1.28876
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.85
ELB improved by 1.07891
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.909
ELB improved by 0.940988
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.19
ELB improved by 0.719062
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.733
ELB improved by 0.4571
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.444
ELB improved by 0.289776
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.243
ELB improved by 0.200211
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.092
ELB improved by 0.151265
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.969
ELB improved by 0.123344
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.862
ELB improved by 0.106626
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.767
ELB improved by 0.0952967
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.681
ELB improved by 0.0853319
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.607
ELB improved by 0.074491
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.544
ELB improved by 0.0628656
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.492
ELB improved by 0.0520301
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.449
ELB improved by 0.0432083
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.412
ELB improved by 0.0365414
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.381
ELB improved by 0.0315847
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.353
ELB improved by 0.0278532
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.328
ELB improved by 0.0249967
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.305
ELB improved by 0.0227899
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.284
ELB improved by 0.0210898
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.264
ELB improved by 0.0198056
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.245
ELB improved by 0.0188777
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.227
ELB improved by 0.0182609
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.209
ELB improved by 0.0179074
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.191
ELB improved by 0.0177514
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.174
ELB improved by 0.0176987
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.156
ELB improved by 0.0176287
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.139
ELB improved by 0.0174142
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.122
ELB improved by 0.0169572
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.105
ELB improved by 0.0162244
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.09
ELB improved by 0.015259
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.076
ELB improved by 0.0141574
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.063
ELB improved by 0.0130255
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.051
ELB improved by 0.0119433
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.04
ELB improved by 0.0109516
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.03
ELB improved by 0.0100596
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.021
ELB improved by 0.009258
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-880.157
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-589.801
ELB improved by 290.356
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-528.278
ELB improved by 61.5238
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-489.323
ELB improved by 38.9543
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.457
ELB improved by 17.8658
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.482
ELB improved by 7.97591
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.336
ELB improved by 5.14577
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.444
ELB improved by 4.89165
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.102
ELB improved by 5.34256
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.285
ELB improved by 5.81703
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.623
ELB improved by 5.66162
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.933
ELB improved by 4.6898
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.481
ELB improved by 3.45256
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.063
ELB improved by 2.41776
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.313
ELB improved by 1.75025
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.92
ELB improved by 1.39246
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.709
ELB improved by 1.21148
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.593
ELB improved by 1.1154
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.536
ELB improved by 1.05697
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.521
ELB improved by 1.0157
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.535
ELB improved by 0.985627
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.565
ELB improved by 0.969564
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.586
ELB improved by 0.979076
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.546
ELB improved by 1.04052
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.351
ELB improved by 1.19507
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.932
ELB improved by 1.41822
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.385
ELB improved by 1.54725
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.807
ELB improved by 1.57776
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.219
ELB improved by 1.58839
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.662
ELB improved by 1.55731
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.215
ELB improved by 1.4471
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.962
ELB improved by 1.25282
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.952
ELB improved by 1.0096
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.182
ELB improved by 0.769964
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.61
ELB improved by 0.571906
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.186
ELB improved by 0.424817
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.867
ELB improved by 0.318806
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.626
ELB improved by 0.240847
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.443
ELB improved by 0.18286
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.302
ELB improved by 0.140598
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.192
ELB improved by 0.110547
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.103
ELB improved by 0.0892275
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.029
ELB improved by 0.0737603
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.967
ELB improved by 0.0621481
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.914
ELB improved by 0.0531323
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.868
ELB improved by 0.0459401
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.828
ELB improved by 0.0400847
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.792
ELB improved by 0.0352448
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.761
ELB improved by 0.0311977
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.733
ELB improved by 0.0277833
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.709
ELB improved by 0.0248826
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.686
ELB improved by 0.0224054
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.666
ELB improved by 0.0202814
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.647
ELB improved by 0.0184553
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.63
ELB improved by 0.0168822
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.615
ELB improved by 0.0155257
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.601
ELB improved by 0.0143555
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.587
ELB improved by 0.0133463
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.575
ELB improved by 0.0124766
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.563
ELB improved by 0.011728
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.552
ELB improved by 0.0110844
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.541
ELB improved by 0.0105318
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.531
ELB improved by 0.0100577
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.522
ELB improved by 0.00965081
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-876.252
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-588.045
ELB improved by 288.206
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-525.418
ELB improved by 62.6272
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-484.243
ELB improved by 41.175
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.429
ELB improved by 20.8142
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.192
ELB improved by 10.2374
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.575
ELB improved by 6.61637
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.328
ELB improved by 6.2474
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.309
ELB improved by 7.01918
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.37
ELB improved by 7.93842
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.529
ELB improved by 7.84171
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.283
ELB improved by 6.24581
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.068
ELB improved by 4.2149
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.334
ELB improved by 2.73346
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.442
ELB improved by 1.89208
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.992
ELB improved by 1.45023
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.789
ELB improved by 1.20276
