Britta Velten
| Snapshot Date: 2024-07-21 14:00 -0400 (Sun, 21 Jul 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 2024-07-24 09:03 -0400 (Wed, 24 Jul 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" | 4747 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4467 |
| 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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings graper_1.20.0.tar.gz |
| StartedAt: 2024-07-22 00:59:42 -0400 (Mon, 22 Jul 2024) |
| EndedAt: 2024-07-22 01:01:05 -0400 (Mon, 22 Jul 2024) |
| EllapsedTime: 82.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings graper_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/graper.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL graper
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘graper’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c fit_graper.cpp -o fit_graper.o
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/math/special_functions/digamma.hpp:15,
from graper_linear_dense_ff.h:2,
from fit_graper.cpp:4:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
| ^~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -llapack -L/home/biocbuild/bbs-3.19-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-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: x86_64-pc-linux-gnu
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=-877.578
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-566.457
ELB improved by 311.121
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-508.187
ELB improved by 58.2698
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.421
ELB improved by 35.7658
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.633
ELB improved by 14.7881
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.357
ELB improved by 6.27619
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.655
ELB improved by 3.70217
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.889
ELB improved by 2.76547
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.469
ELB improved by 2.42043
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.213
ELB improved by 2.25537
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.069
ELB improved by 2.14466
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.024
ELB improved by 2.04454
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.096
ELB improved by 1.92819
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.321
ELB improved by 1.77498
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.747
ELB improved by 1.57373
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.419
ELB improved by 1.32804
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.358
ELB improved by 1.06104
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.548
ELB improved by 0.809798
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.944
ELB improved by 0.604022
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.492
ELB improved by 0.452491
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.144
ELB improved by 0.348028
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.866
ELB improved by 0.277998
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.635
ELB improved by 0.230916
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.436
ELB improved by 0.198484
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.261
ELB improved by 0.175315
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.103
ELB improved by 0.158064
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.958
ELB improved by 0.144679
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.825
ELB improved by 0.133887
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.7
ELB improved by 0.124883
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.583
ELB improved by 0.117145
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.472
ELB improved by 0.110325
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.368
ELB improved by 0.104187
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.269
ELB improved by 0.0985662
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.176
ELB improved by 0.0933472
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.088
ELB improved by 0.0884493
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.004
ELB improved by 0.0838162
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.924
ELB improved by 0.0794097
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.849
ELB improved by 0.0752043
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.778
ELB improved by 0.0711846
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.711
ELB improved by 0.0673414
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.647
ELB improved by 0.0636702
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.587
ELB improved by 0.0601692
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.53
ELB improved by 0.0568381
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.476
ELB improved by 0.0536767
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.426
ELB improved by 0.0506845
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.378
ELB improved by 0.0478603
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.333
ELB improved by 0.0452019
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.29
ELB improved by 0.042706
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.25
ELB improved by 0.0403684
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.211
ELB improved by 0.0381839
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.175
ELB improved by 0.0361471
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.141
ELB improved by 0.0342521
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.108
ELB improved by 0.032493
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.078
ELB improved by 0.0308642
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.048
ELB improved by 0.0293606
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.02
ELB improved by 0.0279778
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.994
ELB improved by 0.0267128
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.968
ELB improved by 0.0255637
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.943
ELB improved by 0.0245303
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.92
ELB improved by 0.023615
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.897
ELB improved by 0.0228225
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.875
ELB improved by 0.0221612
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.853
ELB improved by 0.0216436
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.832
ELB improved by 0.0212877
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.811
ELB improved by 0.0211177
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.79
ELB improved by 0.0211653
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.768
ELB improved by 0.0214701
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.746
ELB improved by 0.022078
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.723
ELB improved by 0.0230376
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.699
ELB improved by 0.0243884
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.673
ELB improved by 0.026141
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.644
ELB improved by 0.028243
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.614
ELB improved by 0.0305369
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.581
ELB improved by 0.0327259
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.547
ELB improved by 0.0343891
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.512
ELB improved by 0.0350883
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.477
ELB improved by 0.034557
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.444
ELB improved by 0.0328558
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.414
ELB improved by 0.0303497
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.386
ELB improved by 0.0275115
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.362
ELB improved by 0.0247179
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.339
ELB improved by 0.0221739
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.319
ELB improved by 0.0199478
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.301
ELB improved by 0.0180348
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.285
ELB improved by 0.0164025
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.27
ELB improved by 0.0150124
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.256
ELB improved by 0.0138284
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.243
ELB improved by 0.0128192
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.231
ELB improved by 0.011958
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.22
ELB improved by 0.0112228
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.21
ELB improved by 0.0105953
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.199
ELB improved by 0.0100603
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.19
ELB improved by 0.00960567
