Britta Velten
| Snapshot Date: 2024-08-07 14:00 -0400 (Wed, 07 Aug 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 2024-08-09 17:42 -0400 (Fri, 09 Aug 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" | 4758 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4493 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4522 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4471 |
| 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: 2024-08-08 22:21:43 -0400 (Thu, 08 Aug 2024) |
| EndedAt: 2024-08-08 22:22:54 -0400 (Thu, 08 Aug 2024) |
| EllapsedTime: 70.4 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_1.20.0.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=-853.193
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-575.167
ELB improved by 278.026
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-516.16
ELB improved by 59.0068
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-482.598
ELB improved by 33.5622
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.462
ELB improved by 15.1354
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.233
ELB improved by 8.22952
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.284
ELB improved by 5.94846
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.09
ELB improved by 5.19473
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.013
ELB improved by 5.07624
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.052
ELB improved by 4.96161
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.616
ELB improved by 4.43597
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.139
ELB improved by 3.47699
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.712
ELB improved by 2.42671
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.117
ELB improved by 1.59456
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.065
ELB improved by 1.05277
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.333
ELB improved by 0.73165
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.789
ELB improved by 0.543884
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.359
ELB improved by 0.430322
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423
ELB improved by 0.35848
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.689
ELB improved by 0.311502
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.409
ELB improved by 0.28038
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.148
ELB improved by 0.260028
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.901
ELB improved by 0.247459
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.66
ELB improved by 0.240892
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.421
ELB improved by 0.239294
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.179
ELB improved by 0.24215
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.929
ELB improved by 0.249381
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.668
ELB improved by 0.261376
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.389
ELB improved by 0.279143
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.084
ELB improved by 0.304572
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.744
ELB improved by 0.340633
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.353
ELB improved by 0.390776
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.897
ELB improved by 0.456018
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.366
ELB improved by 0.530827
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.758
ELB improved by 0.608242
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.062
ELB improved by 0.69612
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.247
ELB improved by 0.815032
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.286
ELB improved by 0.960757
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.214
ELB improved by 1.07156
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.11
ELB improved by 1.1038
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.028
ELB improved by 1.08255
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.998
ELB improved by 1.02949
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.049
ELB improved by 0.94953
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.2
ELB improved by 0.848528
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.463
ELB improved by 0.737002
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.837
ELB improved by 0.625885
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.315
ELB improved by 0.522326
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.886
ELB improved by 0.429632
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.536
ELB improved by 0.349842
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.251
ELB improved by 0.284455
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.018
ELB improved by 0.232833
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.826
ELB improved by 0.191997
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.667
ELB improved by 0.15897
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.535
ELB improved by 0.132727
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.421
ELB improved by 0.113193
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.323
ELB improved by 0.0989384
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.236
ELB improved by 0.0868626
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.161
ELB improved by 0.0742571
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.101
ELB improved by 0.0607624
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.053
ELB improved by 0.0479154
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.016
ELB improved by 0.0372024
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.986
ELB improved by 0.0290613
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.963
ELB improved by 0.0231607
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.944
ELB improved by 0.0189375
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.929
ELB improved by 0.0158846
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.915
ELB improved by 0.0136275
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.903
ELB improved by 0.0119118
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.892
ELB improved by 0.0105706
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.883
ELB improved by 0.00949464
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-852.963
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-579.984
ELB improved by 272.979
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-518.651
ELB improved by 61.333
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-474.651
ELB improved by 44.0004
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.066
ELB improved by 19.5843
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.333
ELB improved by 7.73383
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.899
ELB improved by 5.43373
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.361
ELB improved by 5.53787
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.901
ELB improved by 6.46026
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.275
ELB improved by 7.62603
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.292
ELB improved by 7.98227
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.639
ELB improved by 6.65333
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.267
ELB improved by 4.37247
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.742
ELB improved by 2.52444
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.276
ELB improved by 1.46613
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.358
ELB improved by 0.917628
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.735
ELB improved by 0.623336
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.283
ELB improved by 0.452249
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.939
ELB improved by 0.344166
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.668
ELB improved by 0.270934
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.449
ELB improved by 0.218604
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.269
ELB improved by 0.179757
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.119
ELB improved by 0.150134
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.992
ELB improved by 0.1271
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.883
ELB improved by 0.108901
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.789
ELB improved by 0.0943157
