Britta Velten
| Snapshot Date: 2024-05-17 14:00:11 -0400 (Fri, 17 May 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 2024-05-18 11:37:52 -0400 (Sat, 18 May 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" | 4751 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4515 |
| 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 | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 2024-05-17 21:20:07 -0400 (Fri, 17 May 2024) |
| EndedAt: 2024-05-17 21:21:21 -0400 (Fri, 17 May 2024) |
| EllapsedTime: 74.0 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: 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 ‘1.20.0’
* 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-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-3.19-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-3.19-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-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 4.4.0 (2024-04-24) -- "Puppy Cup"
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=-863.21
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-598.006
ELB improved by 265.204
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-538.218
ELB improved by 59.7881
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-490.211
ELB improved by 48.0068
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.968
ELB improved by 26.2426
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.613
ELB improved by 10.3552
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.95
ELB improved by 5.66264
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.28
ELB improved by 4.67069
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.84
ELB improved by 4.43955
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.3
ELB improved by 4.54057
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.545
ELB improved by 4.75419
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.704
ELB improved by 4.84135
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.12
ELB improved by 4.58382
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.175
ELB improved by 3.94547
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.062
ELB improved by 3.11287
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.781
ELB improved by 2.28077
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.218
ELB improved by 1.56277
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.18
ELB improved by 1.03866
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.475
ELB improved by 0.704935
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.97
ELB improved by 0.505026
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.585
ELB improved by 0.385201
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.274
ELB improved by 0.310503
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.013
ELB improved by 0.26099
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.788
ELB improved by 0.225515
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.59
ELB improved by 0.19763
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.416
ELB improved by 0.173693
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.264
ELB improved by 0.152182
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.131
ELB improved by 0.133071
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.014
ELB improved by 0.116844
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.91
ELB improved by 0.103668
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.817
ELB improved by 0.0932164
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.732
ELB improved by 0.0849238
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.654
ELB improved by 0.0782356
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.581
ELB improved by 0.0727183
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.513
ELB improved by 0.0680646
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.449
ELB improved by 0.0640624
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.389
ELB improved by 0.0605633
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.331
ELB improved by 0.0574602
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.277
ELB improved by 0.0546729
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.224
ELB improved by 0.0521399
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.175
ELB improved by 0.0498125
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.127
ELB improved by 0.0476521
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.081
ELB improved by 0.0456278
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.038
ELB improved by 0.043715
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.996
ELB improved by 0.0418941
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.956
ELB improved by 0.0401497
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.917
ELB improved by 0.03847
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.88
ELB improved by 0.0368462
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.845
ELB improved by 0.0352716
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.811
ELB improved by 0.0337421
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.779
ELB improved by 0.0322546
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.748
ELB improved by 0.0308075
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.719
ELB improved by 0.0294004
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.691
ELB improved by 0.0280333
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.664
ELB improved by 0.0267067
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.639
ELB improved by 0.0254215
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.614
ELB improved by 0.0241788
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.591
ELB improved by 0.0229794
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.57
ELB improved by 0.0218244
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.549
ELB improved by 0.0207144
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.529
ELB improved by 0.01965
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.511
ELB improved by 0.0186315
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.493
ELB improved by 0.0176588
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.476
ELB improved by 0.0167316
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.46
ELB improved by 0.0158495
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.445
ELB improved by 0.0150118
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.431
ELB improved by 0.0142174
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.418
ELB improved by 0.0134652
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.405
ELB improved by 0.012754
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.393
ELB improved by 0.0120824
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.381
ELB improved by 0.0114487
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.371
ELB improved by 0.0108515
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.36
ELB improved by 0.0102891
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.35
ELB improved by 0.0097598
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-850.815
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-578.692
ELB improved by 272.122
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-522.359
ELB improved by 56.3336
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-486.152
ELB improved by 36.2071
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.249
ELB improved by 15.9023
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.327
ELB improved by 5.92222
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.051
ELB improved by 3.2759
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.277
ELB improved by 2.77438
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.432
ELB improved by 2.84514
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.364
ELB improved by 3.06747
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.157
ELB improved by 3.20706
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.075
ELB improved by 3.08175
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.434
ELB improved by 2.64103
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.412
ELB improved by 2.02273
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.977
ELB improved by 1.43452
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.981
ELB improved by 0.996378
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.265
ELB improved by 0.715922
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.715
ELB improved by 0.549988
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.26
ELB improved by 0.454468
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.861
ELB improved by 0.399602
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.493
