Britta Velten
| Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: RELEASE_3_18 |
| git_last_commit: eea1fd2 |
| git_last_commit_date: 2023-10-24 11:10:07 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:37:47 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 896/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.18.0 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 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: 1.18.0 |
| 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_1.18.0.tar.gz |
| StartedAt: 2024-04-16 03:38:49 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 03:40:47 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 117.9 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_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/graper.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* 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 ‘1.18.0’
* 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/4.3-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-3.18-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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.18-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/4.3-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/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/digamma.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/math_fwd.hpp:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11:
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(graper)
>
> test_check("graper")
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-895.409
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-578.837
ELB improved by 316.572
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-525.665
ELB improved by 53.1715
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-493.082
ELB improved by 32.5836
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-478.929
ELB improved by 14.1522
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.164
ELB improved by 5.76577
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.8
ELB improved by 3.36366
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.049
ELB improved by 2.75148
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.515
ELB improved by 2.53362
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.064
ELB improved by 2.45086
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.619
ELB improved by 2.44537
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.116
ELB improved by 2.50283
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.502
ELB improved by 2.61353
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.762
ELB improved by 2.74022
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.964
ELB improved by 2.79838
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.287
ELB improved by 2.67709
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.976
ELB improved by 2.31031
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.21
ELB improved by 1.76659
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.977
ELB improved by 1.23313
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.135
ELB improved by 0.841732
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.536
ELB improved by 0.598569
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.077
ELB improved by 0.459691
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.689
ELB improved by 0.387186
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.333
ELB improved by 0.356148
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.983
ELB improved by 0.350632
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.621
ELB improved by 0.361286
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.238
ELB improved by 0.383351
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.823
ELB improved by 0.415062
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.366
ELB improved by 0.456928
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.854
ELB improved by 0.511641
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.271
ELB improved by 0.583288
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.599
ELB improved by 0.672526
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.831
ELB improved by 0.76781
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.98
ELB improved by 0.850874
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.061
ELB improved by 0.919251
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.079
ELB improved by 0.982088
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.036
ELB improved by 1.043
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.936
ELB improved by 1.0999
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.788
ELB improved by 1.14745
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.615
ELB improved by 1.17308
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.465
ELB improved by 1.15062
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.409
ELB improved by 1.05556
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.508
ELB improved by 0.901091
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.774
ELB improved by 0.733609
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.182
ELB improved by 0.59192
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.697
ELB improved by 0.485021
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.3
ELB improved by 0.397341
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.986
ELB improved by 0.314155
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.747
ELB improved by 0.239036
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.566
ELB improved by 0.180347
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.428
ELB improved by 0.138654
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.318
ELB improved by 0.109773
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.229
ELB improved by 0.0893957
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.154
ELB improved by 0.0744788
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.091
ELB improved by 0.0631233
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.037
ELB improved by 0.0541803
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.99
ELB improved by 0.0469475
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.949
ELB improved by 0.0409815
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.913
ELB improved by 0.0359898
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.881
ELB improved by 0.03177
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.853
ELB improved by 0.0281758
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.828
ELB improved by 0.0250973
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.805
ELB improved by 0.0224487
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.785
ELB improved by 0.020162
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.767
ELB improved by 0.0181818
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.751
ELB improved by 0.0164624
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.736
ELB improved by 0.014966
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.722
ELB improved by 0.0136606
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.709
ELB improved by 0.0125194
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.698
ELB improved by 0.0115197
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.687
ELB improved by 0.010642
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.677
ELB improved by 0.00986989
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-893.6
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-567.042
ELB improved by 326.558
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-506.059
ELB improved by 60.9836
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-474.623
ELB improved by 31.4351
