Britta Velten
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 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 2024-06-11 14:42 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 908/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.20.0 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | 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: 2024-06-09 20:45:10 -0400 (Sun, 09 Jun 2024) |
| EndedAt: 2024-06-09 20:46:20 -0400 (Sun, 09 Jun 2024) |
| EllapsedTime: 69.4 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 4.4.0 (2024-04-24)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.20.0’
* 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-x86_64/Resources/library/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
# warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
See ‘/Users/biocbuild/bbs-3.19-bioc/meat/graper.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking 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-x86_64/Resources/library’
* installing *source* package ‘graper’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fit_graper.cpp -o fit_graper.o
In file included from fit_graper.cpp:4:
In file included from ./graper_linear_dense_ff.h:2:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/digamma.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/math_fwd.hpp:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
# warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o graper.so RcppExports.o fit_graper.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-graper/00new/graper/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (graper)
graper.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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=-832.953
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-557.579
ELB improved by 275.374
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-497.563
ELB improved by 60.0162
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.445
ELB improved by 41.1181
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.023
ELB improved by 19.4223
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.7
ELB improved by 8.32215
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.441
ELB improved by 5.25937
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.075
ELB improved by 4.36633
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.939
ELB improved by 4.13584
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.887
ELB improved by 4.05207
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.032
ELB improved by 3.85478
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.621
ELB improved by 3.41073
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.884
ELB improved by 2.73698
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.892
ELB improved by 1.99227
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.543
ELB improved by 1.34949
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.657
ELB improved by 0.885962
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.065
ELB improved by 0.591979
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.644
ELB improved by 0.42079
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.319
ELB improved by 0.324821
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.048
ELB improved by 0.270907
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.808
ELB improved by 0.239902
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.587
ELB improved by 0.221543
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.376
ELB improved by 0.210342
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.173
ELB improved by 0.203268
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.975
ELB improved by 0.198579
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.779
ELB improved by 0.195252
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.587
ELB improved by 0.192696
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.396
ELB improved by 0.190614
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.207
ELB improved by 0.188917
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.019
ELB improved by 0.187677
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.832
ELB improved by 0.187082
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.645
ELB improved by 0.187403
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.456
ELB improved by 0.188989
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.264
ELB improved by 0.192307
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.066
ELB improved by 0.198041
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.858
ELB improved by 0.207124
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.638
ELB improved by 0.220302
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.402
ELB improved by 0.236609
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.15
ELB improved by 0.251304
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.893
ELB improved by 0.257351
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.64
ELB improved by 0.252707
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.397
ELB improved by 0.24315
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.162
ELB improved by 0.235358
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.929
ELB improved by 0.232177
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.696
ELB improved by 0.233718
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.457
ELB improved by 0.238735
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.212
ELB improved by 0.245117
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.961
ELB improved by 0.251336
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.702
ELB improved by 0.258109
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.437
ELB improved by 0.265764
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.169
ELB improved by 0.267925
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.915
ELB improved by 0.254022
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.69
ELB improved by 0.224815
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.497
ELB improved by 0.192751
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.332
ELB improved by 0.165659
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.188
ELB improved by 0.143848
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.062
ELB improved by 0.125828
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.951
ELB improved by 0.110745
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.853
ELB improved by 0.0982602
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.765
ELB improved by 0.0880985
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.685
ELB improved by 0.0798252
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.612
ELB improved by 0.0728252
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.546
ELB improved by 0.0664206
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.486
ELB improved by 0.0600623
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.432
ELB improved by 0.0534955
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.385
ELB improved by 0.0467969
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.345
ELB improved by 0.0402623
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.311
ELB improved by 0.0342278
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.282
ELB improved by 0.0289318
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.257
ELB improved by 0.0244687
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.237
ELB improved by 0.0208124
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.219
ELB improved by 0.0178666
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.203
ELB improved by 0.0155093
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.19
ELB improved by 0.0136215
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.178
ELB improved by 0.0120997
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.167
ELB improved by 0.0108607
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.157
ELB improved by 0.00983943
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-843.674
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-575.481
ELB improved by 268.193
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-514.159
ELB improved by 61.3217
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-474.342
ELB improved by 39.8176
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.234
ELB improved by 17.1078
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.984
ELB improved by 7.25017
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.186
ELB improved by 4.7978
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.943
ELB improved by 4.24249
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.514