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-898.591
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-563.504
ELB improved by 335.087
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-506.554
ELB improved by 56.9495
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-478.032
ELB improved by 28.5224
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.426
ELB improved by 11.6061
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.167
ELB improved by 6.25848
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.091
ELB improved by 5.07668
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.94
ELB improved by 5.15084
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.147
ELB improved by 5.79336
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.57
ELB improved by 6.57698
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.68
ELB improved by 6.88928
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.49
ELB improved by 6.19026
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.789
ELB improved by 4.70128
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.624
ELB improved by 3.16436
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.567
ELB improved by 2.05792
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.184
ELB improved by 1.3827
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.2
ELB improved by 0.9841
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.459
ELB improved by 0.74084
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.878
ELB improved by 0.581376
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.411
ELB improved by 0.466749
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.032
ELB improved by 0.378673
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.722
ELB improved by 0.310326
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.464
ELB improved by 0.258061
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.246
ELB improved by 0.217938
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.059
ELB improved by 0.186298
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.899
ELB improved by 0.160613
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.759
ELB improved by 0.139419
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.638
ELB improved by 0.121855
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.53
ELB improved by 0.107293
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.435
ELB improved by 0.0951936
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.35
ELB improved by 0.0850843
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.273
ELB improved by 0.0765687
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.204
ELB improved by 0.0693309
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.141
ELB improved by 0.0631247
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.083
ELB improved by 0.0577597
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.03
ELB improved by 0.0530871
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.981
ELB improved by 0.0489899
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.936
ELB improved by 0.0453746
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.894
ELB improved by 0.0421659
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.854
ELB improved by 0.0393023
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.818
ELB improved by 0.0367335
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.783
ELB improved by 0.0344176
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.751
ELB improved by 0.0323202
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.72
ELB improved by 0.0304121
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.692
ELB improved by 0.0286692
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.665
ELB improved by 0.027071
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.639
ELB improved by 0.0256001
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.615
ELB improved by 0.0242418
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.592
ELB improved by 0.0229838
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.57
ELB improved by 0.0218153
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.549
ELB improved by 0.0207273
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.53
ELB improved by 0.0197119
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.511
ELB improved by 0.0187623
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.493
ELB improved by 0.0178728
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.476
ELB improved by 0.0170383
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.46
ELB improved by 0.0162543
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.444
ELB improved by 0.015517
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.429
ELB improved by 0.0148228
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.415
ELB improved by 0.0141688
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.402
ELB improved by 0.0135522
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.389
ELB improved by 0.0129706
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.376
ELB improved by 0.0124216
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.364
ELB improved by 0.0119034
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.353
ELB improved by 0.011414
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.342
ELB improved by 0.0109517
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.331
ELB improved by 0.0105148
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.321
ELB improved by 0.010102
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.312
ELB improved by 0.00971176
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-871.813
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-542.233
ELB improved by 329.581
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-485.86
ELB improved by 56.373
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.027
ELB improved by 30.8325
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.699
ELB improved by 12.3279
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.728
ELB improved by 5.97115
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.844
ELB improved by 3.88451
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.817
ELB improved by 3.02648
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.999
ELB improved by 2.81854
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.058
ELB improved by 2.94096
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.83
ELB improved by 3.22794
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.298
ELB improved by 3.53129
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.629
ELB improved by 3.66977
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.137
ELB improved by 3.49137
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.153
ELB improved by 2.98422
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.861
ELB improved by 2.29212
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.22
ELB improved by 1.64127
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.031
ELB improved by 1.18909
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.085
ELB improved by 0.945478
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.239
ELB improved by 0.845736
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.426
ELB improved by 0.812998
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.63
ELB improved by 0.796401
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.836
ELB improved by 0.79374
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.027
ELB improved by 0.809439
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.192
ELB improved by 0.835144
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.329
ELB improved by 0.862997
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.439
ELB improved by 0.890036
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.522
ELB improved by 0.916234
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.583
ELB improved by 0.939607
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.633
ELB improved by 0.949767
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.701
ELB improved by 0.931926
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.818
ELB improved by 0.883542
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.003
ELB improved by 0.814617
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.268
ELB improved by 0.734883
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.617
ELB improved by 0.650986
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.049
ELB improved by 0.56828
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.558
ELB improved by 0.491186
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.135
ELB improved by 0.422965
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.769
ELB improved by 0.365679
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.449
ELB improved by 0.320246
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.163
ELB improved by 0.286115
