Britta Velten
| Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: RELEASE_3_18 |
| git_last_commit: eea1fd2 |
| git_last_commit_date: 2023-10-24 11:10:07 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:40:46 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 896/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.18.0 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| 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: 1.18.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings graper_1.18.0.tar.gz |
| StartedAt: 2023-11-02 11:07:24 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 11:08:41 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 77.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings graper_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/graper.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
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 ‘1.18.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 7.7Mb
sub-directories of 1Mb or more:
libs 7.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL graper
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘graper’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/lexical_cast.hpp:30,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/convert_from_string.hpp:15,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/constants/constants.hpp:14,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/digamma.hpp:20,
from graper_linear_dense_ff.h:2,
from fit_graper.cpp:4:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -llapack -lblas -lgfortran -lm -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(graper)
>
> test_check("graper")
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-830.6
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-565.61
ELB improved by 264.99
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-505.509
ELB improved by 60.1002
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.624
ELB improved by 36.8853
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.177
ELB improved by 16.447
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.786
ELB improved by 7.39079
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.92
ELB improved by 4.86633
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.691
ELB improved by 4.22857
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.465
ELB improved by 4.22637
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.145
ELB improved by 4.31985
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.013
ELB improved by 4.13215
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.517
ELB improved by 3.49629
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.936
ELB improved by 2.58087
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.216
ELB improved by 1.72032
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.11
ELB improved by 1.10578
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.379
ELB improved by 0.730256
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.866
ELB improved by 0.513698
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.479
ELB improved by 0.387247
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.169
ELB improved by 0.309293
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.911
ELB improved by 0.257788
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.69
ELB improved by 0.221509
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.495
ELB improved by 0.194669
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.321
ELB improved by 0.174136
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.163
ELB improved by 0.158092
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.018
ELB improved by 0.145406
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.882
ELB improved by 0.135326
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.755
ELB improved by 0.12733
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.634
ELB improved by 0.121042
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.518
ELB improved by 0.116184
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.405
ELB improved by 0.112552
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.295
ELB improved by 0.109994
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.187
ELB improved by 0.108397
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.079
ELB improved by 0.107685
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.971
ELB improved by 0.107811
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.863
ELB improved by 0.108756
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.752
ELB improved by 0.110533
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.639
ELB improved by 0.113188
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.522
ELB improved by 0.116806
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.401
ELB improved by 0.121517
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.273
ELB improved by 0.127507
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.138
ELB improved by 0.135027
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.994
ELB improved by 0.1444
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.838
ELB improved by 0.156032
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.667
ELB improved by 0.170422
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.479
ELB improved by 0.188167
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.269
ELB improved by 0.209966
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.032
ELB improved by 0.2366
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.764
ELB improved by 0.268865
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.456
ELB improved by 0.307449
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.103
ELB improved by 0.352813
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.698
ELB improved by 0.405182
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.233
ELB improved by 0.464708
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.702
ELB improved by 0.531693
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.095
ELB improved by 0.606455
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.407
ELB improved by 0.688442
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.632
ELB improved by 0.774308
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.777
ELB improved by 0.855322
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.861
ELB improved by 0.916367
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.92
ELB improved by 0.940695
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.999
ELB improved by 0.921025
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.129
ELB improved by 0.869699
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.308
ELB improved by 0.821565
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.488
ELB improved by 0.819668
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.657
ELB improved by 0.831032
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.95
ELB improved by 0.707288
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.473
ELB improved by 0.476355
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.182
ELB improved by 0.291675
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.997
ELB improved by 0.184713
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.87
ELB improved by 0.127128
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.775
ELB improved by 0.0951247
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.699
ELB improved by 0.0763119
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.634
ELB improved by 0.0647313
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.576
ELB improved by 0.0573183
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.524
ELB improved by 0.0522201
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.476
ELB improved by 0.0480895
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.432
ELB improved by 0.043891
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.393
ELB improved by 0.0390093
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.36
ELB improved by 0.0334129
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.332
ELB improved by 0.0275828
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.31
ELB improved by 0.0221572
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.293
ELB improved by 0.0175741
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.279
ELB improved by 0.0139589
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.267
ELB improved by 0.0112195
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.258
ELB improved by 0.00917997
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-869.569
