Britta Velten
| Snapshot Date: 2024-05-30 18:57:37 -0400 (Thu, 30 May 2024) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: 7b45fcc |
| git_last_commit_date: 2024-04-30 11:11:42 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-31 19:31:18 -0400 (Fri, 31 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
| 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 878/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.21.0 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 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: 1.21.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.21.0.tar.gz |
| StartedAt: 2024-05-31 09:29:31 -0400 (Fri, 31 May 2024) |
| EndedAt: 2024-05-31 09:31:40 -0400 (Fri, 31 May 2024) |
| EllapsedTime: 128.6 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_1.21.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/graper.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.21.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... WARNING
Found the following significant warnings:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
# warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/graper.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) predict.graper.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:23-24: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL graper
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘graper’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fit_graper.cpp -o fit_graper.o
In file included from fit_graper.cpp:4:
In file included from ./graper_linear_dense_ff.h:2:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/digamma.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/math_fwd.hpp:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
# warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o graper.so RcppExports.o fit_graper.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-graper/00new/graper/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (graper)
graper.Rcheck/tests/testthat.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "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=-877.211
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-587.784
ELB improved by 289.427
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-528.663
ELB improved by 59.1204
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-488.548
ELB improved by 40.1151
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.67
ELB improved by 18.8778
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.337
ELB improved by 7.33357
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.231
ELB improved by 4.10607
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.954
ELB improved by 3.27713
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.895
ELB improved by 3.05817
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.825
ELB improved by 3.07025
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.664
ELB improved by 3.16064
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.404
ELB improved by 3.26055
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.094
ELB improved by 3.31033
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.863
ELB improved by 3.23031
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.912
ELB improved by 2.95174
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.407
ELB improved by 2.50445
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.407
ELB improved by 2.00056
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.897
ELB improved by 1.50977
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.832
ELB improved by 1.06479
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.118
ELB improved by 0.714102
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.638
ELB improved by 0.479993
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.298
ELB improved by 0.340122
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.039
ELB improved by 0.259224
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.827
ELB improved by 0.211213
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.646
ELB improved by 0.181226
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.485
ELB improved by 0.161494
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.337
ELB improved by 0.147947
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.198
ELB improved by 0.138388
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.067
ELB improved by 0.131598
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.94
ELB improved by 0.126886
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.816
ELB improved by 0.123858
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.694
ELB improved by 0.122286
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.572
ELB improved by 0.122036
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.449
ELB improved by 0.123038
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.323
ELB improved by 0.125252
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.195
ELB improved by 0.12866
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.061
ELB improved by 0.133249
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.922
ELB improved by 0.139001
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.777
ELB improved by 0.145881
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.623
ELB improved by 0.15383
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.46
ELB improved by 0.162759
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.287
ELB improved by 0.172556
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.104
ELB improved by 0.18309
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.91
ELB improved by 0.194241
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.704
ELB improved by 0.20592
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.486
ELB improved by 0.218103
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.255
ELB improved by 0.23084
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.011
ELB improved by 0.244229
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.753
ELB improved by 0.258328
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.48
ELB improved by 0.273028
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.192
ELB improved by 0.287943
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.889
ELB improved by 0.302467
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.573
ELB improved by 0.315996
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.245
ELB improved by 0.328123
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.906
ELB improved by 0.338609
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.559
ELB improved by 0.347268
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.205
ELB improved by 0.354067
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.846
ELB improved by 0.359561
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.48
ELB improved by 0.36545
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.105
ELB improved by 0.374944
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.713
ELB improved by 0.392674
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.288
ELB improved by 0.424707
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.805
ELB improved by 0.482811
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.207
ELB improved by 0.598059
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.409
ELB improved by 0.798265
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.411
ELB improved by 0.997179
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.238
ELB improved by 1.17392
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.899
ELB improved by 1.33859
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.684
ELB improved by 1.21519
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.79
ELB improved by 0.894068
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.21
ELB improved by 0.579981
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.86
ELB improved by 0.350113
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.649
ELB improved by 0.210714
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.516
ELB improved by 0.133069
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.426
ELB improved by 0.0901584
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.36
ELB improved by 0.0654119
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.31
ELB improved by 0.0501356
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.27
ELB improved by 0.0399994
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.237
