Britta Velten
| Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024) |
| 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 -0500 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-04 11:37:25 -0500 (Mon, 04 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4692 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4445 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4466 |
| 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 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 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: 1.18.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.18.0.tar.gz |
| StartedAt: 2024-03-03 21:00:34 -0500 (Sun, 03 Mar 2024) |
| EndedAt: 2024-03-03 21:01:52 -0500 (Sun, 03 Mar 2024) |
| EllapsedTime: 78.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: graper.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/graper.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* 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 ... WARNING
Found the following significant warnings:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
# warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
See ‘/Users/biocbuild/bbs-3.18-bioc/meat/graper.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.18-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL graper
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘graper’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fit_graper.cpp -o fit_graper.o
In file included from fit_graper.cpp:4:
In file included from ./graper_linear_dense_ff.h:2:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/digamma.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/math_fwd.hpp:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
# warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o graper.so RcppExports.o fit_graper.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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=-871.452
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-586.473
ELB improved by 284.979
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-525.564
ELB improved by 60.909
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-480.118
ELB improved by 45.4459
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.557
ELB improved by 23.5619
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.574
ELB improved by 10.9821
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.391
ELB improved by 7.18351
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.709
ELB improved by 6.68189
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.513
ELB improved by 7.19575
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.898
ELB improved by 7.61578
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.857
ELB improved by 7.0403
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.514
ELB improved by 5.34307
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.134
ELB improved by 3.37986
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.121
ELB improved by 2.01292
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.766
ELB improved by 1.35513
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.702
ELB improved by 1.06381
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.883
ELB improved by 0.819538
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.303
ELB improved by 0.58004
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.894
ELB improved by 0.408693
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.589
ELB improved by 0.305099
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.348
ELB improved by 0.241403
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.149
ELB improved by 0.198206
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.983
ELB improved by 0.166448
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.841
ELB improved by 0.141949
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.719
ELB improved by 0.122479
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.612
ELB improved by 0.10668
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.518
ELB improved by 0.0936473
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.436
ELB improved by 0.0827533
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.362
ELB improved by 0.0735448
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.296
ELB improved by 0.0656869
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.237
ELB improved by 0.058927
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.184
ELB improved by 0.0530707
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.136
ELB improved by 0.047966
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.093
ELB improved by 0.0434922
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.053
ELB improved by 0.0395523
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.017
ELB improved by 0.0360676
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.984
ELB improved by 0.0329733
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.954
ELB improved by 0.0302159
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.926
ELB improved by 0.0277505
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.901
ELB improved by 0.0255397
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.877
ELB improved by 0.0235514
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.855
ELB improved by 0.0217587
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.835
ELB improved by 0.0201384
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.817
ELB improved by 0.0186705
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.799
ELB improved by 0.017338
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.783
ELB improved by 0.0161258
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.768
ELB improved by 0.0150211
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.754
ELB improved by 0.0140125
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.741
ELB improved by 0.0130901
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.729
ELB improved by 0.0122452
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.717
ELB improved by 0.0114701
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.707
ELB improved by 0.010758
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.696
ELB improved by 0.0101029
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.687
ELB improved by 0.00949952
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-894.505
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-592.936
ELB improved by 301.57
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-537.07
ELB improved by 55.8662
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-495.249
ELB improved by 41.8208
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.789
ELB improved by 25.4596
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.539
ELB improved by 13.2497
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.151
ELB improved by 7.38848
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.489
ELB improved by 5.66185
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.106
ELB improved by 5.38317
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.399
ELB improved by 5.70709
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.19
ELB improved by 6.20906
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.823
ELB improved by 6.36646
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.113
ELB improved by 5.71023
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.714
ELB improved by 4.39862
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.614
ELB improved by 3.10009
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.55
ELB improved by 2.06434
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.277
ELB improved by 1.27349
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.485
ELB improved by 0.791293
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.953
ELB improved by 0.532111