ELB improved by 4.42913
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.698
ELB improved by 4.81651
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.847
ELB improved by 4.85115
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.697
ELB improved by 4.15002
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.735
ELB improved by 2.9612
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.849
ELB improved by 1.88628
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.655
ELB improved by 1.19428
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.844
ELB improved by 0.810606
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.243
ELB improved by 0.601629
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.76
ELB improved by 0.482436
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.35
ELB improved by 0.410535
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.984
ELB improved by 0.36553
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.647
ELB improved by 0.337221
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.327
ELB improved by 0.320168
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.015
ELB improved by 0.311313
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.706
ELB improved by 0.308891
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.395
ELB improved by 0.311903
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.075
ELB improved by 0.319846
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.742
ELB improved by 0.332563
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.392
ELB improved by 0.350128
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.019
ELB improved by 0.372688
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.619
ELB improved by 0.400218
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.187
ELB improved by 0.432225
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.719
ELB improved by 0.467613
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.214
ELB improved by 0.50488
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.672
ELB improved by 0.542531
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.092
ELB improved by 0.579449
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.477
ELB improved by 0.615112
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.827
ELB improved by 0.649788
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.143
ELB improved by 0.684652
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.421
ELB improved by 0.721764
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.657
ELB improved by 0.763884
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.843
ELB improved by 0.814542
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.962
ELB improved by 0.880327
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.984
ELB improved by 0.977944
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.849
ELB improved by 1.1356
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.5
ELB improved by 1.34842
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.019
ELB improved by 1.48131
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.395
ELB improved by 1.62424
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.931
ELB improved by 1.46347
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.035
ELB improved by 0.896237
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.486
ELB improved by 0.549036
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.111
ELB improved by 0.374855
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.838
ELB improved by 0.273536
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.633
ELB improved by 0.204367
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.481
ELB improved by 0.152511
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.367
ELB improved by 0.114095
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.28
ELB improved by 0.0871175
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.211
ELB improved by 0.0687045
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.155
ELB improved by 0.0559774
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.108
ELB improved by 0.0468226
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.068
ELB improved by 0.0399153
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.034
ELB improved by 0.0344788
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.004
ELB improved by 0.0300617
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.977
ELB improved by 0.0263935
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.954
ELB improved by 0.0233029
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.933
ELB improved by 0.0206739
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.915
ELB improved by 0.0184231
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.898
ELB improved by 0.0164871
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.884
ELB improved by 0.0148159
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.87
ELB improved by 0.0133693
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.858
ELB improved by 0.0121138
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.847
ELB improved by 0.0110217
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.837
ELB improved by 0.0100698
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.828
ELB improved by 0.00923816
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-840.781
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-567.214
ELB improved by 273.568
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-504.913
ELB improved by 62.3011
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.468
ELB improved by 43.4445
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.907
ELB improved by 18.5608
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.416
ELB improved by 6.49143
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.128
ELB improved by 3.28805
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.91
ELB improved by 2.21766
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.122
ELB improved by 1.78852
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.517
ELB improved by 1.60427
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.996
ELB improved by 1.52147
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.513
ELB improved by 1.48257
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.05
ELB improved by 1.46326
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.595
ELB improved by 1.45479
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.14
ELB improved by 1.45516
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.677
ELB improved by 1.46361
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.2
ELB improved by 1.47694
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.712
ELB improved by 1.4872
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.232
ELB improved by 1.48054
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.793
ELB improved by 1.43873
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.447
ELB improved by 1.34568
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.248
ELB improved by 1.1992
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.229
ELB improved by 1.01944
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.386
ELB improved by 0.842692
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.685
ELB improved by 0.701431
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.076
ELB improved by 0.608722
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.516
ELB improved by 0.559763
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.974
ELB improved by 0.542339
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.429
ELB improved by 0.544355
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.873
ELB improved by 0.55637
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.301
ELB improved by 0.571743
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.715
ELB improved by 0.586267
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.117
ELB improved by 0.597747
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.512
ELB improved by 0.605488
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.902
ELB improved by 0.609705
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.291
ELB improved by 0.610939
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.682
ELB improved by 0.609528
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.076
ELB improved by 0.605222
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.479
ELB improved by 0.597052
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.896
ELB improved by 0.583524
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.333
ELB improved by 0.563076
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.798