ELB improved by 0.0328256
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.21
ELB improved by 0.0274715
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.187
ELB improved by 0.0233057
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.167
ELB improved by 0.0199622
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.149
ELB improved by 0.0172204
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.134
ELB improved by 0.0149421
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.121
ELB improved by 0.0130362
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.11
ELB improved by 0.0114389
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.1
ELB improved by 0.0101012
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.091
ELB improved by 0.00898313
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-844.447
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-587.131
ELB improved by 257.316
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-527.355
ELB improved by 59.7763
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-483.995
ELB improved by 43.3601
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.61
ELB improved by 23.3853
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.604
ELB improved by 10.0056
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.822
ELB improved by 4.78185
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.516
ELB improved by 3.30613
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.671
ELB improved by 2.84474
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.986
ELB improved by 2.68504
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.342
ELB improved by 2.64474
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.698
ELB improved by 2.64365
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.08
ELB improved by 2.61778
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.576
ELB improved by 2.50409
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.303
ELB improved by 2.27367
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.34
ELB improved by 1.96235
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.712
ELB improved by 1.62815
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.406
ELB improved by 1.30563
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.378
ELB improved by 1.02831
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.554
ELB improved by 0.823675
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.858
ELB improved by 0.69628
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.226
ELB improved by 0.632253
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.615
ELB improved by 0.611024
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415
ELB improved by 0.614691
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.37
ELB improved by 0.630212
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.722
ELB improved by 0.648191
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.06
ELB improved by 0.661841
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.393
ELB improved by 0.666837
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.731
ELB improved by 0.661581
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.084
ELB improved by 0.647209
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.457
ELB improved by 0.627003
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.852
ELB improved by 0.605295
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.266
ELB improved by 0.586213
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.693
ELB improved by 0.572689
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.127
ELB improved by 0.56592
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.562
ELB improved by 0.565211
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.994
ELB improved by 0.56797
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.424
ELB improved by 0.569891
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.858
ELB improved by 0.565611
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.308
ELB improved by 0.550044
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.788
ELB improved by 0.520056
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.313
ELB improved by 0.475703
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.892
ELB improved by 0.420381
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.532
ELB improved by 0.359801
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.232
ELB improved by 0.300186
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.986
ELB improved by 0.246462
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.785
ELB improved by 0.201251
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.62
ELB improved by 0.164882
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.484
ELB improved by 0.136141
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.37
ELB improved by 0.113308
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.275
ELB improved by 0.0950411
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.195
ELB improved by 0.0806972
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.124
ELB improved by 0.0700793
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.061
ELB improved by 0.0630835
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.002
ELB improved by 0.0596149
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.942
ELB improved by 0.0597154
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.878
ELB improved by 0.0636971
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.806
ELB improved by 0.0721578
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.72
ELB improved by 0.0857364
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.617
ELB improved by 0.103931
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.495
ELB improved by 0.121488
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.37
ELB improved by 0.125295
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.264
ELB improved by 0.105674
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.191
ELB improved by 0.0732509
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.145
ELB improved by 0.0456381
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.117
ELB improved by 0.0285441
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.097
ELB improved by 0.0193131
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.083
ELB improved by 0.0144627
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.071
ELB improved by 0.0118159
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.061
ELB improved by 0.0102551
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.052
ELB improved by 0.00924417
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-875.429
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-613.685
ELB improved by 261.744
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-557.197
ELB improved by 56.4878
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-508.686
ELB improved by 48.5106
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-478.159
ELB improved by 30.5278
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.135
ELB improved by 14.0233
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.894
ELB improved by 6.24114
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.855
ELB improved by 4.03875
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.484
ELB improved by 3.37179
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.364
ELB improved by 3.11926
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.424
ELB improved by 2.94014
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.758
ELB improved by 2.66593
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.501
ELB improved by 2.25676
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.718
ELB improved by 1.78364
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.369
ELB improved by 1.34842
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.368
ELB improved by 1.00167
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.63
ELB improved by 0.738178
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.091
ELB improved by 0.538998
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.698
ELB improved by 0.392231
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.41
ELB improved by 0.288647
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.192
ELB improved by 0.217834
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.022
ELB improved by 0.169807
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.885
ELB improved by 0.136761
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.772
