Britta Velten
| Snapshot Date: 2024-07-22 14:00 -0400 (Mon, 22 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 2024-07-23 11:41 -0400 (Tue, 23 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" | 4280 |
| 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: 2024-07-22 21:41:04 -0400 (Mon, 22 Jul 2024) |
| EndedAt: 2024-07-22 21:42:19 -0400 (Mon, 22 Jul 2024) |
| EllapsedTime: 75.2 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=-911.718
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-579.183
ELB improved by 332.536
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-521.501
ELB improved by 57.6816
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-486.502
ELB improved by 34.9992
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.66
ELB improved by 16.8413
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.459
ELB improved by 8.20151
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.207
ELB improved by 5.25161
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.923
ELB improved by 4.28401
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.979
ELB improved by 3.94416
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.187
ELB improved by 3.79226
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.548
ELB improved by 3.63864
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.144
ELB improved by 3.40405
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.079
ELB improved by 3.06497
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.443
ELB improved by 2.63656
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.269
ELB improved by 2.17379
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.518
ELB improved by 1.7505
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.12
ELB improved by 1.39858
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.018
ELB improved by 1.1017
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.171
ELB improved by 0.846823
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.533
ELB improved by 0.637992
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.056
ELB improved by 0.477136
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.697
ELB improved by 0.358636
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.423
ELB improved by 0.274459
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.207
ELB improved by 0.216039
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.032
ELB improved by 0.175333
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.885
ELB improved by 0.14615
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.761
ELB improved by 0.124398
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.654
ELB improved by 0.107556
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.559
ELB improved by 0.0940857
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.476
ELB improved by 0.0830327
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.403
ELB improved by 0.0737817
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.337
ELB improved by 0.0659217
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.278
ELB improved by 0.0591666
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.224
ELB improved by 0.0533097
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.176
ELB improved by 0.0481962
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.132
ELB improved by 0.0437063
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.093
ELB improved by 0.0397456
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.056
ELB improved by 0.0362376
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.023
ELB improved by 0.0331194
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.993
ELB improved by 0.0303389
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.965
ELB improved by 0.0278524
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.939
ELB improved by 0.0256228
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.916
ELB improved by 0.0236186
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.894
ELB improved by 0.0218127
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.874
ELB improved by 0.0201819
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.855
ELB improved by 0.0187062
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.838
ELB improved by 0.0173682
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.822
ELB improved by 0.0161527
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.807
ELB improved by 0.0150466
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.793
ELB improved by 0.0140383
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.779
ELB improved by 0.0131177
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.767
ELB improved by 0.0122758
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.756
ELB improved by 0.0115048
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.745
ELB improved by 0.0107977
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.735
ELB improved by 0.0101483
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.725
ELB improved by 0.0095511
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-917.568
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-568.719
ELB improved by 348.849
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-511.162
ELB improved by 57.5565
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-479.871
ELB improved by 31.2916
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.465
ELB improved by 13.4061
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.741
ELB improved by 6.72382
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.991
ELB improved by 4.74959
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.751
ELB improved by 4.24017
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.477
ELB improved by 4.27371
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.928
ELB improved by 4.54975
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.139
ELB improved by 4.7888
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.542
ELB improved by 4.59638
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.779
ELB improved by 3.76308
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.152
ELB improved by 2.62694
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.483
ELB improved by 1.66955
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.435
ELB improved by 1.04824
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.747
ELB improved by 0.687629
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.263
ELB improved by 0.483917
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.896
ELB improved by 0.36696
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.599
ELB improved by 0.296987
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.346
ELB improved by 0.253021
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.122
ELB improved by 0.224308
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.917
ELB improved by 0.205286
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.724
ELB improved by 0.192971
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.538
ELB improved by 0.185682
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.355
ELB improved by 0.182438
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.173
ELB improved by 0.182662
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.987
ELB improved by 0.186034
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.794
ELB improved by 0.192417
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.592
ELB improved by 0.201819
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.378
ELB improved by 0.214365
