Britta Velten
| Snapshot Date: 2024-09-22 14:00 -0400 (Sun, 22 Sep 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 2024-09-24 22:57 -0400 (Tue, 24 Sep 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4760 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4497 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4526 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4475 |
| 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 | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: graper |
| Version: 1.20.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.20.0.tar.gz |
| StartedAt: 2024-09-23 06:02:14 -0400 (Mon, 23 Sep 2024) |
| EndedAt: 2024-09-23 06:04:27 -0400 (Mon, 23 Sep 2024) |
| EllapsedTime: 132.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: graper.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/graper.Rcheck’
* using R version 4.4.1 (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 12.7.5
* 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 4.4.1 (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=-833.674
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-551.323
ELB improved by 282.351
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-495.383
ELB improved by 55.9399
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.11
ELB improved by 32.273
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.684
ELB improved by 13.4256
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.264
ELB improved by 5.42059
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.486
ELB improved by 2.77748
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.519
ELB improved by 1.96731
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.806
ELB improved by 1.71341
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.177
ELB improved by 1.62861
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.563
ELB improved by 1.61385
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.925
ELB improved by 1.63837
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.244
ELB improved by 1.68053
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.537
ELB improved by 1.70684
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.867
ELB improved by 1.67059
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.33
ELB improved by 1.5368
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.015
ELB improved by 1.31528
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.956
ELB improved by 1.05876
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.131
ELB improved by 0.824933
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.485
ELB improved by 0.646102
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.959
ELB improved by 0.525831
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.508
ELB improved by 0.450935
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.103
ELB improved by 0.404795
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.729
ELB improved by 0.374455
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.377
ELB improved by 0.351886
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.044
ELB improved by 0.332838
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.729
ELB improved by 0.315426
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.43
ELB improved by 0.299001
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.146
ELB improved by 0.283339
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.878
ELB improved by 0.268161
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.625
ELB improved by 0.253041
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.388
ELB improved by 0.237661
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.165
ELB improved by 0.222098
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.959
ELB improved by 0.206821
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.766
ELB improved by 0.192406
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.587
ELB improved by 0.179266
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.419
ELB improved by 0.167557
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.262
ELB improved by 0.15724
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.114
ELB improved by 0.148164
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.974
ELB improved by 0.140138
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.841
ELB improved by 0.132962
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.714
ELB improved by 0.126449
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.594
ELB improved by 0.120428
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.479
ELB improved by 0.114751
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.37
ELB improved by 0.109286
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.266
ELB improved by 0.103928
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.167
ELB improved by 0.0985952
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.074
ELB improved by 0.0932328
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.986
ELB improved by 0.087813
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.904
ELB improved by 0.0823352
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.827
ELB improved by 0.0768233
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.756
ELB improved by 0.0713215
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.69
ELB improved by 0.0658885
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.629
ELB improved by 0.0605908
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.574
ELB improved by 0.0554954
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.523
ELB improved by 0.0506639
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.477
ELB improved by 0.0461473
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.435
ELB improved by 0.0419827
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.397
ELB improved by 0.0381925
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.362
ELB improved by 0.0347841
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.33
ELB improved by 0.0317518
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.301
ELB improved by 0.0290786
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.275
ELB improved by 0.0267397
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.25
ELB improved by 0.024704
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.227
ELB improved by 0.0229376
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.206
ELB improved by 0.021405
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.186
ELB improved by 0.0200717
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.167
ELB improved by 0.018905
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.149
ELB improved by 0.0178749
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.132
ELB improved by 0.0169552
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.116
ELB improved by 0.0161236
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.1
ELB improved by 0.0153619
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.086
ELB improved by 0.0146555
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.072
ELB improved by 0.0139933
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.058
ELB improved by 0.0133675
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.046
ELB improved by 0.0127723
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.033
ELB improved by 0.0122041
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.022
ELB improved by 0.0116606
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.011
ELB improved by 0.0111404
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415
ELB improved by 0.0106426
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.99
ELB improved by 0.0101669
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.98
ELB improved by 0.0097126
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-856.077
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-588.974
ELB improved by 267.103
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-529.505
ELB improved by 59.469
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-483.117
ELB improved by 46.3875
