Britta Velten
| Snapshot Date: 2024-05-17 14:00:11 -0400 (Fri, 17 May 2024) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: RELEASE_3_19 |
| git_last_commit: a4dfa52 |
| git_last_commit_date: 2024-04-30 11:11:42 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-18 11:36:54 -0400 (Sat, 18 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4751 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4515 |
| 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 908/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.20.0 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: graper |
| Version: 1.20.0 |
| Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:graper.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings graper_1.20.0.tar.gz |
| StartedAt: 2024-05-18 02:38:50 -0400 (Sat, 18 May 2024) |
| EndedAt: 2024-05-18 02:40:26 -0400 (Sat, 18 May 2024) |
| EllapsedTime: 96.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:graper.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings graper_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/graper.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'graper/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'graper' version '1.20.0'
* 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 whether package 'graper' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) predict.graper.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:23-24: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.19-bioc/R/library/graper/libs/x64/graper.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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: 3 NOTEs
See
'F:/biocbuild/bbs-3.19-bioc/meat/graper.Rcheck/00check.log'
for details.
graper.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL graper
###
##############################################################################
##############################################################################
* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'graper' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
using C++11
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BH/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BH/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fit_graper.cpp -o fit_graper.o
In file included from F:/biocbuild/bbs-3.19-bioc/R/library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11,
from F:/biocbuild/bbs-3.19-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
from F:/biocbuild/bbs-3.19-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:15,
from graper_linear_dense_ff.h:2,
from fit_graper.cpp:4:
F:/biocbuild/bbs-3.19-bioc/R/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++ -shared -s -static-libgcc -o graper.dll tmp.def RcppExports.o fit_graper.o -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-graper/00new/graper/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (graper)
graper.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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=-864.623
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-573.453
ELB improved by 291.171
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-514.994
ELB improved by 58.4583
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-480.57
ELB improved by 34.4245
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.888
ELB improved by 14.6814
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.477
ELB improved by 6.41096
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.125
ELB improved by 4.35282
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.176
ELB improved by 3.94834
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.062
ELB improved by 4.11393
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.565
ELB improved by 4.49764
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.759
ELB improved by 4.80619
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.085
ELB improved by 4.6731
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.266
ELB improved by 3.81924
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.705
ELB improved by 2.561
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.149
ELB improved by 1.55638
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.135
ELB improved by 1.01374
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.35
ELB improved by 0.784655
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.662
ELB improved by 0.688082
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.054
ELB improved by 0.60845
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.522
ELB improved by 0.532256
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.024
ELB improved by 0.497534
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.51
ELB improved by 0.514583
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.958
ELB improved by 0.551803
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.375
ELB improved by 0.582457
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.757
ELB improved by 0.617793
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.093
ELB improved by 0.664177
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.392
ELB improved by 0.701111
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.68
ELB improved by 0.712492
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.97
ELB improved by 0.709768
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.261
ELB improved by 0.709173
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.548
ELB improved by 0.713099
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.83
ELB improved by 0.717689
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.11
ELB improved by 0.72042
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.388
ELB improved by 0.721135
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.67
ELB improved by 0.718687
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.97
ELB improved by 0.70017
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.332
ELB improved by 0.63723
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.805
ELB improved by 0.527203
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.394
ELB improved by 0.410609
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.078
ELB improved by 0.316441
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.831
ELB improved by 0.247062
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.634
ELB improved by 0.196538
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.475
ELB improved by 0.159348
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.344
ELB improved by 0.131605
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.233
ELB improved by 0.110728
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.138
ELB improved by 0.0950256
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.054
ELB improved by 0.0833943
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.979
ELB improved by 0.0751301
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.909
ELB improved by 0.0698457
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.842
ELB improved by 0.0674874
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.773
ELB improved by 0.0684916
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.699
ELB improved by 0.0742295
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.611
ELB improved by 0.0881535
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.492
ELB improved by 0.11859
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.309
ELB improved by 0.183673
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.001
ELB improved by 0.307465
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.527
ELB improved by 0.47454
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.903
ELB improved by 0.624098
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.192
ELB improved by 0.710418
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.657
ELB improved by 0.535717
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.41
ELB improved by 0.24681
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.285
ELB improved by 0.124539
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.205
ELB improved by 0.0801317
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.148
ELB improved by 0.0568256
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.106
ELB improved by 0.0426604
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.071
ELB improved by 0.034119
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.042
ELB improved by 0.0295506
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.014
ELB improved by 0.028148
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.984
ELB improved by 0.0297969
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.949
ELB improved by 0.0351404
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.903
ELB improved by 0.0457142
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.839
ELB improved by 0.0637732
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.749
ELB improved by 0.0905043
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.628
ELB improved by 0.12078
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.489
ELB improved by 0.138766
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.359
ELB improved by 0.129875
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.259
ELB improved by 0.10066
