Britta Velten
| Snapshot Date: 2024-07-05 14:00 -0400 (Fri, 05 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: 7b45fcc |
| git_last_commit_date: 2024-04-30 11:11:42 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-06 11:43 -0400 (Sat, 06 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4643 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4414 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4442 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4391 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 3833 |
| 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 883/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.21.0 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino6 | 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 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: graper |
| Version: 1.21.0 |
| 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_1.21.0.tar.gz |
| StartedAt: 2024-07-06 01:06:06 -0400 (Sat, 06 Jul 2024) |
| EndedAt: 2024-07-06 01:06:44 -0400 (Sat, 06 Jul 2024) |
| EllapsedTime: 38.4 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_1.21.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/graper.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.21.0’
* 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/4.4-arm64/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-3.20-bioc/meat/graper.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* 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 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.20-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/4.4-arm64/Resources/library’
* installing *source* package ‘graper’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/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/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/digamma.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/math_fwd.hpp:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11:
/Library/Frameworks/R.framework/Versions/4.4-arm64/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 arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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=-883.312
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-571.229
ELB improved by 312.083
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-511.776
ELB improved by 59.4522
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.533
ELB improved by 38.2432
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.088
ELB improved by 16.4452
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.768
ELB improved by 6.32003
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.306
ELB improved by 3.46232
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.728
ELB improved by 2.57778
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.486
ELB improved by 2.24211
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.374
ELB improved by 2.11136
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.313
ELB improved by 2.06169
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.274
ELB improved by 2.03858
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.269
ELB improved by 2.00524
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.347
ELB improved by 1.92229
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.592
ELB improved by 1.75478
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.092
ELB improved by 1.49985
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.89
ELB improved by 1.20151
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.967
ELB improved by 0.923273
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.263
ELB improved by 0.704682
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.714
ELB improved by 0.548962
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.272
ELB improved by 0.441435
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.904
ELB improved by 0.367711
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.586
ELB improved by 0.318233
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.3
ELB improved by 0.286312
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.033
ELB improved by 0.266713
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.778
ELB improved by 0.255402
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.528
ELB improved by 0.24944
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.282
ELB improved by 0.246766
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.036
ELB improved by 0.245961
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.79
ELB improved by 0.246062
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.543
ELB improved by 0.24644
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.296
ELB improved by 0.246682
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.05
ELB improved by 0.246458
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.805
ELB improved by 0.24534
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.562
ELB improved by 0.24265
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.324
ELB improved by 0.237556
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.095
ELB improved by 0.229573
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.876
ELB improved by 0.219193
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.668
ELB improved by 0.207972
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.47
ELB improved by 0.19795
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.279
ELB improved by 0.191158
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.089
ELB improved by 0.18983
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.891
ELB improved by 0.19729
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.672
ELB improved by 0.219168
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.409
ELB improved by 0.26311
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.079
ELB improved by 0.329971
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.684
ELB improved by 0.39488
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.259
ELB improved by 0.425234
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.826
ELB improved by 0.433203
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.379
ELB improved by 0.447308
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.907
ELB improved by 0.471615
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.403
ELB improved by 0.503971
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.848
ELB improved by 0.555374
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.26
ELB improved by 0.587828
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.735
ELB improved by 0.52506
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.322
ELB improved by 0.412733
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.006
ELB improved by 0.316255
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.76
ELB improved by 0.245936
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.563
ELB improved by 0.196636
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.399
ELB improved by 0.163733
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.254
ELB improved by 0.145167
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.112
ELB improved by 0.14224
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.951
ELB improved by 0.161003
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.74
ELB improved by 0.211399
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.451
ELB improved by 0.288507
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.116
ELB improved by 0.334953
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.817
ELB improved by 0.299287
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.591
ELB improved by 0.226299
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.424
ELB improved by 0.166943
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.291
ELB improved by 0.132699
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.168
ELB improved by 0.123024
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.033
ELB improved by 0.135378
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.875
ELB improved by 0.157232
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.712
ELB improved by 0.162985
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.568
ELB improved by 0.144741
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.445
ELB improved by 0.122205
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.337
ELB improved by 0.107979
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.236
ELB improved by 0.101447