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.148
ELB improved by 0.230281
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.898
ELB improved by 0.249864
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.625
ELB improved by 0.273465
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.323
ELB improved by 0.301515
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.988
ELB improved by 0.334699
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.614
ELB improved by 0.374366
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.191
ELB improved by 0.423019
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.707
ELB improved by 0.483801
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.152
ELB improved by 0.555355
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.532
ELB improved by 0.619647
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.887
ELB improved by 0.645507
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.26
ELB improved by 0.626218
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.68
ELB improved by 0.580385
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.159
ELB improved by 0.521106
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.704
ELB improved by 0.455272
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.314
ELB improved by 0.38935
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.986
ELB improved by 0.328732
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.709
ELB improved by 0.276416
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.476
ELB improved by 0.233012
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.279
ELB improved by 0.197562
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.11
ELB improved by 0.168434
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.966
ELB improved by 0.143996
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.843
ELB improved by 0.122997
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.738
ELB improved by 0.10468
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.65
ELB improved by 0.0886923
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.575
ELB improved by 0.0748835
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.512
ELB improved by 0.0631319
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.458
ELB improved by 0.0532672
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.413
ELB improved by 0.0450692
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.375
ELB improved by 0.0382973
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.342
ELB improved by 0.0327186
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.314
ELB improved by 0.0281244
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.29
ELB improved by 0.0243358
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.269
ELB improved by 0.0212038
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.25
ELB improved by 0.0186063
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.234
ELB improved by 0.0164438
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.219
ELB improved by 0.0146359
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.206
ELB improved by 0.0131174
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.194
ELB improved by 0.0118359
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.183
ELB improved by 0.0107489
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.174
ELB improved by 0.0098222
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-907.472
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-581.717
ELB improved by 325.755
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-526.824
ELB improved by 54.893
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-497.65
ELB improved by 29.1737
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-485.535
ELB improved by 12.1157
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-478.827
ELB improved by 6.70744
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.236
ELB improved by 5.59074
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.436
ELB improved by 5.80038
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.156
ELB improved by 6.28055
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.856
ELB improved by 6.29993
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.455
ELB improved by 5.40032
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.5
ELB improved by 3.95535
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.781
ELB improved by 2.71872
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.846
ELB improved by 1.93549
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.384
ELB improved by 1.46189
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.224
ELB improved by 1.15988
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.26
ELB improved by 0.964106
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.426
ELB improved by 0.834192
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.683
ELB improved by 0.742183
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.011
ELB improved by 0.672031
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.395
ELB improved by 0.616645
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.82
ELB improved by 0.574889
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.269
ELB improved by 0.55053
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.716
ELB improved by 0.553614
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.115
ELB improved by 0.600486
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.423
ELB improved by 0.692452
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.649
ELB improved by 0.774212
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.87
ELB improved by 0.778292
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.162
ELB improved by 0.707986
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.537
ELB improved by 0.625361
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.973
ELB improved by 0.563696
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.455
ELB improved by 0.518392
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.974
ELB improved by 0.481021
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.526
ELB improved by 0.447482
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.11
ELB improved by 0.416464
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.722
ELB improved by 0.387958
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.359
ELB improved by 0.362518
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.019
ELB improved by 0.34086
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.695
ELB improved by 0.323593
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.384
ELB improved by 0.310972
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.081
ELB improved by 0.3026
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.784
ELB improved by 0.297132
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.492
ELB improved by 0.292248
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.207
ELB improved by 0.285113
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.934
ELB improved by 0.273113
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.679
ELB improved by 0.254587
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.45
ELB improved by 0.229453
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.25
ELB improved by 0.199488
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.083
ELB improved by 0.167737
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.945
ELB improved by 0.137269
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.835
