Britta Velten
| Snapshot Date: 2024-10-09 14:00 -0400 (Wed, 09 Oct 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 2024-10-11 20:42 -0400 (Fri, 11 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4529 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4479 |
| 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 | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | 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: 1.20.0 |
| 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_1.20.0.tar.gz |
| StartedAt: 2024-10-10 23:00:45 -0400 (Thu, 10 Oct 2024) |
| EndedAt: 2024-10-10 23:01:57 -0400 (Thu, 10 Oct 2024) |
| EllapsedTime: 71.9 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_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-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 13.6.6
* 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 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-3.19-bioc/meat/graper.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* 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-3.19-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-1500.0.40.1)’
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=-879.523
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-564.919
ELB improved by 314.604
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-505.314
ELB improved by 59.6049
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.385
ELB improved by 31.9292
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.906
ELB improved by 11.4793
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.116
ELB improved by 4.78965
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.968
ELB improved by 3.14786
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.364
ELB improved by 2.60416
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.941
ELB improved by 2.42311
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.554
ELB improved by 2.38694
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.145
ELB improved by 2.4086
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.708
ELB improved by 2.43727
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.287
ELB improved by 2.42073
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.983
ELB improved by 2.30419
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.921
ELB improved by 2.06177
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.192
ELB improved by 1.72959
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.803
ELB improved by 1.38867
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.699
ELB improved by 1.10381
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.814
ELB improved by 0.885773
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.106
ELB improved by 0.708117
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.557
ELB improved by 0.548204
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.145
ELB improved by 0.41221
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.83
ELB improved by 0.314702
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.578
ELB improved by 0.252244
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.368
ELB improved by 0.209784
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.194
ELB improved by 0.174753
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.051
ELB improved by 0.142594
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.936
ELB improved by 0.114735
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.843
ELB improved by 0.0931817
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.765
ELB improved by 0.0777255
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.699
ELB improved by 0.0667816
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.64
ELB improved by 0.0587772
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.587
ELB improved by 0.0526368
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.539
ELB improved by 0.0477146
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.496
ELB improved by 0.0436305
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.456
ELB improved by 0.040154
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.419
ELB improved by 0.0371383
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.384
ELB improved by 0.0344857
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.352
ELB improved by 0.0321282
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.322
ELB improved by 0.0300164
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.294
ELB improved by 0.0281132
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.267
ELB improved by 0.02639
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.243
ELB improved by 0.0248238
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.219
ELB improved by 0.0233959
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.197
ELB improved by 0.0220906
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.176
ELB improved by 0.0208946
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.156
ELB improved by 0.0197967
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.138
ELB improved by 0.0187868
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.12
ELB improved by 0.0178565
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.103
ELB improved by 0.016998
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.087
ELB improved by 0.0162046
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.071
ELB improved by 0.0154704
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.056
ELB improved by 0.0147901
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.042
ELB improved by 0.0141587
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.029
ELB improved by 0.013572
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.016
ELB improved by 0.0130262
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.003
ELB improved by 0.0125178
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.991
ELB improved by 0.0120435
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.979
ELB improved by 0.0116007
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.968
ELB improved by 0.0111865
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.957
ELB improved by 0.0107988
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.947
ELB improved by 0.0104354
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.937
ELB improved by 0.0100943
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.927
ELB improved by 0.00977372
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-889.052
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-570.025
ELB improved by 319.027
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-512.616
ELB improved by 57.4086
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-479.47
ELB improved by 33.1461
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.925
ELB improved by 14.5449
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.128
ELB improved by 5.7973
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.925
ELB improved by 3.20314
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.524
ELB improved by 2.40065
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.441
ELB improved by 2.08288
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.512
ELB improved by 1.92939
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.664
ELB improved by 1.8477
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.857
ELB improved by 1.80787
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.067
ELB improved by 1.78958
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.302
ELB improved by 1.76469
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.605
ELB improved by 1.69732
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.045
ELB improved by 1.55975
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.692
ELB improved by 1.35353
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.579
ELB improved by 1.11261
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.698
ELB improved by 0.880864
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.011
ELB improved by 0.68742
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.47