ELB improved by 0.53466
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.3
ELB improved by 0.498251
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.845
ELB improved by 0.455093
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.437
ELB improved by 0.407586
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.078
ELB improved by 0.358865
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.766
ELB improved by 0.312242
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.495
ELB improved by 0.270765
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.258
ELB improved by 0.237156
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.044
ELB improved by 0.21434
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.837
ELB improved by 0.20674
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.616
ELB improved by 0.2215
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.354
ELB improved by 0.26156
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.062
ELB improved by 0.291766
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.817
ELB improved by 0.245127
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.661
ELB improved by 0.156518
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.564
ELB improved by 0.0962804
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.5
ELB improved by 0.0643795
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.453
ELB improved by 0.046636
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.417
ELB improved by 0.0359533
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.388
ELB improved by 0.0290648
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.364
ELB improved by 0.0243442
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.343
ELB improved by 0.0209297
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.325
ELB improved by 0.0183415
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.308
ELB improved by 0.0163019
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.294
ELB improved by 0.0146434
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.281
ELB improved by 0.0132618
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.268
ELB improved by 0.012089
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.257
ELB improved by 0.0110796
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.247
ELB improved by 0.0102015
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.238
ELB improved by 0.00943139
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-859.559
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-577.889
ELB improved by 281.67
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-514.893
ELB improved by 62.9962
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.409
ELB improved by 41.4843
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.69
ELB improved by 19.7187
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.254
ELB improved by 8.43549
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.112
ELB improved by 5.14229
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.747
ELB improved by 4.36498
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.504
ELB improved by 4.24338
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.171
ELB improved by 4.33225
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.816
ELB improved by 4.35584
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.723
ELB improved by 4.09242
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.25
ELB improved by 3.47342
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.588
ELB improved by 2.66187
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.682
ELB improved by 1.90576
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.336
ELB improved by 1.34669
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.348
ELB improved by 0.987623
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.579
ELB improved by 0.76903
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.945
ELB improved by 0.634301
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.397
ELB improved by 0.547104
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.911
ELB improved by 0.486854
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.468
ELB improved by 0.442177
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.062
ELB improved by 0.406731
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.685
ELB improved by 0.376967
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.334
ELB improved by 0.350943
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.006
ELB improved by 0.327677
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.699
ELB improved by 0.306746
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.411
ELB improved by 0.288022
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.14
ELB improved by 0.271498
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.883
ELB improved by 0.257183
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.638
ELB improved by 0.245048
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.403
ELB improved by 0.235004
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.176
ELB improved by 0.226906
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.955
ELB improved by 0.220558
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.739
ELB improved by 0.215724
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.527
ELB improved by 0.212136
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.318
ELB improved by 0.209491
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.11
ELB improved by 0.207452
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.905
ELB improved by 0.205653
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.701
ELB improved by 0.203693
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.5
ELB improved by 0.201154
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.302
ELB improved by 0.197615
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.11
ELB improved by 0.192698
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.923
ELB improved by 0.186111
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.746
ELB improved by 0.177703
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.578
ELB improved by 0.167511
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.422
ELB improved by 0.155767
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.28
ELB improved by 0.142878
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.15
ELB improved by 0.129356
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.034
ELB improved by 0.115742
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.932
ELB improved by 0.102528
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.842
ELB improved by 0.0901013
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.763
ELB improved by 0.0787213
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.695
ELB improved by 0.0685232
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.635
ELB improved by 0.0595381
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.583
ELB improved by 0.051722
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.538
ELB improved by 0.044984
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.499
ELB improved by 0.0392089
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.465
ELB improved by 0.0342743
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.435
ELB improved by 0.0300616
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.408
ELB improved by 0.0264621
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.385
ELB improved by 0.02338
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.364
ELB improved by 0.0207327
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.346
ELB improved by 0.0184505
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.329
ELB improved by 0.0164753
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.315
ELB improved by 0.0147589
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.301
ELB improved by 0.0132615
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.289
ELB improved by 0.0119505
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.279
ELB improved by 0.0107988
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.269
ELB improved by 0.00978401
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.546 0.265 2.817
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.057 | 0.018 | 0.074 | |
| getPIPs | 0.053 | 0.015 | 0.068 | |
| graper | 0.075 | 0.018 | 0.094 | |
| makeExampleData | 0.013 | 0.002 | 0.015 | |
| makeExampleDataWithUnequalGroups | 0.033 | 0.002 | 0.035 | |
| plotELBO | 0.234 | 0.021 | 0.255 | |
| plotGroupPenalties | 0.735 | 0.025 | 0.761 | |
| plotPosterior | 0.553 | 0.018 | 0.572 | |
| predict.graper | 1.957 | 0.080 | 2.043 | |
| print.graper | 0.052 | 0.014 | 0.066 | |