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.707
ELB improved by 0.0824704
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.634
ELB improved by 0.0727297
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.569
ELB improved by 0.0646281
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.511
ELB improved by 0.0578204
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.459
ELB improved by 0.0520476
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.412
ELB improved by 0.0471123
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.369
ELB improved by 0.0428619
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.33
ELB improved by 0.0391768
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.294
ELB improved by 0.0359623
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.261
ELB improved by 0.0331424
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.23
ELB improved by 0.0306556
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.202
ELB improved by 0.0284516
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.175
ELB improved by 0.0264893
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.151
ELB improved by 0.0247343
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.128
ELB improved by 0.0231581
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.106
ELB improved by 0.0217368
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.085
ELB improved by 0.0204503
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.066
ELB improved by 0.0192814
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.048
ELB improved by 0.0182156
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.031
ELB improved by 0.0172406
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.014
ELB improved by 0.0163456
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.999
ELB improved by 0.0155215
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.984
ELB improved by 0.0147605
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.97
ELB improved by 0.0140558
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.957
ELB improved by 0.0134013
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.944
ELB improved by 0.0127921
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.932
ELB improved by 0.0122235
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.92
ELB improved by 0.0116917
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.909
ELB improved by 0.0111932
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.898
ELB improved by 0.0107251
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.888
ELB improved by 0.0102847
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.878
ELB improved by 0.00986971
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-832.235
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-572.186
ELB improved by 260.048
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-509.606
ELB improved by 62.5803
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.068
ELB improved by 42.5382
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.342
ELB improved by 19.7261
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.249
ELB improved by 7.09302
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.855
ELB improved by 3.39334
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.433
ELB improved by 2.42209
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.283
ELB improved by 2.15044
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.131
ELB improved by 2.15178
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.836
ELB improved by 2.29514
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.316
ELB improved by 2.52022
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.56
ELB improved by 2.75575
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.676
ELB improved by 2.88342
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.897
ELB improved by 2.77983
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.47
ELB improved by 2.42643
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.521
ELB improved by 1.94964
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.004
ELB improved by 1.51616
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.79
ELB improved by 1.2149
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.748
ELB improved by 1.0415
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.794
ELB improved by 0.954118
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.876
ELB improved by 0.917578
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.963
ELB improved by 0.91328
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.029
ELB improved by 0.933816
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.053
ELB improved by 0.976001
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.017
ELB improved by 1.03583
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.912
ELB improved by 1.10568
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.738
ELB improved by 1.17374
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.514
ELB improved by 1.22354
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.287
ELB improved by 1.22711
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.142
ELB improved by 1.14511
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.165
ELB improved by 0.97682
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.385
ELB improved by 0.780281
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.776
ELB improved by 0.609176
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.282
ELB improved by 0.493527
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.826
ELB improved by 0.456372
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.317
ELB improved by 0.509133
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.743
ELB improved by 0.573578
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.23
ELB improved by 0.513175
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.866
ELB improved by 0.36373
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.634
ELB improved by 0.232462
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.482
ELB improved by 0.151814
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.374
ELB improved by 0.107949
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.291
ELB improved by 0.0835908
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.222
ELB improved by 0.0686812
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.163
ELB improved by 0.0584654
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.113
ELB improved by 0.0508053
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.068
ELB improved by 0.0447087
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.028
ELB improved by 0.0396763
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.993
ELB improved by 0.0354284
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.961
ELB improved by 0.0317907
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.932
ELB improved by 0.0286438
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.906
ELB improved by 0.0259008
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.883
ELB improved by 0.0234955
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.862
ELB improved by 0.0213756
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.842
ELB improved by 0.0194993
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.824
ELB improved by 0.0178326
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.808
ELB improved by 0.0163474
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.793
ELB improved by 0.0150202
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.779
ELB improved by 0.0138312
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.766
ELB improved by 0.0127635
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.755
ELB improved by 0.0118028
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.744
ELB improved by 0.0109368
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.733
ELB improved by 0.0101545
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.724
ELB improved by 0.00944683
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-881.973
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-576.311
ELB improved by 305.662
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-516.85
ELB improved by 59.4607
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-477.294
ELB improved by 39.5562
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.147
ELB improved by 18.1474
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.771