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.332
ELB improved by 13.2918
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.477
ELB improved by 6.85463
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.617
ELB improved by 4.86002
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.399
ELB improved by 4.21838
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.285
ELB improved by 4.1141
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.05
ELB improved by 4.23415
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.648
ELB improved by 4.40225
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.204
ELB improved by 4.44456
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.022
ELB improved by 4.18169
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.437
ELB improved by 3.58491
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.545
ELB improved by 2.89219
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.177
ELB improved by 2.36754
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.187
ELB improved by 1.99041
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.686
ELB improved by 1.50106
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.762
ELB improved by 0.923298
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.234
ELB improved by 0.528609
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.913
ELB improved by 0.320688
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.701
ELB improved by 0.212467
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.549
ELB improved by 0.152224
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.432
ELB improved by 0.116308
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.339
ELB improved by 0.0934692
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.261
ELB improved by 0.077917
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.194
ELB improved by 0.066602
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.136
ELB improved by 0.0579049
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.085
ELB improved by 0.050941
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.04
ELB improved by 0.045202
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409
ELB improved by 0.0403767
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.964
ELB improved by 0.036262
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.931
ELB improved by 0.0327167
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.901
ELB improved by 0.0296378
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.874
ELB improved by 0.026947
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.85
ELB improved by 0.024583
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.827
ELB improved by 0.0224966
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.806
ELB improved by 0.0206479
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.787
ELB improved by 0.0190038
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.77
ELB improved by 0.0175371
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.754
ELB improved by 0.0162245
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.739
ELB improved by 0.0150467
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.725
ELB improved by 0.0139871
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.712
ELB improved by 0.0130316
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.699
ELB improved by 0.0121679
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.688
ELB improved by 0.0113858
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.677
ELB improved by 0.010676
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.667
ELB improved by 0.0100306
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.658
ELB improved by 0.00944294
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-880.845
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-575.301
ELB improved by 305.544
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-515.45
ELB improved by 59.8507
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-479.804
ELB improved by 35.6466
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.277
ELB improved by 14.5272
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.192
ELB improved by 6.08463
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.248
ELB improved by 3.94378
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.685
ELB improved by 3.56364
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.919
ELB improved by 3.76584
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.672
ELB improved by 4.24734
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.907
ELB improved by 4.76482
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.993
ELB improved by 4.91387
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.675
ELB improved by 4.31773
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.521
ELB improved by 3.15438
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.468
ELB improved by 2.05304
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.099
ELB improved by 1.36826
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.059
ELB improved by 1.04033
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.156
ELB improved by 0.903394
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.302
ELB improved by 0.853907
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.462
ELB improved by 0.839663
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.631
ELB improved by 0.831329
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.807
ELB improved by 0.823383
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.975
ELB improved by 0.831928
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.09
ELB improved by 0.885039
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.064
ELB improved by 1.02694
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.779
ELB improved by 1.28417
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.266
ELB improved by 1.5135
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.642
ELB improved by 1.62413
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.894
ELB improved by 1.74786
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.123
ELB improved by 1.77122
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.542
ELB improved by 1.58089
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.23
ELB improved by 1.31168
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.169
ELB improved by 1.06118
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.299
ELB improved by 0.86941
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.539
ELB improved by 0.75997
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.801
ELB improved by 0.738941
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.038
ELB improved by 0.762917
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.274
ELB improved by 0.763676
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.629
ELB improved by 0.645443
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.227
ELB improved by 0.401483
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.01
ELB improved by 0.217008
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.88
ELB improved by 0.12992
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.789
ELB improved by 0.0912252
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.718
ELB improved by 0.0713092
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.659
ELB improved by 0.0588815
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.609
ELB improved by 0.0499551
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.566
ELB improved by 0.0430236
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.528
ELB improved by 0.0374192
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.496
ELB improved by 0.032785
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.467