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.761
ELB improved by 1.0287
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.863
ELB improved by 0.897823
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.046
ELB improved by 0.81642
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.272
ELB improved by 0.774673
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.515
ELB improved by 0.75651
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.764
ELB improved by 0.750786
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.013
ELB improved by 0.751731
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.255
ELB improved by 0.757371
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.487
ELB improved by 0.768181
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.701
ELB improved by 0.785939
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.889
ELB improved by 0.812652
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.039
ELB improved by 0.849266
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.146
ELB improved by 0.893745
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.207
ELB improved by 0.938891
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.235
ELB improved by 0.97204
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.256
ELB improved by 0.978345
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.31
ELB improved by 0.945844
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.44
ELB improved by 0.870773
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.678
ELB improved by 0.761973
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.038
ELB improved by 0.639333
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.513
ELB improved by 0.525572
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.073
ELB improved by 0.439612
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.674
ELB improved by 0.399202
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.242
ELB improved by 0.431481
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.695
ELB improved by 0.547015
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.09
ELB improved by 0.604981
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.586
ELB improved by 0.504186
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.182
ELB improved by 0.403923
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.83
ELB improved by 0.352632
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.526
ELB improved by 0.304036
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.291
ELB improved by 0.234585
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.13
ELB improved by 0.161071
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.025
ELB improved by 0.104929
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.955
ELB improved by 0.0700304
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.905
ELB improved by 0.0500766
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.866
ELB improved by 0.0385045
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.835
ELB improved by 0.0312633
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.809
ELB improved by 0.026277
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.786
ELB improved by 0.0225491
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.767
ELB improved by 0.0195996
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.75
ELB improved by 0.0171838
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.734
ELB improved by 0.015165
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.721
ELB improved by 0.0134578
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.709
ELB improved by 0.0120034
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.698
ELB improved by 0.0107582
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.689
ELB improved by 0.00968792
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-876.699
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-578.648
ELB improved by 298.051
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-519.978
ELB improved by 58.6703
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-483.712
ELB improved by 36.2666
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.253
ELB improved by 16.4581
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.226
ELB improved by 7.02768
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.048
ELB improved by 4.17752
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.457
ELB improved by 3.5908
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.878
ELB improved by 3.57991
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.226
ELB improved by 3.65202
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.673
ELB improved by 3.55207
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.529
ELB improved by 3.14466
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.043
ELB improved by 2.4858
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.265
ELB improved by 1.77817
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.058
ELB improved by 1.20678
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.226
ELB improved by 0.831983
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.607
ELB improved by 0.618967
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.098
ELB improved by 0.50942
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.646
ELB improved by 0.452048
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.235
ELB improved by 0.410566
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.862
ELB improved by 0.37336
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.516
ELB improved by 0.345812
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.185
ELB improved by 0.331009
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.859
ELB improved by 0.3263
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.53
ELB improved by 0.328116
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.196
ELB improved by 0.334001
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.854
ELB improved by 0.342658
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.5
ELB improved by 0.353853
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.132
ELB improved by 0.368431
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.743
ELB improved by 0.388315
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.326
ELB improved by 0.41672
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.867
ELB improved by 0.459031
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.343
ELB improved by 0.524326
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.719
ELB improved by 0.624501
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.96
ELB improved by 0.758803
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.077
ELB improved by 0.882712
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.138
ELB improved by 0.938637
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.204
ELB improved by 0.934735
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.295
ELB improved by 0.908823
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.405
ELB improved by 0.890113
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.478
ELB improved by 0.926569
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.377
ELB improved by 1.10075
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.133
ELB improved by 1.2443
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.208
ELB improved by 0.925128
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.534
ELB improved by 0.674343
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.984
ELB improved by 0.549326
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.564
ELB improved by 0.420306
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.259
ELB improved by 0.304984
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.04
ELB improved by 0.219274
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.879
ELB improved by 0.16048
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.758
ELB improved by 0.121453
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.662
ELB improved by 0.0962577
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.581
ELB improved by 0.0810483
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.507
ELB improved by 0.0739267
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.432
ELB improved by 0.0749075
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.346
ELB improved by 0.0859524
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.237
ELB improved by 0.109091
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.1
ELB improved by 0.137136
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.956
ELB improved by 0.143744
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.842
ELB improved by 0.113393
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.771
ELB improved by 0.0715928
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.729
ELB improved by 0.0421376
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.703
ELB improved by 0.0261296
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.685
ELB improved by 0.017961
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.671
ELB improved by 0.0136176
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.66
ELB improved by 0.0110807
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.65
ELB improved by 0.00943126
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.630 0.276 2.922
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.059 | 0.023 | 0.083 | |
| getPIPs | 0.052 | 0.016 | 0.068 | |
| graper | 0.088 | 0.024 | 0.115 | |
| makeExampleData | 0.010 | 0.001 | 0.011 | |
| makeExampleDataWithUnequalGroups | 0.029 | 0.003 | 0.032 | |
| plotELBO | 0.239 | 0.022 | 0.262 | |
| plotGroupPenalties | 0.846 | 0.033 | 0.886 | |
| plotPosterior | 0.659 | 0.024 | 0.686 | |
| predict.graper | 2.127 | 0.103 | 2.246 | |
| print.graper | 0.050 | 0.014 | 0.065 | |