Britta Velten
| Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 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 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| 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: 2024-11-20 08:32:47 -0000 (Wed, 20 Nov 2024) |
| EndedAt: 2024-11-20 08:33:58 -0000 (Wed, 20 Nov 2024) |
| EllapsedTime: 71.1 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=-854.54
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-556.11
ELB improved by 298.431
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-494.898
ELB improved by 61.2115
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.349
ELB improved by 37.549
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.056
ELB improved by 18.2931
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.702
ELB improved by 9.35439
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.67
ELB improved by 6.03174
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.645
ELB improved by 5.0251
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.67
ELB improved by 4.97452
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.175
ELB improved by 5.49524
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.918
ELB improved by 6.25741
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.243
ELB improved by 6.6746
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.192
ELB improved by 6.05117
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.702
ELB improved by 4.48959
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.691
ELB improved by 3.01155
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.562
ELB improved by 2.12898
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.062
ELB improved by 1.49953
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.073
ELB improved by 0.989391
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.418
ELB improved by 0.65493
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.965
ELB improved by 0.452989
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.631
ELB improved by 0.334027
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.367
ELB improved by 0.263604
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.147
ELB improved by 0.220011
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.956
ELB improved by 0.191375
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.784
ELB improved by 0.171544
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.627
ELB improved by 0.15725
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.481
ELB improved by 0.146633
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.342
ELB improved by 0.138554
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.21
ELB improved by 0.132262
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.082
ELB improved by 0.127232
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.959
ELB improved by 0.123084
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.84
ELB improved by 0.11953
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.723
ELB improved by 0.116351
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.61
ELB improved by 0.113375
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.5
ELB improved by 0.110473
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.392
ELB improved by 0.107552
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.288
ELB improved by 0.104552
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.186
ELB improved by 0.101442
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.088
ELB improved by 0.098221
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.993
ELB improved by 0.0949171
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.901
ELB improved by 0.0915845
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.813
ELB improved by 0.088306
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.728
ELB improved by 0.0851986
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.645
ELB improved by 0.0824286
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.565
ELB improved by 0.0802458
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.486
ELB improved by 0.0790601
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.407
ELB improved by 0.0796089
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.323
ELB improved by 0.083323
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.23
ELB improved by 0.0930725
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.116
ELB improved by 0.114218
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.963
ELB improved by 0.153355
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.758
ELB improved by 0.204887
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.525
ELB improved by 0.232489
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.311
ELB improved by 0.213897
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.129
ELB improved by 0.182292
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.966
ELB improved by 0.162765
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.812
ELB improved by 0.153967
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.663
ELB improved by 0.149639
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.516
ELB improved by 0.146323
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.373
ELB improved by 0.143058
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.233
ELB improved by 0.1398
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.097
ELB improved by 0.136449
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.964
ELB improved by 0.132702
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.836
ELB improved by 0.128221
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.713
ELB improved by 0.122763
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.597
ELB improved by 0.116221
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.488
ELB improved by 0.108629
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.388
ELB improved by 0.100147
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.297
ELB improved by 0.0910242
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.216
ELB improved by 0.0815669
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.144
ELB improved by 0.0720936
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.081
ELB improved by 0.0629003
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.026
ELB improved by 0.0542343
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.98
ELB improved by 0.0462775
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.941
ELB improved by 0.0391421
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.908
ELB improved by 0.0328752
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.881
ELB improved by 0.0274696
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.858
ELB improved by 0.0228781
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.839
ELB improved by 0.0190277
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.823
ELB improved by 0.015832
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.81
ELB improved by 0.0132012
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.799
ELB improved by 0.0110485
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.789
ELB improved by 0.0092946
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-841.979
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-563.936
ELB improved by 278.043
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-505.822
ELB improved by 58.1139
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.973
ELB improved by 38.8493
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.624
ELB improved by 17.3496
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.031
ELB improved by 7.59247
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.759
ELB improved by 5.27186
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.506
ELB improved by 5.25318
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.507
ELB improved by 5.9989
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.799
ELB improved by 6.70811
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.291
ELB improved by 6.50815
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.174
ELB improved by 5.117
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.82
ELB improved by 3.3539
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.759
ELB improved by 2.0609
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.42
ELB improved by 1.33929
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.444
ELB improved by 0.975288
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.643