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.353
ELB improved by 23.7643
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.259
ELB improved by 10.0937
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.778
ELB improved by 5.48111
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.47
ELB improved by 4.30805
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.465
ELB improved by 4.00481
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.615
ELB improved by 3.8505
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.936
ELB improved by 3.67894
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.495
ELB improved by 3.44112
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.464
ELB improved by 3.03133
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.042
ELB improved by 2.42148
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.215
ELB improved by 1.8267
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.81
ELB improved by 1.40579
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.678
ELB improved by 1.13107
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.725
ELB improved by 0.953312
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.88
ELB improved by 0.845258
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.1
ELB improved by 0.780222
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.36
ELB improved by 0.739259
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.645
ELB improved by 0.715165
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.937
ELB improved by 0.708263
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.22
ELB improved by 0.717258
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.496
ELB improved by 0.724
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.794
ELB improved by 0.701778
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.136
ELB improved by 0.65805
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.513
ELB improved by 0.62273
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.898
ELB improved by 0.615031
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.252
ELB improved by 0.646402
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.547
ELB improved by 0.704362
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.826
ELB improved by 0.721575
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.161
ELB improved by 0.664918
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.575
ELB improved by 0.585411
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.063
ELB improved by 0.51291
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.614
ELB improved by 0.448693
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.223
ELB improved by 0.390465
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.886
ELB improved by 0.337495
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.595
ELB improved by 0.290578
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.344
ELB improved by 0.25144
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.121
ELB improved by 0.222469
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.914
ELB improved by 0.207345
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.702
ELB improved by 0.212494
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.456
ELB improved by 0.245795
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.158
ELB improved by 0.297855
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.844
ELB improved by 0.314046
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.584
ELB improved by 0.26027
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.4
ELB improved by 0.183961
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.275
ELB improved by 0.125023
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.187
ELB improved by 0.0872875
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.123
ELB improved by 0.064139
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.074
ELB improved by 0.0497032
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.033
ELB improved by 0.0402821
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.999
ELB improved by 0.0337635
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.971
ELB improved by 0.0289786
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.945
ELB improved by 0.0252819
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.923
ELB improved by 0.0223101
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.903
ELB improved by 0.0198512
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.885
ELB improved by 0.0177757
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.869
ELB improved by 0.0159999
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.855
ELB improved by 0.0144665
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.842
ELB improved by 0.0131339
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.83
ELB improved by 0.0119705
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.819
ELB improved by 0.010951
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.809
ELB improved by 0.0100549
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.799
ELB improved by 0.00926529
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-878.226
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-602.58
ELB improved by 275.646
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-542.233
ELB improved by 60.3466
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-496.231
ELB improved by 46.002
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.572
ELB improved by 24.659
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.746
ELB improved by 10.8259
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.888
ELB improved by 6.85871
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.989
ELB improved by 5.89888
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.43
ELB improved by 5.55843
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.403
ELB improved by 5.02727
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.32
ELB improved by 4.08336
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.344
ELB improved by 2.9758
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.296
ELB improved by 2.04789
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.868
ELB improved by 1.42758
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.817
ELB improved by 1.05146
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.009
ELB improved by 0.80823
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.383
ELB improved by 0.62557
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.899
ELB improved by 0.484243
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.517
ELB improved by 0.381571
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.208
ELB improved by 0.308989
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.952
ELB improved by 0.256385
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.735
ELB improved by 0.216656
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.55
ELB improved by 0.185549
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.389
ELB improved by 0.160394
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.25
ELB improved by 0.139272
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.129
ELB improved by 0.120762
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.025
ELB improved by 0.104061
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.936
ELB improved by 0.0890609
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.86
ELB improved by 0.0760869
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.795
ELB improved by 0.065407
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.738
ELB improved by 0.056944
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.687
ELB improved by 0.0503321
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.642
ELB improved by 0.0451178
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.601
ELB improved by 0.0409056
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.564
ELB improved by 0.0374045
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.53
ELB improved by 0.0344178
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.498
ELB improved by 0.0318169