ELB improved by 7.37555
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.332
ELB improved by 4.43893
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.765
ELB improved by 3.56705
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.591
ELB improved by 3.17404
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.684
ELB improved by 2.9071
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.025
ELB improved by 2.65916
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.622
ELB improved by 2.40288
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.482
ELB improved by 2.14024
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.595
ELB improved by 1.88648
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.934
ELB improved by 1.66106
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.457
ELB improved by 1.47758
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.127
ELB improved by 1.32931
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.95
ELB improved by 1.1776
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.966
ELB improved by 0.983762
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.196
ELB improved by 0.769741
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.61
ELB improved by 0.586321
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.159
ELB improved by 0.451328
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.801
ELB improved by 0.357107
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.511
ELB improved by 0.290786
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.269
ELB improved by 0.241777
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.065
ELB improved by 0.203445
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.893
ELB improved by 0.172487
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.746
ELB improved by 0.147426
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.618
ELB improved by 0.127333
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.507
ELB improved by 0.111325
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.408
ELB improved by 0.0985451
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.32
ELB improved by 0.0882551
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.24
ELB improved by 0.0798778
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.167
ELB improved by 0.0729858
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.1
ELB improved by 0.0672687
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.037
ELB improved by 0.0625003
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.979
ELB improved by 0.0585135
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.924
ELB improved by 0.0551827
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.871
ELB improved by 0.0524117
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.821
ELB improved by 0.0501262
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.773
ELB improved by 0.0482683
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.726
ELB improved by 0.0467934
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.681
ELB improved by 0.045667
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.636
ELB improved by 0.0448633
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.591
ELB improved by 0.0443633
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.547
ELB improved by 0.0441547
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.503
ELB improved by 0.0442301
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.458
ELB improved by 0.0445876
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.413
ELB improved by 0.0452297
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.367
ELB improved by 0.0461639
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.32
ELB improved by 0.0474025
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.271
ELB improved by 0.0489629
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.22
ELB improved by 0.050868
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.167
ELB improved by 0.0531468
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.111
ELB improved by 0.0558354
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.052
ELB improved by 0.0589777
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.989
ELB improved by 0.062627
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.922
ELB improved by 0.066848
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.851
ELB improved by 0.071719
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.773
ELB improved by 0.0773357
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.689
ELB improved by 0.0838167
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.598
ELB improved by 0.091312
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.498
ELB improved by 0.100016
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.388
ELB improved by 0.110189
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.266
ELB improved by 0.122191
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.129
ELB improved by 0.136539
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.975
ELB improved by 0.153998
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.799
ELB improved by 0.17574
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.596
ELB improved by 0.203607
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.355
ELB improved by 0.2406
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.063
ELB improved by 0.291789
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.697
ELB improved by 0.366123
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.217
ELB improved by 0.48009
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.553
ELB improved by 0.664632
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.58
ELB improved by 0.972698
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.126
ELB improved by 1.45342
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.107
ELB improved by 2.01975
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.692
ELB improved by 2.41465
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.204
ELB improved by 2.48791
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.94
ELB improved by 2.26374
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.113
ELB improved by 1.82769
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.801
ELB improved by 1.31207
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.94
ELB improved by 0.860166
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.402
ELB improved by 0.538579
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.066
ELB improved by 0.33629
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.85
ELB improved by 0.215586
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.706
ELB improved by 0.143898
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.606
ELB improved by 0.100361
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.533
ELB improved by 0.0729981
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.478
ELB improved by 0.0551368
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.435
ELB improved by 0.0430346
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.4
ELB improved by 0.0345403
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.372
ELB improved by 0.0283808
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.348
ELB improved by 0.0237799
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.328
ELB improved by 0.0202512
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.31
ELB improved by 0.0174819
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.295
ELB improved by 0.0152655
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.281
ELB improved by 0.013462
iteration 99
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.269
ELB improved by 0.0119743
iteration 100
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.259
ELB improved by 0.0107332
iteration 101
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.249
ELB improved by 0.00968818
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.724 0.218 2.970
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.086 | 0.016 | 0.102 | |
| getPIPs | 0.081 | 0.013 | 0.094 | |
| graper | 0.134 | 0.018 | 0.152 | |
| makeExampleData | 0.013 | 0.001 | 0.014 | |
| makeExampleDataWithUnequalGroups | 0.034 | 0.002 | 0.037 | |
| plotELBO | 0.262 | 0.018 | 0.281 | |
| plotGroupPenalties | 0.751 | 0.024 | 0.777 | |
| plotPosterior | 0.612 | 0.018 | 0.633 | |
| predict.graper | 3.021 | 0.084 | 3.121 | |
| print.graper | 0.081 | 0.010 | 0.091 | |