ELB improved by 0.801185
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.917
ELB improved by 0.725895
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.234
ELB improved by 0.68376
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.607
ELB improved by 0.626391
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.052
ELB improved by 0.555675
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.559
ELB improved by 0.492424
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.118
ELB improved by 0.441266
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.718
ELB improved by 0.399536
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.353
ELB improved by 0.365078
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.017
ELB improved by 0.336741
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.703
ELB improved by 0.31382
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.407
ELB improved by 0.29584
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.124
ELB improved by 0.282587
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.85
ELB improved by 0.274158
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.579
ELB improved by 0.27077
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.308
ELB improved by 0.271834
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.034
ELB improved by 0.273887
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.764
ELB improved by 0.269489
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.512
ELB improved by 0.252576
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.285
ELB improved by 0.226363
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.086
ELB improved by 0.199367
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.91
ELB improved by 0.176242
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.752
ELB improved by 0.157187
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.611
ELB improved by 0.14117
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.484
ELB improved by 0.127413
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.368
ELB improved by 0.115556
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.263
ELB improved by 0.105536
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.165
ELB improved by 0.0975082
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.073
ELB improved by 0.0918713
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.984
ELB improved by 0.0893817
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.893
ELB improved by 0.0913226
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.793
ELB improved by 0.0994461
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.679
ELB improved by 0.114626
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.546
ELB improved by 0.132607
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.405
ELB improved by 0.140819
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.276
ELB improved by 0.129582
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.169
ELB improved by 0.106246
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.086
ELB improved by 0.0835196
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.02
ELB improved by 0.0661118
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.966
ELB improved by 0.053397
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.922
ELB improved by 0.043918
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.886
ELB improved by 0.0366504
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.855
ELB improved by 0.0309783
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.828
ELB improved by 0.0265129
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.805
ELB improved by 0.022979
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.785
ELB improved by 0.0201652
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.767
ELB improved by 0.0179042
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.751
ELB improved by 0.0160654
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.737
ELB improved by 0.0145486
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.723
ELB improved by 0.0132786
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.711
ELB improved by 0.0121994
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.7
ELB improved by 0.0112701
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.689
ELB improved by 0.0104603
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.68
ELB improved by 0.00974752
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-856.922
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-555.583
ELB improved by 301.339
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-499.262
ELB improved by 56.3217
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.589
ELB improved by 34.673
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.057
ELB improved by 14.5319
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.9
ELB improved by 6.15698
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.005
ELB improved by 3.89477
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.637
ELB improved by 3.36764
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.318
ELB improved by 3.31903
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.777
ELB improved by 3.54176
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.814
ELB improved by 3.96279
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.373
ELB improved by 4.44077
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.696
ELB improved by 4.67671
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.363
ELB improved by 4.33376
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.939
ELB improved by 3.42386
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.571
ELB improved by 2.36789
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.036
ELB improved by 1.53523
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.032
ELB improved by 1.00415
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.337
ELB improved by 0.694658
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.821
ELB improved by 0.515717
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.413
ELB improved by 0.408372
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.072
ELB improved by 0.340476
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.777
ELB improved by 0.295209
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.513
ELB improved by 0.263627
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.273
ELB improved by 0.240797
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.049
ELB improved by 0.223895
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.837
ELB improved by 0.211278
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.635
ELB improved by 0.202011
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.44
ELB improved by 0.195626
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.248
ELB improved by 0.19201
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.056
ELB improved by 0.191356
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.862
ELB improved by 0.194166
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.661
ELB improved by 0.201259
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.447
ELB improved by 0.213728
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.215
ELB improved by 0.232745
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.955
ELB improved by 0.259144
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.663
ELB improved by 0.292936
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.33
ELB improved by 0.332868
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.955
ELB improved by 0.375062
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.543
ELB improved by 0.411704
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.107
ELB improved by 0.435667
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.66
ELB improved by 0.447322
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.208
ELB improved by 0.451533
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.757
ELB improved by 0.451228
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.311
ELB improved by 0.446189
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.876
ELB improved by 0.434568
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.462
ELB improved by 0.414473
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.077
ELB improved by 0.385202
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.729
ELB improved by 0.347894
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.423
ELB improved by 0.305406