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.468
ELB improved by 0.0295172
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.441
ELB improved by 0.0274614
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.415
ELB improved by 0.0256092
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.391
ELB improved by 0.0239309
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.369
ELB improved by 0.0224037
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.348
ELB improved by 0.0210091
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.328
ELB improved by 0.0197322
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.31
ELB improved by 0.0185603
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.292
ELB improved by 0.0174826
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.276
ELB improved by 0.0164898
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.26
ELB improved by 0.0155735
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.245
ELB improved by 0.0147267
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.231
ELB improved by 0.0139429
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.218
ELB improved by 0.0132165
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.206
ELB improved by 0.0125424
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.194
ELB improved by 0.011916
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.182
ELB improved by 0.0113333
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.172
ELB improved by 0.0107905
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.161
ELB improved by 0.0102845
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.151
ELB improved by 0.00981219
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-856.592
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-561.659
ELB improved by 294.932
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-495.567
ELB improved by 66.0922
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.389
ELB improved by 37.178
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.96
ELB improved by 14.429
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.047
ELB improved by 5.91323
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.333
ELB improved by 3.71425
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.137
ELB improved by 3.19564
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.955
ELB improved by 3.18217
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.52
ELB improved by 3.43447
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.677
ELB improved by 3.84298
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.423
ELB improved by 4.25445
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.034
ELB improved by 4.3892
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.118
ELB improved by 3.91581
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.214
ELB improved by 2.90367
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.323
ELB improved by 1.89123
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.128
ELB improved by 1.19481
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.347
ELB improved by 0.781613
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.8
ELB improved by 0.546586
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.385
ELB improved by 0.41458
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.047
ELB improved by 0.338621
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.754
ELB improved by 0.292742
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.49
ELB improved by 0.263745
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.245
ELB improved by 0.244809
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.013
ELB improved by 0.232147
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.79
ELB improved by 0.223492
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.572
ELB improved by 0.217405
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.359
ELB improved by 0.212955
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.15
ELB improved by 0.20956
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.943
ELB improved by 0.20693
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.738
ELB improved by 0.205053
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.534
ELB improved by 0.204226
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.329
ELB improved by 0.20515
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.119
ELB improved by 0.209147
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.901
ELB improved by 0.218675
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.662
ELB improved by 0.238677
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.382
ELB improved by 0.280442
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.008
ELB improved by 0.373637
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.411
ELB improved by 0.597436
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.337
ELB improved by 1.07364
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.691
ELB improved by 1.64579
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.71
ELB improved by 1.98085
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.502
ELB improved by 2.20871
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.362
ELB improved by 2.1398
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.43
ELB improved by 1.93168
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.771
ELB improved by 1.65931
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.45
ELB improved by 1.32034
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.477
ELB improved by 0.973476
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.792
ELB improved by 0.684438
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.309
ELB improved by 0.483147
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.946
ELB improved by 0.363733
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.647
ELB improved by 0.29882
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.399
ELB improved by 0.247534
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.218
ELB improved by 0.181612
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.098
ELB improved by 0.119462
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.015
ELB improved by 0.0826592
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.951
ELB improved by 0.0647001
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.895
ELB improved by 0.0553612
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.845
ELB improved by 0.0501468
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.798
ELB improved by 0.0474644
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.751
ELB improved by 0.046588
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.704
ELB improved by 0.046884
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.657
ELB improved by 0.047409
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.61
ELB improved by 0.0467894
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.566
ELB improved by 0.0437012
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.529
ELB improved by 0.0378719
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.498
ELB improved by 0.0305215
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.475
ELB improved by 0.0234545
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.457
ELB improved by 0.0178291
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.443
ELB improved by 0.0138497
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.432
ELB improved by 0.0111889
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.422
ELB improved by 0.00942092
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
4.621 0.449 6.182
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.084 | 0.043 | 0.138 | |
| getPIPs | 0.079 | 0.037 | 0.125 | |
| graper | 0.128 | 0.053 | 0.193 | |
| makeExampleData | 0.019 | 0.003 | 0.022 | |
| makeExampleDataWithUnequalGroups | 0.047 | 0.006 | 0.061 | |
| plotELBO | 0.422 | 0.045 | 0.807 | |
| plotGroupPenalties | 1.717 | 0.070 | 2.369 | |
| plotPosterior | 1.211 | 0.043 | 1.472 | |
| predict.graper | 3.152 | 0.197 | 3.961 | |
| print.graper | 0.077 | 0.032 | 0.130 | |