Britta Velten
| Snapshot Date: 2024-11-06 13:40 -0500 (Wed, 06 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: RELEASE_3_20 |
| git_last_commit: 04d5a90 |
| git_last_commit_date: 2024-10-29 10:33:50 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-07 12:08 -0500 (Thu, 07 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4505 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4765 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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 899/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.22.0 (landing page) Britta Velten
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: graper |
| Version: 1.22.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings graper_1.22.0.tar.gz |
| StartedAt: 2024-11-07 09:13:19 -0000 (Thu, 07 Nov 2024) |
| EndedAt: 2024-11-07 09:14:24 -0000 (Thu, 07 Nov 2024) |
| EllapsedTime: 65.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings graper_1.22.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/graper.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.22.0’
* 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 ... OK
* used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 6.0Mb
sub-directories of 1Mb or more:
libs 5.9Mb
* 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 loading without being on the library search path ... 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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.20-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL graper
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘graper’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c fit_graper.cpp -o fit_graper.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11,
from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/special_functions/digamma.hpp:15,
from graper_linear_dense_ff.h:2,
from fit_graper.cpp:4:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
| ^~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -lopenblas -L/usr/lib/gcc/aarch64-linux-gnu/10.3.1 -lgfortran -lm -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/site-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: aarch64-unknown-linux-gnu
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=-907.683
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-578.765
ELB improved by 328.918
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-520.502
ELB improved by 58.2633
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-490.497
ELB improved by 30.0046
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-478.879
ELB improved by 11.6179
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.631
ELB improved by 6.24842
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.786
ELB improved by 4.8444
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.274
ELB improved by 4.51274
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.607
ELB improved by 4.66663
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.399
ELB improved by 5.20808
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.284
ELB improved by 6.11506
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.509
ELB improved by 6.77497
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.467
ELB improved by 6.04192
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.329
ELB improved by 4.13789
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.893
ELB improved by 2.43604
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.497
ELB improved by 1.39579
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.662
ELB improved by 0.834851
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.116
ELB improved by 0.54609
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.72
ELB improved by 0.396431
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.405
ELB improved by 0.314637
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.138
ELB improved by 0.266949
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.9
ELB improved by 0.238327
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.678
ELB improved by 0.222396
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.461
ELB improved by 0.216989
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.238
ELB improved by 0.222588
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.996
ELB improved by 0.242447
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.712
ELB improved by 0.283244
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.364
ELB improved by 0.348454
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.955
ELB improved by 0.408661
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.556
ELB improved by 0.399601
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.235
ELB improved by 0.320286
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421
ELB improved by 0.235475
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.818
ELB improved by 0.181865
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.662
ELB improved by 0.155614
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.519
ELB improved by 0.143651
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.381
ELB improved by 0.13768
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.248
ELB improved by 0.13356
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.118
ELB improved by 0.129106
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.995
ELB improved by 0.123413
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.878
ELB improved by 0.116784
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.768
ELB improved by 0.110174
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.664
ELB improved by 0.104341
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.564
ELB improved by 0.0994909
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.469
ELB improved by 0.0954629
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.377
ELB improved by 0.0920126
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.288
ELB improved by 0.0889516
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.202
ELB improved by 0.0861703
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.118
ELB improved by 0.0836171
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.037
ELB improved by 0.0812746
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.958
ELB improved by 0.0791431
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.88
ELB improved by 0.0772316
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.805
ELB improved by 0.0755523
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.731
ELB improved by 0.0741182
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.658
ELB improved by 0.072942
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.586
ELB improved by 0.0720359
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.514
ELB improved by 0.0714117
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.443
ELB improved by 0.0710819
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.372
ELB improved by 0.0710611
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.301
ELB improved by 0.0713679
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.229
ELB improved by 0.0720281
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.156
ELB improved by 0.0730795
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.081
ELB improved by 0.0745787
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.004
ELB improved by 0.0766134
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.925
ELB improved by 0.0793216
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.842
ELB improved by 0.0829266
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.754
ELB improved by 0.0878019
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.66
ELB improved by 0.0945936
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.555
ELB improved by 0.104464
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.436
ELB improved by 0.119565
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.292
ELB improved by 0.14388
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.108
ELB improved by 0.184068
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.861
ELB improved by 0.247076
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.535
ELB improved by 0.326026
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.149
ELB improved by 0.385893
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.746
ELB improved by 0.40323
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.343
ELB improved by 0.402399
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.928
ELB improved by 0.415265
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.462
ELB improved by 0.466006
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.892
ELB improved by 0.569909
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.236
ELB improved by 0.656447