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.162
ELB improved by 0.261433
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.943
ELB improved by 0.219356
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.761
ELB improved by 0.181419
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.613
ELB improved by 0.148618
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.491
ELB improved by 0.121109
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.393
ELB improved by 0.0986198
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.312
ELB improved by 0.0806331
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.246
ELB improved by 0.0664549
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.19
ELB improved by 0.0553294
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.144
ELB improved by 0.0465613
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.104
ELB improved by 0.0395838
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.07
ELB improved by 0.0339664
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.041
ELB improved by 0.0293924
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.015
ELB improved by 0.0256301
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.993
ELB improved by 0.0225081
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.973
ELB improved by 0.0198976
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.955
ELB improved by 0.0176998
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.939
ELB improved by 0.0158379
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.925
ELB improved by 0.0142512
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.912
ELB improved by 0.0128915
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.9
ELB improved by 0.01172
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.89
ELB improved by 0.0107055
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.88
ELB improved by 0.00982251
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-897.396
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-574.457
ELB improved by 322.939
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-513.176
ELB improved by 61.2806
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-477.002
ELB improved by 36.174
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.109
ELB improved by 14.8932
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.056
ELB improved by 7.05281
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.378
ELB improved by 4.67772
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.405
ELB improved by 3.97358
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.507
ELB improved by 3.89807
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.335
ELB improved by 4.17173
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.639
ELB improved by 4.69555
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.285
ELB improved by 5.35451
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.407
ELB improved by 5.87835
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.556
ELB improved by 5.85006
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.5
ELB improved by 5.05661
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.702
ELB improved by 3.7982
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.114
ELB improved by 2.58739
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.409
ELB improved by 1.70498
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.254
ELB improved by 1.15575
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.422
ELB improved by 0.831158
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.795
ELB improved by 0.627732
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.307
ELB improved by 0.487586
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.919
ELB improved by 0.388399
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.599
ELB improved by 0.319546
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.327
ELB improved by 0.272062
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.089
ELB improved by 0.238551
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.875
ELB improved by 0.213871
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.68
ELB improved by 0.194824
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.5
ELB improved by 0.179536
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.333
ELB improved by 0.166947
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.177
ELB improved by 0.156488
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.029
ELB improved by 0.147915
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.888
ELB improved by 0.141234
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.751
ELB improved by 0.136727
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.616
ELB improved by 0.13509
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.478
ELB improved by 0.137763
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.331
ELB improved by 0.147576
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.161
ELB improved by 0.169627
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.95
ELB improved by 0.210503
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.682
ELB improved by 0.268353
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.369
ELB improved by 0.313
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.059
ELB improved by 0.310412
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.776
ELB improved by 0.282624
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.511
ELB improved by 0.264831
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.248
ELB improved by 0.2635
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.973
ELB improved by 0.275042
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.679
ELB improved by 0.294051
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.368
ELB improved by 0.311098
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.051
ELB improved by 0.316406
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.743
ELB improved by 0.308381
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.45
ELB improved by 0.29231
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.178
ELB improved by 0.272336
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.928
ELB improved by 0.249712
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.703
ELB improved by 0.225022
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.504
ELB improved by 0.199292
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.33
ELB improved by 0.173863
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.18
ELB improved by 0.14996
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.052
ELB improved by 0.128408
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.942
ELB improved by 0.109552
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.849
ELB improved by 0.0933417
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.769
ELB improved by 0.0794849
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.702
ELB improved by 0.0676111
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.644
ELB improved by 0.0573834
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.596
ELB improved by 0.048549
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.555
ELB improved by 0.0409357
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.521
ELB improved by 0.0344218
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.492
ELB improved by 0.0289036
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.467
ELB improved by 0.0242781
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.447
ELB improved by 0.0204374
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.43
ELB improved by 0.0172724
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.415
ELB improved by 0.0146784
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.402
ELB improved by 0.0125598
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.392
ELB improved by 0.0108326
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.382
ELB improved by 0.00942466
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
3.053 0.138 2.776
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.101 | 0.000 | 0.053 | |
| getPIPs | 0.095 | 0.000 | 0.048 | |
| graper | 0.150 | 0.000 | 0.075 | |
| makeExampleData | 0.012 | 0.004 | 0.008 | |
| makeExampleDataWithUnequalGroups | 0.013 | 0.004 | 0.010 | |
| plotELBO | 0.354 | 0.004 | 0.259 | |
| plotGroupPenalties | 1.105 | 0.008 | 1.022 | |
| plotPosterior | 0.970 | 0.008 | 0.886 | |
| predict.graper | 1.117 | 0.000 | 1.002 | |
| print.graper | 0.091 | 0.004 | 0.049 | |