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.564
ELB improved by 0.389614
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.259
ELB improved by 0.304935
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.009
ELB improved by 0.250056
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.797
ELB improved by 0.211787
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.613
ELB improved by 0.183599
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.451
ELB improved by 0.16199
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.306
ELB improved by 0.144916
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.175
ELB improved by 0.131089
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.056
ELB improved by 0.119652
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.946
ELB improved by 0.110013
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.844
ELB improved by 0.101743
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.749
ELB improved by 0.0945306
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.661
ELB improved by 0.0881454
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.579
ELB improved by 0.0824143
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.501
ELB improved by 0.0772079
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.429
ELB improved by 0.07243
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.361
ELB improved by 0.0680093
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.297
ELB improved by 0.0638934
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.237
ELB improved by 0.0600447
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.181
ELB improved by 0.0564361
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.128
ELB improved by 0.0530483
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.078
ELB improved by 0.049867
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.031
ELB improved by 0.0468814
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.987
ELB improved by 0.0440821
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.945
ELB improved by 0.0414599
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.906
ELB improved by 0.0390053
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.87
ELB improved by 0.0367072
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.835
ELB improved by 0.0345531
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.803
ELB improved by 0.0325294
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.772
ELB improved by 0.0306216
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.743
ELB improved by 0.0288152
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.716
ELB improved by 0.0270977
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.691
ELB improved by 0.0254587
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.667
ELB improved by 0.0238914
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.644
ELB improved by 0.0223929
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.623
ELB improved by 0.0209632
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.604
ELB improved by 0.0196046
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.585
ELB improved by 0.0183204
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.568
ELB improved by 0.0171131
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.552
ELB improved by 0.0159843
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.537
ELB improved by 0.0149339
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.523
ELB improved by 0.0139598
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.51
ELB improved by 0.0130592
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.498
ELB improved by 0.0122278
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.487
ELB improved by 0.011461
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.476
ELB improved by 0.0107542
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.466
ELB improved by 0.0101025
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.456
ELB improved by 0.00950144
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-843.053
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-559.598
ELB improved by 283.455
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-500.661
ELB improved by 58.9368
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.688
ELB improved by 33.9724
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.425
ELB improved by 14.2636
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.223
ELB improved by 7.2019
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.033
ELB improved by 5.18997
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.766
ELB improved by 4.26724
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.831
ELB improved by 3.93419
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.021
ELB improved by 3.80997
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.455
ELB improved by 3.56607
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.396
ELB improved by 3.05956
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.016
ELB improved by 2.38018
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.285
ELB improved by 1.73031
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.048
ELB improved by 1.23755
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.135
ELB improved by 0.91311
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.422
ELB improved by 0.713007
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.833
ELB improved by 0.588351
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.328
ELB improved by 0.505312
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.88
ELB improved by 0.447744
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.471
ELB improved by 0.409591
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.084
ELB improved by 0.386734
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.709
ELB improved by 0.374771
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.339
ELB improved by 0.369904
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.97
ELB improved by 0.369484
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.598
ELB improved by 0.371884
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.222
ELB improved by 0.376224
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.84
ELB improved by 0.38215
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.45
ELB improved by 0.389676
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.051
ELB improved by 0.399021
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.64
ELB improved by 0.410435
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.216
ELB improved by 0.424032
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.777
ELB improved by 0.439716
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.319
ELB improved by 0.45724
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.843
ELB improved by 0.476389
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.346
ELB improved by 0.497195
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.826
ELB improved by 0.520149
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.279
ELB improved by 0.546538
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.7
ELB improved by 0.579355
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.074
ELB improved by 0.62563
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.372
ELB improved by 0.702507
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.518
ELB improved by 0.853408
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.35
ELB improved by 1.16842
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.743
ELB improved by 1.60676
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.017
ELB improved by 1.72639
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.505
ELB improved by 1.51173
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.298
ELB improved by 1.20702
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.391