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.134
ELB improved by 0.101892
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.02
ELB improved by 0.114371
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.869
ELB improved by 0.150519
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.644
ELB improved by 0.224667
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.323
ELB improved by 0.321063
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.979
ELB improved by 0.344155
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.731
ELB improved by 0.248271
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.594
ELB improved by 0.137024
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.524
ELB improved by 0.070347
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.486
ELB improved by 0.0380234
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.463
ELB improved by 0.0228965
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.447
ELB improved by 0.0155678
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.435
ELB improved by 0.0117745
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.426
ELB improved by 0.00964371
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-860.398
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-568.028
ELB improved by 292.369
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-507.035
ELB improved by 60.993
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.374
ELB improved by 40.6615
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.787
ELB improved by 19.5864
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.758
ELB improved by 9.02922
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.124
ELB improved by 5.63387
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.415
ELB improved by 4.70923
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.741
ELB improved by 4.67421
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.633
ELB improved by 5.10773
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.909
ELB improved by 5.72438
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.891
ELB improved by 6.0175
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.516
ELB improved by 5.37543
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.614
ELB improved by 3.90123
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.164
ELB improved by 2.45082
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.634
ELB improved by 1.5298
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.588
ELB improved by 1.04616
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.793
ELB improved by 0.794512
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.137
ELB improved by 0.655978
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.561
ELB improved by 0.576131
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.032
ELB improved by 0.528971
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.533
ELB improved by 0.499274
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.057
ELB improved by 0.475664
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.607
ELB improved by 0.450368
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.185
ELB improved by 0.421306
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.795
ELB improved by 0.390682
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.434
ELB improved by 0.361189
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.099
ELB improved by 0.334339
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.789
ELB improved by 0.310713
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.498
ELB improved by 0.290377
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.225
ELB improved by 0.273074
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.967
ELB improved by 0.258337
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.721
ELB improved by 0.245597
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.487
ELB improved by 0.23426
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.263
ELB improved by 0.22377
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.049
ELB improved by 0.213645
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.846
ELB improved by 0.203504
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.653
ELB improved by 0.193079
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.471
ELB improved by 0.182229
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.3
ELB improved by 0.170929
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.14
ELB improved by 0.15926
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.993
ELB improved by 0.147383
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.858
ELB improved by 0.135509
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.734
ELB improved by 0.123862
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.621
ELB improved by 0.112651
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.519
ELB improved by 0.10205
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.427
ELB improved by 0.0921815
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.344
ELB improved by 0.0831191
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.269
ELB improved by 0.0748896
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.201
ELB improved by 0.0674824
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.14
ELB improved by 0.0608597
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.086
ELB improved by 0.0549663
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.036
ELB improved by 0.0497371
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.991
ELB improved by 0.0451039
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.95
ELB improved by 0.0409993
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.912
ELB improved by 0.0373598
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.878
ELB improved by 0.0341275
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.847
ELB improved by 0.0312503
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.818
ELB improved by 0.0286828
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.792
ELB improved by 0.0263852
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.768
ELB improved by 0.0243235
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.745
ELB improved by 0.0224687
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.724
ELB improved by 0.020796
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.705
ELB improved by 0.0192841
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.687
ELB improved by 0.0179151
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.67
ELB improved by 0.0166735
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.655
ELB improved by 0.015546
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.64
ELB improved by 0.0145212
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.627
ELB improved by 0.0135888
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.614
ELB improved by 0.0127401
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.602
ELB improved by 0.0119673
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.591
ELB improved by 0.0112633
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.58
ELB improved by 0.0106218
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.57
ELB improved by 0.0100371
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.561
ELB improved by 0.00950407
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-901.42
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-569.508
ELB improved by 331.911
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-512.913
ELB improved by 56.595
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-482.418
ELB improved by 30.4948
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.021
ELB improved by 12.3975
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.347
ELB improved by 6.67373
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.806
ELB improved by 5.54145
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.46
ELB improved by 5.34542
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.516
ELB improved by 4.94418
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.511
ELB improved by 4.00495
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.712
ELB improved by 2.79912
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.914
ELB improved by 1.79772
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.74
ELB improved by 1.17393
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.91
ELB improved by 0.830384
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.282