ELB improved by 0.368231
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.142
ELB improved by 0.350862
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.8
ELB improved by 0.341934
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.462
ELB improved by 0.337794
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.126
ELB improved by 0.335871
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.792
ELB improved by 0.33438
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.46
ELB improved by 0.332209
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.131
ELB improved by 0.328867
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.806
ELB improved by 0.32445
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.487
ELB improved by 0.319626
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.171
ELB improved by 0.315607
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.857
ELB improved by 0.31409
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.54
ELB improved by 0.317029
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.214
ELB improved by 0.325838
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.874
ELB improved by 0.339691
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.521
ELB improved by 0.353801
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.161
ELB improved by 0.359881
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.811
ELB improved by 0.349608
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.489
ELB improved by 0.322016
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.203
ELB improved by 0.286511
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.95
ELB improved by 0.252772
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.726
ELB improved by 0.224201
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.525
ELB improved by 0.200669
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.344
ELB improved by 0.181368
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.178
ELB improved by 0.165572
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.025
ELB improved by 0.152671
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.883
ELB improved by 0.142136
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.75
ELB improved by 0.133503
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.623
ELB improved by 0.126369
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.503
ELB improved by 0.120389
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.388
ELB improved by 0.115263
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.277
ELB improved by 0.110736
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.17
ELB improved by 0.106587
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.068
ELB improved by 0.102626
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.969
ELB improved by 0.0986921
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.874
ELB improved by 0.0946525
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.784
ELB improved by 0.0904022
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.698
ELB improved by 0.0858677
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.617
ELB improved by 0.081011
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.541
ELB improved by 0.0758323
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.471
ELB improved by 0.0703713
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.406
ELB improved by 0.0647039
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.347
ELB improved by 0.0589348
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.294
ELB improved by 0.0531855
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.246
ELB improved by 0.0475813
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.204
ELB improved by 0.0422373
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.167
ELB improved by 0.0372479
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.134
ELB improved by 0.032681
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.106
ELB improved by 0.0285755
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.081
ELB improved by 0.0249438
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.059
ELB improved by 0.0217759
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.04
ELB improved by 0.0190458
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.023
ELB improved by 0.0167161
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.008
ELB improved by 0.0147442
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.995
ELB improved by 0.0130853
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.984
ELB improved by 0.0116961
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.973
ELB improved by 0.0105361
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.964
ELB improved by 0.00956868
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-881.281
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-565.953
ELB improved by 315.328
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-510.285
ELB improved by 55.668
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-478.413
ELB improved by 31.872
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.289
ELB improved by 15.1238
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.389
ELB improved by 7.89986
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.031
ELB improved by 5.35794
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.529
ELB improved by 4.50219
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.265
ELB improved by 4.26418
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.164
ELB improved by 4.10098
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.437
ELB improved by 3.7266
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.356
ELB improved by 3.08095
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.049
ELB improved by 2.30687
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.445
ELB improved by 1.60444
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.362
ELB improved by 1.08294
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.62
ELB improved by 0.742026
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.089
ELB improved by 0.531281
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.688
ELB improved by 0.400577
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.372
ELB improved by 0.316166
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.113
ELB improved by 0.258536
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.896
ELB improved by 0.216957
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.711
ELB improved by 0.185506
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.55
ELB improved by 0.160813
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.409
ELB improved by 0.140866
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.285
ELB improved by 0.124404
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.174
ELB improved by 0.110596
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.075
ELB improved by 0.0988674
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.986
ELB improved by 0.0888033
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.906
ELB improved by 0.0800961
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.834
ELB improved by 0.0725101
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.768
ELB improved by 0.0658609
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.708
ELB improved by 0.0600018
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.653
ELB improved by 0.0548144
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.603
ELB improved by 0.050202
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.557
ELB improved by 0.0460848
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.514
ELB improved by 0.0423966
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.475
ELB improved by 0.0390818
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.439
ELB improved by 0.0360935
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.406
ELB improved by 0.0333921
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.375
ELB improved by 0.0309436
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.346
ELB improved by 0.028719
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.32
ELB improved by 0.0266932
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.295
ELB improved by 0.0248447
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.272
ELB improved by 0.0231544
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.25
ELB improved by 0.0216061
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.23
ELB improved by 0.0201853
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.211
ELB improved by 0.0188794
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.193
ELB improved by 0.0176773
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.177