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.902
ELB improved by 0.260251
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.666
ELB improved by 0.236705
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.456
ELB improved by 0.210049
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.275
ELB improved by 0.180758
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.121
ELB improved by 0.15377
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.989
ELB improved by 0.132503
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.871
ELB improved by 0.117429
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.763
ELB improved by 0.108077
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.658
ELB improved by 0.104682
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.549
ELB improved by 0.10928
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.422
ELB improved by 0.127053
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.256
ELB improved by 0.166533
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.027
ELB improved by 0.22846
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.751
ELB improved by 0.275883
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.49
ELB improved by 0.260869
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.283
ELB improved by 0.207727
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.123
ELB improved by 0.159245
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.999
ELB improved by 0.12478
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.898
ELB improved by 0.100416
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.816
ELB improved by 0.0819157
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.75
ELB improved by 0.0667501
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.696
ELB improved by 0.0538621
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.653
ELB improved by 0.0430322
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.618
ELB improved by 0.0342595
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.591
ELB improved by 0.0274281
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.569
ELB improved by 0.0222659
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.55
ELB improved by 0.0184315
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.535
ELB improved by 0.0155977
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.521
ELB improved by 0.0134938
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.509
ELB improved by 0.0119137
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.499
ELB improved by 0.010708
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.489
ELB improved by 0.00977114
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-853.654
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-580.078
ELB improved by 273.575
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-515.63
ELB improved by 64.4485
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.06
ELB improved by 46.5701
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.379
ELB improved by 23.6809
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.494
ELB improved by 9.88507
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.67
ELB improved by 4.82416
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.631
ELB improved by 3.03894
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.303
ELB improved by 2.32781
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.251
ELB improved by 2.05241
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.271
ELB improved by 1.97996
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.261
ELB improved by 2.00944
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.174
ELB improved by 2.08671
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.01
ELB improved by 2.16483
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.822
ELB improved by 2.18741
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.722
ELB improved by 2.10045
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.832
ELB improved by 1.88982
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.229
ELB improved by 1.60278
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.914
ELB improved by 1.31537
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.835
ELB improved by 1.0786
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.934
ELB improved by 0.90169
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.163
ELB improved by 0.770638
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.496
ELB improved by 0.667308
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.918
ELB improved by 0.577247
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.425
ELB improved by 0.492916
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.011
ELB improved by 0.414672
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.664
ELB improved by 0.346542
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.373
ELB improved by 0.290755
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.127
ELB improved by 0.246579
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.915
ELB improved by 0.211906
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.73
ELB improved by 0.184572
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.568
ELB improved by 0.162837
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.422
ELB improved by 0.145432
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.291
ELB improved by 0.131491
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.17
ELB improved by 0.120481
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.058
ELB improved by 0.112173
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.951
ELB improved by 0.106673
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.847
ELB improved by 0.104566
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.74
ELB improved by 0.107191
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.623
ELB improved by 0.117017
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.485
ELB improved by 0.137429
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.316
ELB improved by 0.169448
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.112
ELB improved by 0.204016
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.887
ELB improved by 0.224476
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.656
ELB improved by 0.230753
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.415
ELB improved by 0.241454
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.141
ELB improved by 0.273808
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.794
ELB improved by 0.347218
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.292
ELB improved by 0.50231
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.483
ELB improved by 0.808813
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.199
ELB improved by 1.28429
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.509
ELB improved by 1.68936
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.717
ELB improved by 1.79249
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.989
ELB improved by 1.72796
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.429
ELB improved by 1.5597
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.199
ELB improved by 1.2301
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.435
ELB improved by 0.763948
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.02
ELB improved by 0.414786
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.792
ELB improved by 0.227922
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.661
ELB improved by 0.131354
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.581
ELB improved by 0.0802894
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.528
ELB improved by 0.0524352
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.492
ELB improved by 0.0366351
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.464
ELB improved by 0.0272566
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.443
ELB improved by 0.0214076
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.425
ELB improved by 0.0175666
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.41
ELB improved by 0.0149103
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.397
ELB improved by 0.0129798
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.386
ELB improved by 0.011512
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.376
ELB improved by 0.0103519
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.366
ELB improved by 0.00940504
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.399 0.125 2.511
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.064 | 0.008 | 0.071 | |
| getPIPs | 0.057 | 0.012 | 0.070 | |
| graper | 0.072 | 0.032 | 0.105 | |
| makeExampleData | 0.01 | 0.00 | 0.01 | |
| makeExampleDataWithUnequalGroups | 0.013 | 0.000 | 0.013 | |
| plotELBO | 0.231 | 0.008 | 0.239 | |
| plotGroupPenalties | 0.778 | 0.012 | 0.789 | |
| plotPosterior | 0.520 | 0.016 | 0.536 | |
| predict.graper | 2.080 | 0.060 | 2.141 | |
| print.graper | 0.047 | 0.019 | 0.064 | |