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.189
ELB improved by 0.0694916
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.143
ELB improved by 0.046161
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.112
ELB improved by 0.0311964
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.09
ELB improved by 0.0222114
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.073
ELB improved by 0.01691
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.059
ELB improved by 0.0137203
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.047
ELB improved by 0.011702
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.037
ELB improved by 0.0103311
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.028
ELB improved by 0.00932625
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-874.142
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-582.686
ELB improved by 291.455
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-524.656
ELB improved by 58.0307
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-486.718
ELB improved by 37.9381
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.394
ELB improved by 18.3232
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.341
ELB improved by 8.05369
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.886
ELB improved by 4.45465
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.553
ELB improved by 3.33342
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.595
ELB improved by 2.95787
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.76
ELB improved by 2.83499
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.997
ELB improved by 2.76312
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.35
ELB improved by 2.64662
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.91
ELB improved by 2.44046
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.764
ELB improved by 2.14507
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.977
ELB improved by 1.78715
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.577
ELB improved by 1.40054
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.534
ELB improved by 1.04312
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.769
ELB improved by 0.7645
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.199
ELB improved by 0.569749
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.76
ELB improved by 0.439407
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.408
ELB improved by 0.352204
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.115
ELB improved by 0.292424
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.865
ELB improved by 0.25001
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.646
ELB improved by 0.218903
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.451
ELB improved by 0.195503
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.273
ELB improved by 0.177645
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.109
ELB improved by 0.163984
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.956
ELB improved by 0.153654
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.81
ELB improved by 0.146081
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.669
ELB improved by 0.140876
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.531
ELB improved by 0.137773
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.394
ELB improved by 0.136593
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.257
ELB improved by 0.137225
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.117
ELB improved by 0.139605
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.974
ELB improved by 0.143712
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.824
ELB improved by 0.149565
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.667
ELB improved by 0.157213
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.5
ELB improved by 0.166747
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.322
ELB improved by 0.178298
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.13
ELB improved by 0.192043
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.922
ELB improved by 0.208212
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.695
ELB improved by 0.227087
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.446
ELB improved by 0.248998
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.171
ELB improved by 0.274308
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.868
ELB improved by 0.303389
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.531
ELB improved by 0.33658
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.157
ELB improved by 0.374133
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.741
ELB improved by 0.416158
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.278
ELB improved by 0.462581
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.765
ELB improved by 0.513112
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.198
ELB improved by 0.567161
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.575
ELB improved by 0.623638
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.894
ELB improved by 0.680674
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.159
ELB improved by 0.735389
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.375
ELB improved by 0.783541
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.556
ELB improved by 0.818621
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.725
ELB improved by 0.830892
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.915
ELB improved by 0.810007
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.161
ELB improved by 0.754351
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.482
ELB improved by 0.679064
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.871
ELB improved by 0.611342
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.292
ELB improved by 0.578232
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.701
ELB improved by 0.591733
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.08
ELB improved by 0.620266
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.493
ELB improved by 0.587695
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.021
ELB improved by 0.47149
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.689
ELB improved by 0.33221
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.47
ELB improved by 0.21901
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.329
ELB improved by 0.141377
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.237
ELB improved by 0.0917713
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.176
ELB improved by 0.0607579
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.135
ELB improved by 0.0413329
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.106
ELB improved by 0.0290101
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.085
ELB improved by 0.021054
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.069
ELB improved by 0.0158147
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.057
ELB improved by 0.0122924
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.047
ELB improved by 0.00987351
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-854.978
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-582.817
ELB improved by 272.161
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-526.16
ELB improved by 56.6569
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-479.39
ELB improved by 46.7696
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.772
ELB improved by 26.6182
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.217
ELB improved by 10.5552
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.726
ELB improved by 4.49103
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.329
ELB improved by 2.39716
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.836
ELB improved by 1.49281
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.75
ELB improved by 1.08626
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.844
ELB improved by 0.905692
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.011
ELB improved by 0.833015
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.193
ELB improved by 0.817894
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.353
ELB improved by 0.839701
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.462
ELB improved by 0.891279
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.49
ELB improved by 0.971797
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.407
ELB improved by 1.08305
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.181
ELB improved by 1.2265
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.781
ELB improved by 1.40002
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.186
ELB improved by 1.59447
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.394
ELB improved by 1.79247
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.424
ELB improved by 1.96962
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.331
ELB improved by 2.09318
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.208
ELB improved by 2.12335
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.176
ELB improved by 2.03201
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.348
ELB improved by 1.82764
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.764
ELB improved by 1.58348
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.369