ELB improved by 0.628435
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.792
ELB improved by 0.489406
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.403
ELB improved by 0.389146
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.083
ELB improved by 0.319846
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.81
ELB improved by 0.272782
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.57
ELB improved by 0.240167
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.353
ELB improved by 0.217117
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.152
ELB improved by 0.201097
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.961
ELB improved by 0.191031
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.774
ELB improved by 0.186604
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.587
ELB improved by 0.187118
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.398
ELB improved by 0.189095
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.214
ELB improved by 0.184131
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.051
ELB improved by 0.163567
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.921
ELB improved by 0.129813
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.825
ELB improved by 0.0956218
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.755
ELB improved by 0.0701479
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.701
ELB improved by 0.0539997
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.657
ELB improved by 0.0441477
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.619
ELB improved by 0.0378426
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.586
ELB improved by 0.0334449
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.555
ELB improved by 0.0301098
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.528
ELB improved by 0.0274154
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.503
ELB improved by 0.0251446
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.48
ELB improved by 0.0231781
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.458
ELB improved by 0.0214448
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.438
ELB improved by 0.019899
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.42
ELB improved by 0.0185092
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.403
ELB improved by 0.0172523
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.386
ELB improved by 0.0161104
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.371
ELB improved by 0.0150695
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.357
ELB improved by 0.0141177
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.344
ELB improved by 0.0132455
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.332
ELB improved by 0.0124443
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.32
ELB improved by 0.0117072
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.309
ELB improved by 0.0110278
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.298
ELB improved by 0.0104006
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.289
ELB improved by 0.00982083
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-850.086
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-578.289
ELB improved by 271.797
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-517.9
ELB improved by 60.3896
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-478.166
ELB improved by 39.7339
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.987
ELB improved by 18.1782
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.142
ELB improved by 7.84522
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.798
ELB improved by 4.34451
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.493
ELB improved by 3.30521
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.491
ELB improved by 3.00122
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.554
ELB improved by 2.93768
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.567
ELB improved by 2.98659
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.472
ELB improved by 3.095
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.274
ELB improved by 3.19768
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.086
ELB improved by 3.18801
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.144
ELB improved by 2.94226
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.689
ELB improved by 2.45515
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.788
ELB improved by 1.90115
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.335
ELB improved by 1.45297
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.172
ELB improved by 1.16333
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.164
ELB improved by 1.00766
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.223
ELB improved by 0.941182
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.297
ELB improved by 0.925687
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.36
ELB improved by 0.937091
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.397
ELB improved by 0.962568
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.402
ELB improved by 0.995215
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.37
ELB improved by 1.03256
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.29
ELB improved by 1.07965
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.139
ELB improved by 1.15074
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.871
ELB improved by 1.26841
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.412
ELB improved by 1.4586
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.694
ELB improved by 1.71804
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.735
ELB improved by 1.95884
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.657
ELB improved by 2.07862
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.574
ELB improved by 2.08259
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.623
ELB improved by 1.951
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.102
ELB improved by 1.52121
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.117
ELB improved by 0.984408
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.506
ELB improved by 0.611169
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.113
ELB improved by 0.393494
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.848
ELB improved by 0.265208
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.662
ELB improved by 0.185702
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.527
ELB improved by 0.134519
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.427
ELB improved by 0.100616
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.349
ELB improved by 0.077527
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.288
ELB improved by 0.0613575
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.238
ELB improved by 0.0497201
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.197
ELB improved by 0.0411214
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.162
ELB improved by 0.0346084
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.133
ELB improved by 0.029561
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.107
ELB improved by 0.0255679
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.085
ELB improved by 0.0223502
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.065
ELB improved by 0.0197155
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.048
ELB improved by 0.0175277
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.032
ELB improved by 0.015689
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.018
ELB improved by 0.0141277
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.005
ELB improved by 0.01279
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.993
ELB improved by 0.0116354
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.983
ELB improved by 0.0106323
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.973
ELB improved by 0.00975585
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
1.167 0.107 1.539
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.039 | 0.007 | 0.058 | |
| getPIPs | 0.032 | 0.005 | 0.042 | |
| graper | 0.048 | 0.006 | 0.067 | |
| makeExampleData | 0.009 | 0.000 | 0.014 | |
| makeExampleDataWithUnequalGroups | 0.013 | 0.001 | 0.016 | |
| plotELBO | 0.095 | 0.006 | 0.121 | |
| plotGroupPenalties | 0.278 | 0.009 | 0.360 | |
| plotPosterior | 0.207 | 0.008 | 0.283 | |
| predict.graper | 1.119 | 0.025 | 1.492 | |
| print.graper | 0.033 | 0.004 | 0.037 | |