ELB improved by 0.907342
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.73
ELB improved by 0.660138
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.249
ELB improved by 0.481505
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.886
ELB improved by 0.362708
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.601
ELB improved by 0.285545
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.368
ELB improved by 0.232727
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.178
ELB improved by 0.190433
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.027
ELB improved by 0.150699
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.913
ELB improved by 0.113948
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.828
ELB improved by 0.0845086
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.765
ELB improved by 0.0638588
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.714
ELB improved by 0.0501175
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.674
ELB improved by 0.0407422
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.64
ELB improved by 0.0338975
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.611
ELB improved by 0.0285051
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.587
ELB improved by 0.023992
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.567
ELB improved by 0.0200934
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.55
ELB improved by 0.0167182
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.537
ELB improved by 0.0138497
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.525
ELB improved by 0.0114785
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.516
ELB improved by 0.00957181
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-834.577
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-566.18
ELB improved by 268.397
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-504.094
ELB improved by 62.0863
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.158
ELB improved by 40.9359
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.833
ELB improved by 17.3254
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.123
ELB improved by 6.71017
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.592
ELB improved by 3.53011
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.113
ELB improved by 2.4791
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.041
ELB improved by 2.07202
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.163
ELB improved by 1.87804
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.413
ELB improved by 1.75044
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.768
ELB improved by 1.64491
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.218
ELB improved by 1.54971
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.758
ELB improved by 1.4603
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.386
ELB improved by 1.37191
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.107
ELB improved by 1.27857
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.932
ELB improved by 1.17519
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.872
ELB improved by 1.06057
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.933
ELB improved by 0.938952
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.114
ELB improved by 0.81893
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.403
ELB improved by 0.710476
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.781
ELB improved by 0.622102
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.222
ELB improved by 0.559153
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.699
ELB improved by 0.523479
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.184
ELB improved by 0.514111
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.656
ELB improved by 0.528247
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.094
ELB improved by 0.562068
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.483
ELB improved by 0.611288
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.811
ELB improved by 0.67159
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.072
ELB improved by 0.739084
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.261
ELB improved by 0.811111
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.373
ELB improved by 0.887761
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.399
ELB improved by 0.974106
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.316
ELB improved by 1.08328
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.073
ELB improved by 1.24329
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.553
ELB improved by 1.5193
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.504
ELB improved by 2.04898
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.74
ELB improved by 2.76384
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.705
ELB improved by 3.03581
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.857
ELB improved by 2.84751
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.412
ELB improved by 2.44538
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.338
ELB improved by 2.07388
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.335
ELB improved by 2.00244
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.392
ELB improved by 1.94371
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.927
ELB improved by 1.46452
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.977
ELB improved by 0.950212
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.405
ELB improved by 0.571785
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.063
ELB improved by 0.342014
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.846
ELB improved by 0.216888
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.697
ELB improved by 0.149125
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.587
ELB improved by 0.110347
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.501
ELB improved by 0.0862858
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.431
ELB improved by 0.0700745
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.372
ELB improved by 0.0583627
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.323
ELB improved by 0.0494401
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.28
ELB improved by 0.0423794
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.244
ELB improved by 0.0366428
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.212
ELB improved by 0.0318966
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.184
ELB improved by 0.0279196
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.159
ELB improved by 0.0245571
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.138
ELB improved by 0.021695
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.118
ELB improved by 0.0192466
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.101
ELB improved by 0.0171436
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.086
ELB improved by 0.0153311
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.072
ELB improved by 0.0137645
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.06
ELB improved by 0.0124069
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.049
ELB improved by 0.0112276
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.038
ELB improved by 0.0102009
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.029
ELB improved by 0.00930496
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.634 0.307 2.966
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.060 | 0.023 | 0.086 | |
| getPIPs | 0.049 | 0.015 | 0.064 | |
| graper | 0.073 | 0.017 | 0.092 | |
| makeExampleData | 0.008 | 0.001 | 0.009 | |
| makeExampleDataWithUnequalGroups | 0.010 | 0.001 | 0.011 | |
| plotELBO | 0.247 | 0.027 | 0.276 | |
| plotGroupPenalties | 0.969 | 0.048 | 1.025 | |
| plotPosterior | 0.527 | 0.025 | 0.555 | |
| predict.graper | 2.031 | 0.094 | 2.145 | |
| print.graper | 0.047 | 0.012 | 0.059 | |