ELB improved by 1.39561
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.122
ELB improved by 1.24667
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.062
ELB improved by 1.06007
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.181
ELB improved by 0.880648
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.461
ELB improved by 0.720269
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.896
ELB improved by 0.565586
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.469
ELB improved by 0.426782
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.153
ELB improved by 0.316102
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.914
ELB improved by 0.23852
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.726
ELB improved by 0.187931
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.571
ELB improved by 0.155196
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.438
ELB improved by 0.13338
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.32
ELB improved by 0.118053
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.213
ELB improved by 0.106428
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.116
ELB improved by 0.096803
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.028
ELB improved by 0.0883826
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.947
ELB improved by 0.0811633
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.871
ELB improved by 0.0756945
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.798
ELB improved by 0.0727917
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.725
ELB improved by 0.0733878
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.646
ELB improved by 0.0785368
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.557
ELB improved by 0.089277
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.451
ELB improved by 0.105788
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.326
ELB improved by 0.125734
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.182
ELB improved by 0.143961
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.026
ELB improved by 0.15569
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.868
ELB improved by 0.15755
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.724
ELB improved by 0.144945
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.607
ELB improved by 0.116839
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.525
ELB improved by 0.0816356
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.474
ELB improved by 0.0512305
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.442
ELB improved by 0.0313149
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.422
ELB improved by 0.0202424
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.408
ELB improved by 0.0142953
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.397
ELB improved by 0.0109064
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.388
ELB improved by 0.00880051
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-871.577
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-583.044
ELB improved by 288.533
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-520.54
ELB improved by 62.504
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-479.494
ELB improved by 41.0459
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.208
ELB improved by 18.2858
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.591
ELB improved by 7.61734
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.4
ELB improved by 4.1911
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.434
ELB improved by 2.96528
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.914
ELB improved by 2.52018
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.57
ELB improved by 2.34373
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.32
ELB improved by 2.25063
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.163
ELB improved by 2.15681
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.158
ELB improved by 2.00439
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.393
ELB improved by 1.76597
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.926
ELB improved by 1.46676
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.756
ELB improved by 1.16964
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.828
ELB improved by 0.927964
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.069
ELB improved by 0.758789
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.418
ELB improved by 0.651484
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.831
ELB improved by 0.586907
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.282
ELB improved by 0.548581
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.757
ELB improved by 0.52526
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.247
ELB improved by 0.509959
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.749
ELB improved by 0.498558
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.26
ELB improved by 0.488908
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.779
ELB improved by 0.480384
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.306
ELB improved by 0.47366
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.835
ELB improved by 0.470504
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.362
ELB improved by 0.473437
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.877
ELB improved by 0.484945
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.371
ELB improved by 0.505773
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.838
ELB improved by 0.532753
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.279
ELB improved by 0.559709
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.695
ELB improved by 0.583296
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.09
ELB improved by 0.605214
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.464
ELB improved by 0.626389
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.82
ELB improved by 0.643842
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.166
ELB improved by 0.654043
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.507
ELB improved by 0.658746
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.834
ELB improved by 0.672918
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.096
ELB improved by 0.737855
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.171
ELB improved by 0.925314
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.962
ELB improved by 1.20855
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.681
ELB improved by 1.28156
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.535
ELB improved by 1.14606
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.421
ELB improved by 1.11328
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.348
ELB improved by 1.07374
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.443
ELB improved by 0.904257
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.683
ELB improved by 0.760637
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.936
ELB improved by 0.746448
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.068
ELB improved by 0.868311
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.116
ELB improved by 0.95185
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.379
ELB improved by 0.737614
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.958
ELB improved by 0.420874
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.733
ELB improved by 0.224543
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.605
ELB improved by 0.128038
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.524
ELB improved by 0.0816641
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.465
ELB improved by 0.0582295
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.42
ELB improved by 0.0451039
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.383
ELB improved by 0.0368014
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.352
ELB improved by 0.0309686
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.326
ELB improved by 0.0265557
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.303
ELB improved by 0.0230562
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.283
ELB improved by 0.0201996
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.265
ELB improved by 0.0178254
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.249
ELB improved by 0.0158292
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.235
ELB improved by 0.0141375
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.222
ELB improved by 0.0126959
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.211
ELB improved by 0.0114621
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.2
ELB improved by 0.0104022
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.191
ELB improved by 0.00948896
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.84 0.29 4.04
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.06 | 0.05 | 0.16 | |
| getPIPs | 0.08 | 0.00 | 0.08 | |
| graper | 0.10 | 0.03 | 0.13 | |
| makeExampleData | 0.01 | 0.00 | 0.01 | |
| makeExampleDataWithUnequalGroups | 0.02 | 0.00 | 0.02 | |
| plotELBO | 0.31 | 0.03 | 0.58 | |
| plotGroupPenalties | 1.22 | 0.03 | 1.25 | |
| plotPosterior | 0.63 | 0.03 | 0.66 | |
| predict.graper | 2.26 | 0.03 | 2.31 | |
| print.graper | 0.05 | 0.02 | 0.06 | |