Britta Velten
| Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: RELEASE_3_15 |
| git_last_commit: d7ee5fa |
| git_last_commit_date: 2022-04-26 11:52:37 -0400 (Tue, 26 Apr 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:20:21 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 | ||||
|
To the developers/maintainers of the graper package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 841/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.12.0 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: graper |
| Version: 1.12.0 |
| Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings graper_1.12.0.tar.gz |
| StartedAt: 2022-10-18 20:00:47 -0400 (Tue, 18 Oct 2022) |
| EndedAt: 2022-10-18 20:01:39 -0400 (Tue, 18 Oct 2022) |
| EllapsedTime: 51.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings graper_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/graper.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘graper/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘graper’ version ‘1.12.0’ * 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 * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking 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 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: 1 NOTE See ‘/home/biocbuild/bbs-3.15-bioc/meat/graper.Rcheck/00check.log’ for details.
graper.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL graper
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘graper’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.15-bioc/R/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/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/lexical_cast.hpp:30,
from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/tools/lexical_cast.hpp:12,
from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/tools/convert_from_string.hpp:14,
from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/constants/constants.hpp:14,
from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:20,
from graper_linear_dense_ff.h:2,
from fit_graper.cpp:4:
/home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.15-bioc/R/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/bbs-3.15-bioc/R/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.15-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-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=-839.093
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-556.928
ELB improved by 282.165
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-501.674
ELB improved by 55.2538
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.014
ELB improved by 31.6595
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.347
ELB improved by 12.6669
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.94
ELB improved by 5.40787
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.537
ELB improved by 3.40207
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.587
ELB improved by 2.95037
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.72
ELB improved by 2.86738
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.804
ELB improved by 2.91545
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.822
ELB improved by 2.98228
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.884
ELB improved by 2.93797
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.216
ELB improved by 2.66841
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.035
ELB improved by 2.18075
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.409
ELB improved by 1.62599
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.243
ELB improved by 1.16569
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.386
ELB improved by 0.856808
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.713
ELB improved by 0.673222
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.142
ELB improved by 0.57101
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.624
ELB improved by 0.518114
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.128
ELB improved by 0.495966
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.633
ELB improved by 0.494755
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.123
ELB improved by 0.509932
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.583
ELB improved by 0.540226
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.997
ELB improved by 0.586196
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.348
ELB improved by 0.648576
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.621
ELB improved by 0.727075
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.799
ELB improved by 0.822623
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.855
ELB improved by 0.943187
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.753
ELB improved by 1.10216
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.454
ELB improved by 1.29952
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.945
ELB improved by 1.50908
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.252
ELB improved by 1.69271
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.456
ELB improved by 1.79647
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.694
ELB improved by 1.76134
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.118
ELB improved by 1.57598
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.822
ELB improved by 1.29601
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.815
ELB improved by 1.00672
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.046
ELB improved by 0.769296
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.453
ELB improved by 0.593123
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.996
ELB improved by 0.457322
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.643
ELB improved by 0.352901
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.359
ELB improved by 0.283874
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.108
ELB improved by 0.251348
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.853
ELB improved by 0.255008
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.565
ELB improved by 0.287257
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.265
ELB improved by 0.300674
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.025
ELB improved by 0.239724
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.872
ELB improved by 0.152467
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.777
ELB improved by 0.095691
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.711
ELB improved by 0.0659472
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.661
ELB improved by 0.0495568
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.622
ELB improved by 0.0394895
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.589
ELB improved by 0.0327139
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.561
ELB improved by 0.027833
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.537
ELB improved by 0.0241337
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.516
ELB improved by 0.0212196
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.497
ELB improved by 0.0188552
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.48
ELB improved by 0.0168929
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.465
ELB improved by 0.0152355
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.451
ELB improved by 0.0138167
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.438
ELB improved by 0.0125895
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.427
ELB improved by 0.0115194
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.416
ELB improved by 0.0105802
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.407
ELB improved by 0.00975164
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-904.682
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-568.651