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-569.572
ELB improved by 299.997
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-508.219
ELB improved by 61.353
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.215
ELB improved by 40.0043
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.636
ELB improved by 17.5783
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.241
ELB improved by 7.39588
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.919
ELB improved by 4.32176
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.427
ELB improved by 3.49147
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.092
ELB improved by 3.33554
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.654
ELB improved by 3.43736
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.071
ELB improved by 3.58331
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.49
ELB improved by 3.58148
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.211
ELB improved by 3.27826
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.524
ELB improved by 2.6878
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.515
ELB improved by 2.00855
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.067
ELB improved by 1.4477
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.982
ELB improved by 1.08565
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.088
ELB improved by 0.893757
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.294
ELB improved by 0.793543
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.583
ELB improved by 0.71093
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.944
ELB improved by 0.638971
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.344
ELB improved by 0.60078
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.75
ELB improved by 0.593898
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.143
ELB improved by 0.606292
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.513
ELB improved by 0.630819
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.848
ELB improved by 0.665056
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.14
ELB improved by 0.707499
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.389
ELB improved by 0.750596
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.613
ELB improved by 0.776077
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.843
ELB improved by 0.770245
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.101
ELB improved by 0.742599
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.39
ELB improved by 0.710157
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.711
ELB improved by 0.679408
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.062
ELB improved by 0.649015
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.446
ELB improved by 0.616182
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.866
ELB improved by 0.579568
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.326
ELB improved by 0.540296
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.824
ELB improved by 0.502397
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.35
ELB improved by 0.473568
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.884
ELB improved by 0.466217
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.394
ELB improved by 0.489919
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.883
ELB improved by 0.510934
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.428
ELB improved by 0.454681
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.08
ELB improved by 0.348296
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.819
ELB improved by 0.260912
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.618
ELB improved by 0.200894
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.46
ELB improved by 0.157811
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.335
ELB improved by 0.125246
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.235
ELB improved by 0.100293
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.153
ELB improved by 0.0812773
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.087
ELB improved by 0.0668776
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.031
ELB improved by 0.055995
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.983
ELB improved by 0.047748
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.941
ELB improved by 0.0414441
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.905
ELB improved by 0.0365499
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.872
ELB improved by 0.0326682
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.843
ELB improved by 0.0295131
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.816
ELB improved by 0.0268843
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.791
ELB improved by 0.0246415
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.768
ELB improved by 0.0226856
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.748
ELB improved by 0.0209443
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.728
ELB improved by 0.0193641
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.71
ELB improved by 0.0179053
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.694
ELB improved by 0.0165398
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.678
ELB improved by 0.01525
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.664
ELB improved by 0.0140272
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.652
ELB improved by 0.0128699
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.64
ELB improved by 0.011782
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.629
ELB improved by 0.0107696
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.619
ELB improved by 0.00983881
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-886.082
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-566.619
ELB improved by 319.463
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-506.491
ELB improved by 60.1275
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.978
ELB improved by 34.5136
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.821
ELB improved by 13.1567
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.844
ELB improved by 5.97741
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.351
ELB improved by 4.49228
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.954
ELB improved by 4.39764
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.097
ELB improved by 4.85675
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.413
ELB improved by 5.684
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.789
ELB improved by 6.62427
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.76
ELB improved by 7.02831
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.561
ELB improved by 6.19946
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.127
ELB improved by 4.43349
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.372
ELB improved by 2.75505
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.716
ELB improved by 1.65628
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.677
ELB improved by 1.03894
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.975
ELB improved by 0.701924
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.463
ELB improved by 0.512496
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.063
ELB improved by 0.400148
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.733
ELB improved by 0.32971
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.449
ELB improved by 0.283482
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.198
ELB improved by 0.251447
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.972
ELB improved by 0.226254
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.77
ELB improved by 0.201886
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.594
ELB improved by 0.175701
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.444
ELB improved by 0.14981
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.316
ELB improved by 0.127858
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.205
ELB improved by 0.111265
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.106
ELB improved by 0.0992098
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.016
ELB improved by 0.0902476
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.932
ELB improved by 0.0832201
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.855
ELB improved by 0.0773901
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.783
ELB improved by 0.0723263
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.715
ELB improved by 0.0677804
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.651