ELB improved by 0.0288992
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.441
ELB improved by 0.0256092
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.418
ELB improved by 0.0228033
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.398
ELB improved by 0.0203963
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.379
ELB improved by 0.0183214
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.363
ELB improved by 0.0165252
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.348
ELB improved by 0.0149646
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.334
ELB improved by 0.0136039
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.322
ELB improved by 0.0124138
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.311
ELB improved by 0.0113699
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.3
ELB improved by 0.0104515
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.291
ELB improved by 0.00964145
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-877.226
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-567.99
ELB improved by 309.236
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-508
ELB improved by 59.9893
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-477.348
ELB improved by 30.6522
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.033
ELB improved by 12.3157
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.108
ELB improved by 6.92417
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.339
ELB improved by 5.76904
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.333
ELB improved by 6.00586
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.488
ELB improved by 6.84496
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.105
ELB improved by 7.38382
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.374
ELB improved by 6.73116
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.174
ELB improved by 5.19913
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.363
ELB improved by 3.81089
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.565
ELB improved by 2.79803
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.54
ELB improved by 2.02544
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.028
ELB improved by 1.51171
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.831
ELB improved by 1.1978
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.825
ELB improved by 1.00517
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.909
ELB improved by 0.916767
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.096
ELB improved by 0.812763
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.487
ELB improved by 0.609213
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.045
ELB improved by 0.441394
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.694
ELB improved by 0.350882
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.391
ELB improved by 0.303737
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.113
ELB improved by 0.277579
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.85
ELB improved by 0.262706
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.596
ELB improved by 0.254789
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.344
ELB improved by 0.251617
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.092
ELB improved by 0.251869
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.837
ELB improved by 0.254651
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.578
ELB improved by 0.259317
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.313
ELB improved by 0.265389
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.04
ELB improved by 0.272543
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.76
ELB improved by 0.280608
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.47
ELB improved by 0.289571
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.17
ELB improved by 0.29958
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.859
ELB improved by 0.310923
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.535
ELB improved by 0.323987
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.196
ELB improved by 0.339194
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.839
ELB improved by 0.356919
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.462
ELB improved by 0.377386
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.061
ELB improved by 0.400552
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.635
ELB improved by 0.425963
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.183
ELB improved by 0.452599
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.704
ELB improved by 0.478689
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.203
ELB improved by 0.50156
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.685
ELB improved by 0.517615
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.162
ELB improved by 0.522719
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.649
ELB improved by 0.513335
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.161
ELB improved by 0.488155
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.712
ELB improved by 0.449117
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.311
ELB improved by 0.400798
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.962
ELB improved by 0.34866
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.665
ELB improved by 0.297427
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.414
ELB improved by 0.250298
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.206
ELB improved by 0.208906
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.032
ELB improved by 0.173678
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.888
ELB improved by 0.144285
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.768
ELB improved by 0.120038
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.667
ELB improved by 0.100145
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.584
ELB improved by 0.0838465
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.513
ELB improved by 0.070482
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.454
ELB improved by 0.0594974
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.403
ELB improved by 0.0504405
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.36
ELB improved by 0.0429464
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.323
ELB improved by 0.0367217
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.292
ELB improved by 0.0315317
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.265
ELB improved by 0.0271875
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.241
ELB improved by 0.0235376
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.221
ELB improved by 0.0204597
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.203
ELB improved by 0.0178549
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.187
ELB improved by 0.0156428
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.174
ELB improved by 0.013758
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.161
ELB improved by 0.0121469
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.151
ELB improved by 0.0107655
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.141
ELB improved by 0.00957746
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
4.409 0.433 4.971
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.082 | 0.036 | 0.129 | |
| getPIPs | 0.076 | 0.035 | 0.116 | |
| graper | 0.125 | 0.048 | 0.180 | |
| makeExampleData | 0.019 | 0.002 | 0.022 | |
| makeExampleDataWithUnequalGroups | 0.022 | 0.003 | 0.025 | |
| plotELBO | 0.421 | 0.046 | 0.488 | |
| plotGroupPenalties | 1.760 | 0.113 | 1.957 | |
| plotPosterior | 1.050 | 0.046 | 1.155 | |
| predict.graper | 3.120 | 0.191 | 3.591 | |
| print.graper | 0.074 | 0.032 | 0.112 | |