ELB improved by 0.110209
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.748
ELB improved by 0.0875007
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.678
ELB improved by 0.0691912
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.624
ELB improved by 0.054825
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.58
ELB improved by 0.0437502
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.545
ELB improved by 0.0352987
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.516
ELB improved by 0.0288743
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.492
ELB improved by 0.0239839
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.471
ELB improved by 0.0202392
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.454
ELB improved by 0.017344
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.439
ELB improved by 0.0150774
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.426
ELB improved by 0.0132773
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.414
ELB improved by 0.0118255
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.403
ELB improved by 0.0106364
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.394
ELB improved by 0.00964804
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-860.277
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-544.113
ELB improved by 316.165
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-488.526
ELB improved by 55.5863
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.936
ELB improved by 29.5898
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.181
ELB improved by 11.755
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.727
ELB improved by 5.45433
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.089
ELB improved by 3.63768
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.98
ELB improved by 3.10984
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.909
ELB improved by 3.07079
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.633
ELB improved by 3.2757
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.06
ELB improved by 3.57301
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.296
ELB improved by 3.76395
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.693
ELB improved by 3.6034
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.678
ELB improved by 3.01513
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.456
ELB improved by 2.22125
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.939
ELB improved by 1.51729
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.909
ELB improved by 1.03009
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.173
ELB improved by 0.73579
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.604
ELB improved by 0.56931
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.126
ELB improved by 0.477883
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.697
ELB improved by 0.428968
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.292
ELB improved by 0.40459
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.897
ELB improved by 0.395268
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.501
ELB improved by 0.396192
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.096
ELB improved by 0.405199
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.674
ELB improved by 0.421812
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.227
ELB improved by 0.446751
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.746
ELB improved by 0.481379
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.22
ELB improved by 0.526151
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.642
ELB improved by 0.577174
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.019
ELB improved by 0.623413
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.366
ELB improved by 0.652748
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.703
ELB improved by 0.663692
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.039
ELB improved by 0.66342
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.382
ELB improved by 0.657439
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.734
ELB improved by 0.647304
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.102
ELB improved by 0.632596
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.49
ELB improved by 0.611856
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.907
ELB improved by 0.583148
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.362
ELB improved by 0.54511
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.864
ELB improved by 0.497891
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.42
ELB improved by 0.443455
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.035
ELB improved by 0.385551
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.706
ELB improved by 0.329367
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.425
ELB improved by 0.280208
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.183
ELB improved by 0.241914
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.966
ELB improved by 0.217032
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.757
ELB improved by 0.20925
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.531
ELB improved by 0.226206
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.255
ELB improved by 0.275714
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.913
ELB improved by 0.342185
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.522
ELB improved by 0.391396
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.054
ELB improved by 0.468033
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.447
ELB improved by 0.606309
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.804
ELB improved by 0.64322
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.26
ELB improved by 0.543831
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.77
ELB improved by 0.489869
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.309
ELB improved by 0.460872
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.984
ELB improved by 0.325427
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.806
ELB improved by 0.178306
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.709
ELB improved by 0.0965138
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.651
ELB improved by 0.0577544
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.613
ELB improved by 0.0385569
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.585
ELB improved by 0.0281662
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.563
ELB improved by 0.0220366
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.545
ELB improved by 0.018127
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.529
ELB improved by 0.0154458
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.516
ELB improved by 0.0134824
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.504
ELB improved by 0.0119629
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.493
ELB improved by 0.0107356
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.483
ELB improved by 0.00971307
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.698 0.284 3.002
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.057 | 0.023 | 0.081 | |
| getPIPs | 0.048 | 0.017 | 0.065 | |
| graper | 0.088 | 0.027 | 0.116 | |
| makeExampleData | 0.013 | 0.001 | 0.014 | |
| makeExampleDataWithUnequalGroups | 0.032 | 0.003 | 0.036 | |
| plotELBO | 0.244 | 0.020 | 0.269 | |
| plotGroupPenalties | 0.810 | 0.032 | 0.848 | |
| plotPosterior | 0.677 | 0.024 | 0.705 | |
| predict.graper | 2.053 | 0.100 | 2.172 | |
| print.graper | 0.051 | 0.013 | 0.064 | |