ELB improved by 0.0636069
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.592
ELB improved by 0.0597191
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.536
ELB improved by 0.056064
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.483
ELB improved by 0.0526092
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.434
ELB improved by 0.0493351
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.387
ELB improved by 0.0462301
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.344
ELB improved by 0.0432876
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.304
ELB improved by 0.0405036
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.266
ELB improved by 0.0378753
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.23
ELB improved by 0.0354003
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.197
ELB improved by 0.0330758
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.166
ELB improved by 0.0308984
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.137
ELB improved by 0.0288638
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.111
ELB improved by 0.0269669
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.085
ELB improved by 0.025202
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.062
ELB improved by 0.0235628
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.04
ELB improved by 0.0220426
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.019
ELB improved by 0.0206345
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399
ELB improved by 0.0193313
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.982
ELB improved by 0.0181263
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.965
ELB improved by 0.0170125
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.949
ELB improved by 0.0159835
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.934
ELB improved by 0.015033
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.919
ELB improved by 0.0141551
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.906
ELB improved by 0.0133444
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.894
ELB improved by 0.0125958
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.882
ELB improved by 0.0119045
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.87
ELB improved by 0.0112663
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.86
ELB improved by 0.0106771
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.85
ELB improved by 0.0101334
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.84
ELB improved by 0.00963197
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-886.842
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-598.07
ELB improved by 288.772
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-533.741
ELB improved by 64.3283
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-486.2
ELB improved by 47.5416
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.904
ELB improved by 22.2956
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.37
ELB improved by 9.53379
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.623
ELB improved by 6.74749
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.572
ELB improved by 7.05104
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.349
ELB improved by 8.22251
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.601
ELB improved by 8.74857
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.977
ELB improved by 7.62365
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.442
ELB improved by 5.53516
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.566
ELB improved by 3.87626
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.775
ELB improved by 2.79087
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.843
ELB improved by 1.93196
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.431
ELB improved by 1.41186
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.31
ELB improved by 1.1213
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.43
ELB improved by 0.879988
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.749
ELB improved by 0.680967
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.198
ELB improved by 0.551161
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.729
ELB improved by 0.469031
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.317
ELB improved by 0.411344
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.951
ELB improved by 0.366011
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.623
ELB improved by 0.32785
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.329
ELB improved by 0.294919
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.062
ELB improved by 0.26644
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.82
ELB improved by 0.241841
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.6
ELB improved by 0.220583
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.397
ELB improved by 0.202286
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.211
ELB improved by 0.186837
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.036
ELB improved by 0.174512
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.87
ELB improved by 0.166286
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.705
ELB improved by 0.164895
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.526
ELB improved by 0.17855
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.291
ELB improved by 0.235183
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.861
ELB improved by 0.43029
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.932
ELB improved by 0.928826
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.452
ELB improved by 1.47976
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.995
ELB improved by 1.4571
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.576
ELB improved by 1.41866
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.951
ELB improved by 1.62509
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.39
ELB improved by 1.56183
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.031
ELB improved by 1.35839
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.842
ELB improved by 1.18921
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.766
ELB improved by 1.07555
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.718
ELB improved by 1.04825
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.513
ELB improved by 1.20557
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.963
ELB improved by 1.54965
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.565
ELB improved by 1.3978
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.634
ELB improved by 0.931597
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.999
ELB improved by 0.635022
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.574
ELB improved by 0.424075
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.295
ELB improved by 0.279283
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.108
ELB improved by 0.187073
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.978
ELB improved by 0.129864
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.884
ELB improved by 0.0938171
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.814
ELB improved by 0.0701882
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.76
ELB improved by 0.0539711
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.718
ELB improved by 0.0423837
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.684
ELB improved by 0.0338508
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.657
ELB improved by 0.0274353
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.634
ELB improved by 0.0225437
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.615
ELB improved by 0.018777
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.599
ELB improved by 0.0158537
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.586
ELB improved by 0.0135684
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.574
ELB improved by 0.011768
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.564
ELB improved by 0.0103379
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.555
ELB improved by 0.00919145
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.928 0.299 3.237
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.084 | 0.008 | 0.095 | |
| getPIPs | 0.086 | 0.000 | 0.086 | |
| graper | 0.127 | 0.008 | 0.135 | |
| makeExampleData | 0.014 | 0.000 | 0.014 | |
| makeExampleDataWithUnequalGroups | 0.017 | 0.000 | 0.017 | |
| plotELBO | 0.299 | 0.020 | 0.331 | |
| plotGroupPenalties | 1.140 | 0.012 | 1.155 | |
| plotPosterior | 0.723 | 0.012 | 0.736 | |
| predict.graper | 3.125 | 0.020 | 3.150 | |
| print.graper | 0.076 | 0.011 | 0.087 | |