ELB improved by 336.031
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-507.993
ELB improved by 60.6571
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.531
ELB improved by 36.462
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.007
ELB improved by 14.5246
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.003
ELB improved by 6.004
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.091
ELB improved by 3.91213
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.937
ELB improved by 3.15341
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.058
ELB improved by 2.87887
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.225
ELB improved by 2.83308
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.338
ELB improved by 2.88745
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.36
ELB improved by 2.9776
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.296
ELB improved by 3.06411
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.186
ELB improved by 3.11055
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.118
ELB improved by 3.06809
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.232
ELB improved by 2.88592
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.673
ELB improved by 2.55836
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.539
ELB improved by 2.13465
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.856
ELB improved by 1.6824
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.583
ELB improved by 1.27286
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.64
ELB improved by 0.943256
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.944
ELB improved by 0.695682
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.424
ELB improved by 0.52025
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.024
ELB improved by 0.400579
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.705
ELB improved by 0.318817
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.444
ELB improved by 0.261081
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.225
ELB improved by 0.218486
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.04
ELB improved by 0.185772
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.88
ELB improved by 0.159838
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.741
ELB improved by 0.138783
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.619
ELB improved by 0.121381
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.513
ELB improved by 0.106798
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.418
ELB improved by 0.0944401
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.334
ELB improved by 0.0838706
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.26
ELB improved by 0.0747603
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.193
ELB improved by 0.0668564
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.133
ELB improved by 0.0599621
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.079
ELB improved by 0.0539217
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.03
ELB improved by 0.0486109
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.986
ELB improved by 0.0439282
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.947
ELB improved by 0.0397896
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.91
ELB improved by 0.0361243
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.878
ELB improved by 0.0328721
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.848
ELB improved by 0.0299812
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.82
ELB improved by 0.0274065
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.795
ELB improved by 0.0251092
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.772
ELB improved by 0.0230551
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.751
ELB improved by 0.021215
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.731
ELB improved by 0.0195631
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.713
ELB improved by 0.0180773
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.696
ELB improved by 0.0167383
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.681
ELB improved by 0.0155291
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.666
ELB improved by 0.0144353
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.653
ELB improved by 0.0134441
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.64
ELB improved by 0.0125442
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.629
ELB improved by 0.011726
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.618
ELB improved by 0.0109808
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.607
ELB improved by 0.0103011
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.598
ELB improved by 0.00968032
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-874.414
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-564.309
ELB improved by 310.105
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-504.243
ELB improved by 60.0665
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.41
ELB improved by 36.833
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.424
ELB improved by 15.9861
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.819
ELB improved by 7.60469
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.829
ELB improved by 5.99033
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.666
ELB improved by 6.1621
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.693
ELB improved by 6.97378
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.881
ELB improved by 7.81171
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.964
ELB improved by 7.9168
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.017
ELB improved by 6.94685
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.569
ELB improved by 5.44839
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.528
ELB improved by 4.04091
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.644
ELB improved by 2.88376
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.577
ELB improved by 2.06683
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.045
ELB improved by 1.53248
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.871
ELB improved by 1.17376
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.893
ELB improved by 0.977874
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.005
ELB improved by 0.888114
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.211
ELB improved by 0.793923
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.515
ELB improved by 0.69591
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.908
ELB improved by 0.607668
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.414
ELB improved by 0.493387
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.035
ELB improved by 0.37896
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.74
ELB improved by 0.295251
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.501
ELB improved by 0.239577
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.299
ELB improved by 0.201063
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.127
ELB improved by 0.17242
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.977
ELB improved by 0.149805
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.846
ELB improved by 0.131217
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.73
ELB improved by 0.115535
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.628
ELB improved by 0.102078
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.538
ELB improved by 0.0904087
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.458
ELB improved by 0.0802336
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.386
ELB improved by 0.0713419
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.323
ELB improved by 0.0635706