ELB improved by 0.0165692
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.161
ELB improved by 0.0155462
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.147
ELB improved by 0.0146006
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.133
ELB improved by 0.0137255
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.12
ELB improved by 0.0129147
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.108
ELB improved by 0.0121626
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.096
ELB improved by 0.0114643
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.085
ELB improved by 0.0108151
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.075
ELB improved by 0.0102112
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.066
ELB improved by 0.00964885
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-877.124
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-560.779
ELB improved by 316.345
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-504.182
ELB improved by 56.597
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.639
ELB improved by 30.5436
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.903
ELB improved by 12.7354
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.958
ELB improved by 5.94552
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.929
ELB improved by 4.02914
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.621
ELB improved by 3.30779
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.618
ELB improved by 3.0028
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.724
ELB improved by 2.89391
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.833
ELB improved by 2.8912
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.911
ELB improved by 2.92162
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.039
ELB improved by 2.87269
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.402
ELB improved by 2.63714
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.191
ELB improved by 2.21083
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.486
ELB improved by 1.70465
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.24
ELB improved by 1.24644
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.342
ELB improved by 0.898049
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.683
ELB improved by 0.658347
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.182
ELB improved by 0.501036
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.783
ELB improved by 0.39911
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.451
ELB improved by 0.332426
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.164
ELB improved by 0.286292
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.916
ELB improved by 0.248544
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.705
ELB improved by 0.210946
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.532
ELB improved by 0.173301
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.391
ELB improved by 0.141029
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.273
ELB improved by 0.117474
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.171
ELB improved by 0.101707
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.08
ELB improved by 0.0912838
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.996
ELB improved by 0.0842273
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.917
ELB improved by 0.0793325
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.841
ELB improved by 0.0759184
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.767
ELB improved by 0.0735954
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.695
ELB improved by 0.0721295
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.624
ELB improved by 0.0713746
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.552
ELB improved by 0.0712368
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.481
ELB improved by 0.0716557
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.408
ELB improved by 0.0725931
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.334
ELB improved by 0.0740275
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.258
ELB improved by 0.0759489
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.18
ELB improved by 0.0783575
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.098
ELB improved by 0.0812618
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.014
ELB improved by 0.0846788
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.925
ELB improved by 0.0886336
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.832
ELB improved by 0.0931614
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.734
ELB improved by 0.0983085
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.63
ELB improved by 0.104136
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.519
ELB improved by 0.110724
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.401
ELB improved by 0.118175
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.274
ELB improved by 0.126628
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.138
ELB improved by 0.136265
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.99
ELB improved by 0.147333
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.83
ELB improved by 0.16018
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.655
ELB improved by 0.175293
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.462
ELB improved by 0.193372
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.246
ELB improved by 0.215377
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.004
ELB improved by 0.24246
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.728
ELB improved by 0.275491
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.414
ELB improved by 0.313926
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.059
ELB improved by 0.355026
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.663
ELB improved by 0.396285
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.223
ELB improved by 0.440258
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.729
ELB improved by 0.493664
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.17
ELB improved by 0.55863
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.547
ELB improved by 0.623371
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.882
ELB improved by 0.665399
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.208
ELB improved by 0.673776
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.545
ELB improved by 0.662433
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.887
ELB improved by 0.658911
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.228
ELB improved by 0.658846
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.632
ELB improved by 0.59578
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.156
ELB improved by 0.475954
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.794
ELB improved by 0.362126
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.532
ELB improved by 0.261608
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.358
ELB improved by 0.17466
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.246
ELB improved by 0.111448
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.174
ELB improved by 0.0724714
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.123
ELB improved by 0.0501912
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.086
ELB improved by 0.0374021
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.056
ELB improved by 0.0296454
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.032
ELB improved by 0.0245649
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.011
ELB improved by 0.0209766
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.993
ELB improved by 0.0182808
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.976
ELB improved by 0.0161601
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.962
ELB improved by 0.014436
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.949
ELB improved by 0.0130007
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.937
ELB improved by 0.0117851
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.926
ELB improved by 0.0107418
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.917
ELB improved by 0.00983717
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.593 0.293 2.898
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.050 | 0.018 | 0.070 | |
| getPIPs | 0.049 | 0.016 | 0.065 | |
| graper | 0.088 | 0.026 | 0.116 | |
| makeExampleData | 0.013 | 0.001 | 0.015 | |
| makeExampleDataWithUnequalGroups | 0.034 | 0.003 | 0.037 | |
| plotELBO | 0.235 | 0.023 | 0.260 | |
| plotGroupPenalties | 0.871 | 0.038 | 0.918 | |
| plotPosterior | 0.650 | 0.025 | 0.683 | |
| predict.graper | 2.014 | 0.095 | 2.130 | |
| print.graper | 0.050 | 0.012 | 0.063 | |