ELB improved by 0.540445
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.035
ELB improved by 0.434979
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.673
ELB improved by 0.362005
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.361
ELB improved by 0.312525
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.083
ELB improved by 0.277877
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.832
ELB improved by 0.250607
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.606
ELB improved by 0.226406
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.402
ELB improved by 0.204371
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.216
ELB improved by 0.185265
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.047
ELB improved by 0.1698
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.889
ELB improved by 0.157999
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.739
ELB improved by 0.149359
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.596
ELB improved by 0.143225
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.457
ELB improved by 0.139047
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.32
ELB improved by 0.136486
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.185
ELB improved by 0.135442
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.049
ELB improved by 0.136056
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.91
ELB improved by 0.138754
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.766
ELB improved by 0.144362
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.611
ELB improved by 0.154285
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.441
ELB improved by 0.170648
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.245
ELB improved by 0.196288
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.01
ELB improved by 0.234922
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.717
ELB improved by 0.292719
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.336
ELB improved by 0.381062
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.823
ELB improved by 0.512642
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.146
ELB improved by 0.677627
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.314
ELB improved by 0.831574
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.352
ELB improved by 0.962079
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.248
ELB improved by 1.10371
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.004
ELB improved by 1.2438
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.677
ELB improved by 1.32696
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.351
ELB improved by 1.32636
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.119
ELB improved by 1.23207
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.062
ELB improved by 1.05707
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.218
ELB improved by 0.843791
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.586
ELB improved by 0.632305
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.134
ELB improved by 0.451861
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.815
ELB improved by 0.319366
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.58
ELB improved by 0.234645
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.391
ELB improved by 0.189372
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.213
ELB improved by 0.17804
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.011
ELB improved by 0.2016
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.75
ELB improved by 0.260933
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.417
ELB improved by 0.332636
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.065
ELB improved by 0.352439
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.78
ELB improved by 0.28539
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.586
ELB improved by 0.193369
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.452
ELB improved by 0.134132
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.344
ELB improved by 0.108195
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.242
ELB improved by 0.102292
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.135
ELB improved by 0.106282
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.026
ELB improved by 0.109632
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.924
ELB improved by 0.101623
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.843
ELB improved by 0.0808926
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.786
ELB improved by 0.0570869
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.747
ELB improved by 0.0386065
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.721
ELB improved by 0.0269239
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.7
ELB improved by 0.0201261
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.684
ELB improved by 0.016163
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.671
ELB improved by 0.013712
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.658
ELB improved by 0.0120578
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.648
ELB improved by 0.01084
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.638
ELB improved by 0.00987927
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-860.079
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-554.471
ELB improved by 305.608
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-501.481
ELB improved by 52.9901
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.253
ELB improved by 29.2282
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.748
ELB improved by 11.5044
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.109
ELB improved by 5.6397
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.991
ELB improved by 4.11763
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.235
ELB improved by 3.75568
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.404
ELB improved by 3.83178
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.298
ELB improved by 4.10537
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.886
ELB improved by 4.41208
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.373
ELB improved by 4.51336
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.198
ELB improved by 4.1749
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.801
ELB improved by 3.39675
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.312
ELB improved by 2.48954
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.558
ELB improved by 1.75324
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.301
ELB improved by 1.25748
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.337
ELB improved by 0.963553
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.525
ELB improved by 0.811792
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.776
ELB improved by 0.749033
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.04
ELB improved by 0.73681
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.293
ELB improved by 0.747053
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.523
ELB improved by 0.769514
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.715
ELB improved by 0.80835
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.849
ELB improved by 0.865738
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.91
ELB improved by 0.938617
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.888
ELB improved by 1.02281
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.773
ELB improved by 1.11477
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.562
ELB improved by 1.21123
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.254
ELB improved by 1.30789
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.856
ELB improved by 1.39817
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.381
ELB improved by 1.47442
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.843
ELB improved by 1.53821
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.222
ELB improved by 1.6208
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.456
ELB improved by 1.76579
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.606