ELB improved by 0.11333
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.676
ELB improved by 0.0960876
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.593
ELB improved by 0.0829136
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.52
ELB improved by 0.0725084
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.456
ELB improved by 0.0640638
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.399
ELB improved by 0.0570633
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.348
ELB improved by 0.0511651
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.302
ELB improved by 0.0461332
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.26
ELB improved by 0.0417984
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.222
ELB improved by 0.0380351
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.187
ELB improved by 0.0347467
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.156
ELB improved by 0.0318579
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.126
ELB improved by 0.029308
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.099
ELB improved by 0.0270482
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.074
ELB improved by 0.0250382
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.051
ELB improved by 0.0232446
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.029
ELB improved by 0.0216396
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.009
ELB improved by 0.0201998
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.99
ELB improved by 0.0189053
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.972
ELB improved by 0.0177394
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.956
ELB improved by 0.0166877
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.94
ELB improved by 0.0157377
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.925
ELB improved by 0.0148788
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.911
ELB improved by 0.0141019
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.898
ELB improved by 0.0133988
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.885
ELB improved by 0.0127628
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.873
ELB improved by 0.0121875
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.861
ELB improved by 0.0116679
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.85
ELB improved by 0.0111992
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.839
ELB improved by 0.0107773
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.829
ELB improved by 0.0103988
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.819
ELB improved by 0.0100605
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.809
ELB improved by 0.00975968
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-877.891
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-566.998
ELB improved by 310.893
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-511.789
ELB improved by 55.2089
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-482.264
ELB improved by 29.525
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.908
ELB improved by 13.3558
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.924
ELB improved by 6.98443
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.203
ELB improved by 4.72085
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.072
ELB improved by 4.13099
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.922
ELB improved by 4.1497
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.606
ELB improved by 4.31572
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.319
ELB improved by 4.28723
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.543
ELB improved by 3.77637
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.666
ELB improved by 2.87641
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.647
ELB improved by 2.01981
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.186
ELB improved by 1.46054
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.03
ELB improved by 1.15593
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.046
ELB improved by 0.983951
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.181
ELB improved by 0.864909
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.412
ELB improved by 0.769493
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.721
ELB improved by 0.69059
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.097
ELB improved by 0.623772
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.532
ELB improved by 0.565044
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.02
ELB improved by 0.512118
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.556
ELB improved by 0.464097
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.135
ELB improved by 0.420704
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.754
ELB improved by 0.381816
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.406
ELB improved by 0.347288
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.089
ELB improved by 0.316936
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.799
ELB improved by 0.290584
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.531
ELB improved by 0.268123
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.281
ELB improved by 0.249571
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.046
ELB improved by 0.235104
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.821
ELB improved by 0.224972
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.602
ELB improved by 0.219106
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.386
ELB improved by 0.216332
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.172
ELB improved by 0.214018
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.961
ELB improved by 0.210106
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.754
ELB improved by 0.20701
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.541
ELB improved by 0.213156
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.298
ELB improved by 0.242853
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.985
ELB improved by 0.31299
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.584
ELB improved by 0.401768
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.177
ELB improved by 0.406886
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.854
ELB improved by 0.322444
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.614
ELB improved by 0.240671
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.429
ELB improved by 0.184248
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.285
ELB improved by 0.144823
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.169
ELB improved by 0.115972
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.074
ELB improved by 0.0942391
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.997
ELB improved by 0.0775286
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.932
ELB improved by 0.0644353
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.878
ELB improved by 0.05399
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.833
ELB improved by 0.0455254
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.794
ELB improved by 0.0385818
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.761
ELB improved by 0.0328368
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.733
ELB improved by 0.0280572
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.709
ELB improved by 0.0240671
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.689
ELB improved by 0.0207287
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.671
ELB improved by 0.0179309
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.655
ELB improved by 0.0155824
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.642
ELB improved by 0.0136077
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.63
ELB improved by 0.0119439
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.619
ELB improved by 0.0105385
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.61
ELB improved by 0.00934824
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
4.642 0.494 5.512
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.088 | 0.053 | 0.192 | |
| getPIPs | 0.079 | 0.047 | 0.147 | |
| graper | 0.132 | 0.065 | 0.226 | |
| makeExampleData | 0.019 | 0.003 | 0.023 | |
| makeExampleDataWithUnequalGroups | 0.045 | 0.006 | 0.059 | |
| plotELBO | 0.425 | 0.049 | 0.536 | |
| plotGroupPenalties | 1.730 | 0.072 | 1.971 | |
| plotPosterior | 1.222 | 0.058 | 1.383 | |
| predict.graper | 3.118 | 0.224 | 3.610 | |
| print.graper | 0.074 | 0.033 | 0.126 | |