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.646
ELB improved by 0.589462
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.211
ELB improved by 0.435502
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.906
ELB improved by 0.304636
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.693
ELB improved by 0.212673
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.543
ELB improved by 0.15046
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.434
ELB improved by 0.108537
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.354
ELB improved by 0.0798583
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.295
ELB improved by 0.0598008
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.249
ELB improved by 0.0454754
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.214
ELB improved by 0.0350695
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.187
ELB improved by 0.0274114
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.165
ELB improved by 0.021717
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.148
ELB improved by 0.0174461
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.133
ELB improved by 0.0142177
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.122
ELB improved by 0.0117595
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.112
ELB improved by 0.009874
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-870.56
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-584.202
ELB improved by 286.358
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-524.229
ELB improved by 59.9729
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-480.566
ELB improved by 43.6631
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.902
ELB improved by 23.6639
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.632
ELB improved by 9.26977
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.021
ELB improved by 4.611
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.814
ELB improved by 3.20751
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.113
ELB improved by 2.70073
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.55
ELB improved by 2.56336
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.958
ELB improved by 2.59198
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.254
ELB improved by 2.70338
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.42
ELB improved by 2.83452
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.527
ELB improved by 2.8922
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.763
ELB improved by 2.76408
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.355
ELB improved by 2.40881
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.422
ELB improved by 1.93214
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.91
ELB improved by 1.51196
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.658
ELB improved by 1.25266
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.504
ELB improved by 1.1535
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.339
ELB improved by 1.1653
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.111
ELB improved by 1.22799
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.821
ELB improved by 1.28974
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.486
ELB improved by 1.33571
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.093
ELB improved by 1.39289
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.599
ELB improved by 1.49388
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.947
ELB improved by 1.65189
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.1
ELB improved by 1.84691
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.104
ELB improved by 1.9963
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.126
ELB improved by 1.97777
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.37
ELB improved by 1.75593
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.942
ELB improved by 1.42837
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.84
ELB improved by 1.1014
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.043
ELB improved by 0.797093
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.514
ELB improved by 0.52904
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.176
ELB improved by 0.3378
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.956
ELB improved by 0.220654
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.805
ELB improved by 0.15109
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.695
ELB improved by 0.109486
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.61
ELB improved by 0.0848425
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.539
ELB improved by 0.0713456
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.473
ELB improved by 0.0662157
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.404
ELB improved by 0.0685674
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.326
ELB improved by 0.0784049
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.231
ELB improved by 0.0944789
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.121
ELB improved by 0.110429
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.006
ELB improved by 0.114589
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.905
ELB improved by 0.101003
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.828
ELB improved by 0.0771013
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.774
ELB improved by 0.0537895
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.738
ELB improved by 0.0365292
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.712
ELB improved by 0.025658
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.693
ELB improved by 0.0193295
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.677
ELB improved by 0.0156401
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.664
ELB improved by 0.0133463
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.652
ELB improved by 0.0117814
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.641
ELB improved by 0.0106155
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.632
ELB improved by 0.00968712
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-870
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-567.489
ELB improved by 302.51
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-513.137
ELB improved by 54.3524
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-481.621
ELB improved by 31.5164
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.811
ELB improved by 13.8094
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.06
ELB improved by 6.75102
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.655
ELB improved by 4.40505
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.933
ELB improved by 3.72252
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.14
ELB improved by 3.79297
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.913
ELB improved by 4.2263
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.217
ELB improved by 4.69644
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.444
ELB improved by 4.77301
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.285
ELB improved by 4.1588
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.255
ELB improved by 3.03022
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.365
ELB improved by 1.88933
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.28
ELB improved by 1.08507
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.637
ELB improved by 0.64376
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.206
ELB improved by 0.430218
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.88
ELB improved by 0.326892
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.606
ELB improved by 0.273909
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.361
ELB improved by 0.244936
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.133
ELB improved by 0.227899
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.916
ELB improved by 0.21678
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.708
ELB improved by 0.208518
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.506
ELB improved by 0.201679
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.31
ELB improved by 0.195734
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.119
ELB improved by 0.190623
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.933
ELB improved by 0.186558
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.749
ELB improved by 0.183992
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.565
ELB improved by 0.183673
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.378
ELB improved by 0.186772
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.183
ELB improved by 0.195038
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.973
ELB improved by 0.210742
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.737