ELB improved by 1.84996
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.988
ELB improved by 1.61881
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.766
ELB improved by 1.22175
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.864
ELB improved by 0.901473
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.168
ELB improved by 0.696236
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.623
ELB improved by 0.544775
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.227
ELB improved by 0.396776
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.956
ELB improved by 0.270508
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.77
ELB improved by 0.186262
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.635
ELB improved by 0.134865
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.533
ELB improved by 0.102307
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.453
ELB improved by 0.08
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.389
ELB improved by 0.0637284
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.337
ELB improved by 0.0514937
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.295
ELB improved by 0.0422116
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.26
ELB improved by 0.035142
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.23
ELB improved by 0.0297128
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.205
ELB improved by 0.0254818
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.183
ELB improved by 0.0221227
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.163
ELB improved by 0.0194039
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.146
ELB improved by 0.0171644
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.131
ELB improved by 0.0152924
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.117
ELB improved by 0.0137088
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.105
ELB improved by 0.0123568
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.094
ELB improved by 0.011194
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.083
ELB improved by 0.0101881
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.074
ELB improved by 0.00931367
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-855.524
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-568.7
ELB improved by 286.824
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-508.874
ELB improved by 59.8265
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.468
ELB improved by 35.4058
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.911
ELB improved by 15.5573
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.035
ELB improved by 7.87547
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.603
ELB improved by 6.43226
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.879
ELB improved by 6.72437
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.823
ELB improved by 7.05583
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.402
ELB improved by 6.42098
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.555
ELB improved by 4.84654
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.336
ELB improved by 3.21938
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.263
ELB improved by 2.07326
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.911
ELB improved by 1.35178
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.998
ELB improved by 0.912425
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.338
ELB improved by 0.660719
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.82
ELB improved by 0.518042
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.386
ELB improved by 0.433552
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.006
ELB improved by 0.38034
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.661
ELB improved by 0.344686
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.342
ELB improved by 0.319329
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.042
ELB improved by 0.30021
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.757
ELB improved by 0.284968
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.484
ELB improved by 0.272213
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.223
ELB improved by 0.261158
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.972
ELB improved by 0.251399
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.729
ELB improved by 0.242792
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.494
ELB improved by 0.235358
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.265
ELB improved by 0.229228
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.04
ELB improved by 0.224594
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.818
ELB improved by 0.221685
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.597
ELB improved by 0.220738
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.375
ELB improved by 0.221991
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.15
ELB improved by 0.225668
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.918
ELB improved by 0.231969
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.677
ELB improved by 0.241042
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.424
ELB improved by 0.252944
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.156
ELB improved by 0.267557
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.872
ELB improved by 0.284487
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.569
ELB improved by 0.302923
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.247
ELB improved by 0.32153
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.909
ELB improved by 0.338406
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.558
ELB improved by 0.351235
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.2
ELB improved by 0.357682
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.844
ELB improved by 0.356076
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.498
ELB improved by 0.346208
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.168
ELB improved by 0.329999
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.856
ELB improved by 0.311759
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.558
ELB improved by 0.297627
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.266
ELB improved by 0.292501
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.975
ELB improved by 0.291267
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.702
ELB improved by 0.272879
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.477
ELB improved by 0.224829
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.311
ELB improved by 0.166166
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.192
ELB improved by 0.11842
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.107
ELB improved by 0.0854421
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.044
ELB improved by 0.0631121
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.996
ELB improved by 0.0475182
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.96
ELB improved by 0.0362838
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.932
ELB improved by 0.0280257
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.91
ELB improved by 0.0218808
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.893
ELB improved by 0.0172703
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.879
ELB improved by 0.0137881
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.868
ELB improved by 0.0111424
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.859
ELB improved by 0.00912049
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.718 0.233 2.972
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.085 | 0.018 | 0.103 | |
| getPIPs | 0.079 | 0.014 | 0.096 | |
| graper | 0.131 | 0.019 | 0.155 | |
| makeExampleData | 0.013 | 0.001 | 0.015 | |
| makeExampleDataWithUnequalGroups | 0.039 | 0.004 | 0.044 | |
| plotELBO | 0.267 | 0.021 | 0.300 | |
| plotGroupPenalties | 0.790 | 0.026 | 0.833 | |
| plotPosterior | 0.602 | 0.018 | 0.629 | |
| predict.graper | 3.038 | 0.083 | 3.132 | |
| print.graper | 0.082 | 0.011 | 0.095 | |