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.266
ELB improved by 0.0567826
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.215
ELB improved by 0.0508553
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.17
ELB improved by 0.045677
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.128
ELB improved by 0.0411463
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.091
ELB improved by 0.0371729
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.058
ELB improved by 0.0336781
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.027
ELB improved by 0.0305942
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.999
ELB improved by 0.0278638
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.974
ELB improved by 0.0254385
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.95
ELB improved by 0.0232775
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.929
ELB improved by 0.0213466
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.909
ELB improved by 0.0196166
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.891
ELB improved by 0.0180629
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.875
ELB improved by 0.0166643
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.859
ELB improved by 0.0154027
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.845
ELB improved by 0.0142625
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.832
ELB improved by 0.01323
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.819
ELB improved by 0.0122935
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.808
ELB improved by 0.0114427
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.797
ELB improved by 0.0106684
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.787
ELB improved by 0.00996263
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-864.547
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-593.352
ELB improved by 271.195
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-537.453
ELB improved by 55.8987
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-494.332
ELB improved by 43.1219
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.25
ELB improved by 24.0814
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.733
ELB improved by 9.51689
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.911
ELB improved by 4.82226
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.09
ELB improved by 3.82083
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.521
ELB improved by 3.56964
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.039
ELB improved by 3.4814
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.718
ELB improved by 3.321
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.757
ELB improved by 2.96079
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.351
ELB improved by 2.40588
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.557
ELB improved by 1.79445
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.279
ELB improved by 1.27791
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.362
ELB improved by 0.916939
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.671
ELB improved by 0.691452
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.116
ELB improved by 0.554916
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.649
ELB improved by 0.467166
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.245
ELB improved by 0.403561
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.892
ELB improved by 0.353159
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.579
ELB improved by 0.312442
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.3
ELB improved by 0.279156
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.051
ELB improved by 0.249801
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.83
ELB improved by 0.220905
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.638
ELB improved by 0.191304
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.476
ELB improved by 0.162581
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.338
ELB improved by 0.137235
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.222
ELB improved by 0.116675
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.121
ELB improved by 0.100771
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.032
ELB improved by 0.0885603
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.953
ELB improved by 0.0789906
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.882
ELB improved by 0.0712461
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.817
ELB improved by 0.0647814
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.758
ELB improved by 0.0592517
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.704
ELB improved by 0.0544392
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.654
ELB improved by 0.0502004
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.607
ELB improved by 0.0464357
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.564
ELB improved by 0.0430716
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.524
ELB improved by 0.0400508
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.487
ELB improved by 0.0373273
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.452
ELB improved by 0.0348628
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.419
ELB improved by 0.0326252
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.389
ELB improved by 0.0305871
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.36
ELB improved by 0.0287247
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.333
ELB improved by 0.027018
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.307
ELB improved by 0.0254493
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.283
ELB improved by 0.0240034
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.261
ELB improved by 0.0226673
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.239
ELB improved by 0.0214294
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.219
ELB improved by 0.0202799
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.2
ELB improved by 0.0192102
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.182
ELB improved by 0.0182127
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.164
ELB improved by 0.0172808
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.148
ELB improved by 0.0164088
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.132
ELB improved by 0.0155915
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.117
ELB improved by 0.0148246
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.103
ELB improved by 0.014104
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.09
ELB improved by 0.0134261
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.077
ELB improved by 0.0127879
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.065
ELB improved by 0.0121865
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.053
ELB improved by 0.0116193
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.042
ELB improved by 0.011084
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.032
ELB improved by 0.0105786
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.022
ELB improved by 0.010101
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.012
ELB improved by 0.00964955
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.385 0.168 2.535
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.042 | 0.019 | 0.064 | |
| getPIPs | 0.046 | 0.011 | 0.057 | |
| graper | 0.071 | 0.024 | 0.095 | |
| makeExampleData | 0.005 | 0.004 | 0.010 | |
| makeExampleDataWithUnequalGroups | 0.011 | 0.000 | 0.011 | |
| plotELBO | 0.186 | 0.028 | 0.215 | |
| plotGroupPenalties | 0.718 | 0.044 | 0.763 | |
| plotPosterior | 0.478 | 0.036 | 0.515 | |
| predict.graper | 1.945 | 0.088 | 2.033 | |
| print.graper | 0.049 | 0.020 | 0.070 | |