ELB improved by 0.235664
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.469
ELB improved by 0.268042
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.169
ELB improved by 0.299995
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.844
ELB improved by 0.325104
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.491
ELB improved by 0.353146
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.085
ELB improved by 0.405377
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.606
ELB improved by 0.479585
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.079
ELB improved by 0.526803
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.526
ELB improved by 0.553075
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.89
ELB improved by 0.635913
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.178
ELB improved by 0.71249
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.521
ELB improved by 0.656468
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.918
ELB improved by 0.603411
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.332
ELB improved by 0.585202
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.826
ELB improved by 0.5069
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.425
ELB improved by 0.400978
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.105
ELB improved by 0.31967
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.842
ELB improved by 0.263063
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.619
ELB improved by 0.223005
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.423
ELB improved by 0.195366
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.243
ELB improved by 0.18
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.061
ELB improved by 0.182305
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.844
ELB improved by 0.217616
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.537
ELB improved by 0.306078
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.125
ELB improved by 0.412715
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.671
ELB improved by 0.453891
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.151
ELB improved by 0.519501
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.499
ELB improved by 0.652249
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.914
ELB improved by 0.585158
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.526
ELB improved by 0.387623
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.281
ELB improved by 0.245
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.121
ELB improved by 0.159821
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.012
ELB improved by 0.108989
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.935
ELB improved by 0.0779902
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.876
ELB improved by 0.0584648
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.83
ELB improved by 0.0456491
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.794
ELB improved by 0.03685
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.763
ELB improved by 0.0305385
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.737
ELB improved by 0.0258307
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.715
ELB improved by 0.0222008
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.696
ELB improved by 0.0193251
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.679
ELB improved by 0.016997
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.664
ELB improved by 0.0150795
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.65
ELB improved by 0.0134784
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.638
ELB improved by 0.0121269
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.627
ELB improved by 0.0109758
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.617
ELB improved by 0.00998834
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-887.226
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-585.084
ELB improved by 302.142
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-522.967
ELB improved by 62.1175
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-479.688
ELB improved by 43.279
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.957
ELB improved by 20.7305
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.148
ELB improved by 8.80972
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.368
ELB improved by 4.78006
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.23
ELB improved by 3.13741
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.724
ELB improved by 2.50575
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.342
ELB improved by 2.38216
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.843
ELB improved by 2.49873
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.126
ELB improved by 2.71754
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.217
ELB improved by 2.90917
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.301
ELB improved by 2.91621
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.64
ELB improved by 2.66104
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.36
ELB improved by 2.27965
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.319
ELB improved by 2.04043
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.206
ELB improved by 2.11304
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.84
ELB improved by 2.36592
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.353
ELB improved by 2.48747
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.864
ELB improved by 2.4895
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.37
ELB improved by 2.49395
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.845
ELB improved by 2.52476
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.247
ELB improved by 2.59757
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.529
ELB improved by 2.71827
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.68
ELB improved by 2.84927
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.79
ELB improved by 2.88953
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.083
ELB improved by 2.70715
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.824
ELB improved by 2.25914
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.143
ELB improved by 1.6808
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.973
ELB improved by 1.17051
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.139
ELB improved by 0.833199
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.46
ELB improved by 0.679033
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.823
ELB improved by 0.637405
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.276
ELB improved by 0.54708
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.9
ELB improved by 0.376337
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.667
ELB improved by 0.23209
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.523
ELB improved by 0.144823
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.426
ELB improved by 0.0969666
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.355
ELB improved by 0.0702531
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.301
ELB improved by 0.0541163
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.258
ELB improved by 0.0434741
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.222
ELB improved by 0.0359457
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.192
ELB improved by 0.0303384
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.166
ELB improved by 0.0259973
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.143
ELB improved by 0.022536
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.123
ELB improved by 0.0197139
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.106
ELB improved by 0.0173751
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.09
ELB improved by 0.0154132
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.077
ELB improved by 0.013753
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.064
ELB improved by 0.0123387
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.053
ELB improved by 0.0111276
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.043
ELB improved by 0.0100859
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.034
ELB improved by 0.00918665
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
3.116 0.122 2.819
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.104 | 0.000 | 0.055 | |
| getPIPs | 0.097 | 0.000 | 0.048 | |
| graper | 0.154 | 0.004 | 0.078 | |
| makeExampleData | 0.016 | 0.000 | 0.008 | |
| makeExampleDataWithUnequalGroups | 0.014 | 0.004 | 0.009 | |
| plotELBO | 0.376 | 0.004 | 0.283 | |
| plotGroupPenalties | 1.200 | 0.004 | 1.113 | |
| plotPosterior | 1.009 | 0.012 | 0.928 | |
| predict.graper | 1.136 | 0.016 | 1.036 | |
| print.graper | 0.143 | 0.008 | 0.078 | |