Britta Velten
| Snapshot Date: 2024-05-15 14:05:05 -0400 (Wed, 15 May 2024) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: 7b45fcc |
| git_last_commit_date: 2024-04-30 11:11:42 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-17 11:36:38 -0400 (Fri, 17 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4663 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4398 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4425 |
| 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 878/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.21.0 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: graper |
| Version: 1.21.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings graper_1.21.0.tar.gz |
| StartedAt: 2024-05-15 22:59:08 -0400 (Wed, 15 May 2024) |
| EndedAt: 2024-05-15 23:00:30 -0400 (Wed, 15 May 2024) |
| EllapsedTime: 81.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings graper_1.21.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/graper.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* 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 ‘1.21.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... 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 ... NOTE
installed size is 6.2Mb
sub-directories of 1Mb or more:
libs 6.1Mb
* 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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.20-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL graper
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-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-3.20-bioc/R/site-library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11,
from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
from /home/biocbuild/bbs-3.20-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-3.20-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-3.20-bioc/R/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -llapack -L/home/biocbuild/bbs-3.20-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-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 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
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=-870.127
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-573.134
ELB improved by 296.993
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-515.282
ELB improved by 57.8529
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-478.768
ELB improved by 36.5136
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.456
ELB improved by 15.3116
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.568
ELB improved by 5.8887
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.106
ELB improved by 3.46123
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.164
ELB improved by 2.9425
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.225
ELB improved by 2.93843
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.08
ELB improved by 3.1451
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.615
ELB improved by 3.46513
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.765
ELB improved by 3.85029
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.549
ELB improved by 4.21597
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.217
ELB improved by 4.33174
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.25
ELB improved by 3.96684
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.997
ELB improved by 3.2531
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.527
ELB improved by 2.47029
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.71
ELB improved by 1.81652
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.317
ELB improved by 1.39393
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.176
ELB improved by 1.14063
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.212
ELB improved by 0.964313
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.377
ELB improved by 0.834171
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.625
ELB improved by 0.752302
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.914
ELB improved by 0.711184
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.215
ELB improved by 0.698416
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.51
ELB improved by 0.70592
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.779
ELB improved by 0.730414
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.007
ELB improved by 0.771933
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.173
ELB improved by 0.833936
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.246
ELB improved by 0.927222
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.166
ELB improved by 1.08041
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.834
ELB improved by 1.33135
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.26
ELB improved by 1.57476
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.687
ELB improved by 1.57209
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.306
ELB improved by 1.38101
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.174
ELB improved by 1.13266
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.286
ELB improved by 0.887354
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.611
ELB improved by 0.674994
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.109
ELB improved by 0.502688
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.741
ELB improved by 0.367482
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.475
ELB improved by 0.26617
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.28
ELB improved by 0.194773
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.134
ELB improved by 0.146525
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.02
ELB improved by 0.113862
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.929
ELB improved by 0.0908965
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.855
ELB improved by 0.0740298
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.794
ELB improved by 0.0613315
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.742
ELB improved by 0.0517317
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.697
ELB improved by 0.0445098
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.658
ELB improved by 0.0391034
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.623
ELB improved by 0.0350624
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.591
ELB improved by 0.0320266
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.562
ELB improved by 0.029692
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.534
ELB improved by 0.0277769
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.508
ELB improved by 0.0260109
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.484
ELB improved by 0.0241581
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.462
ELB improved by 0.0220731
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.442
ELB improved by 0.0197505
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.424
ELB improved by 0.0173222
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.409
ELB improved by 0.014987
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.397
ELB improved by 0.0129175
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.385
ELB improved by 0.0112026
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.376
ELB improved by 0.00984603
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-838.463
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-556.847
ELB improved by 281.616
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-491.875
ELB improved by 64.9715
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.826
ELB improved by 43.0492
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.786
ELB improved by 18.0402
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.291
ELB improved by 7.49545
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.879
ELB improved by 4.41137
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.649
ELB improved by 3.23069
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.938
ELB improved by 2.71004
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.465
ELB improved by 2.47355
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.089
ELB improved by 2.37551
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.741
ELB improved by 2.34868
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.378
ELB improved by 2.36279
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.975
ELB improved by 2.40333
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.518
ELB improved by 2.4571
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.017
ELB improved by 2.5009
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.523
ELB improved by 2.49348
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.142
ELB improved by 2.38065
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.015
ELB improved by 2.12717
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.256
ELB improved by 1.75883
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.896
ELB improved by 1.36072
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.876
ELB improved by 1.01944
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.103
ELB improved by 0.773528
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.489
ELB improved by 0.613985
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.98
ELB improved by 0.508648
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.558
ELB improved by 0.42252
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.222
ELB improved by 0.335511
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.97
ELB improved by 0.251761
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.786
ELB improved by 0.184493
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.648
ELB improved by 0.137957
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.54
ELB improved by 0.107718
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.452
ELB improved by 0.0877849
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.379
ELB improved by 0.0739119
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.315
ELB improved by 0.0636479
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.259
ELB improved by 0.05565
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.21
ELB improved by 0.04917
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.166
ELB improved by 0.0437722
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.127
ELB improved by 0.0391882
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.092
ELB improved by 0.0352425
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.06
ELB improved by 0.0318131
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.031
ELB improved by 0.028811
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.005
ELB improved by 0.026168
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.981
ELB improved by 0.0238306
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.959
ELB improved by 0.0217552
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.94
ELB improved by 0.0199064
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.921
ELB improved by 0.0182543
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.905
ELB improved by 0.0167739
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.889
ELB improved by 0.0154441
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.875
ELB improved by 0.0142467
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.862
ELB improved by 0.0131661
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.849
ELB improved by 0.0121889
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.838
ELB improved by 0.0113035
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.828
ELB improved by 0.0104998
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.818
ELB improved by 0.00976901
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-862.685
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-575.842
ELB improved by 286.842
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-516.976
ELB improved by 58.8663
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-476.219
ELB improved by 40.7565
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.836
ELB improved by 20.3833
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.291
ELB improved by 8.54495
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.694
ELB improved by 4.59761
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.275
ELB improved by 3.41822
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.248
ELB improved by 3.02702
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.329
ELB improved by 2.91962
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.42
ELB improved by 2.90915
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.515
ELB improved by 2.90453
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.679
ELB improved by 2.83619
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.038
ELB improved by 2.64138
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.741
ELB improved by 2.29667
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.888
ELB improved by 1.85278
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.479
ELB improved by 1.40876
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.44
ELB improved by 1.03883
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.68
ELB improved by 0.760812
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.12
ELB improved by 0.559619
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.704
ELB improved by 0.415637
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.39
ELB improved by 0.314316
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.146
ELB improved by 0.244501
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.949
ELB improved by 0.196666
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.786
ELB improved by 0.163237
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.647
ELB improved by 0.138942
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.526
ELB improved by 0.12046
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.42
ELB improved by 0.105806
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.327
ELB improved by 0.0938054
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.243
ELB improved by 0.0837439
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.168
ELB improved by 0.0751662
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.1
ELB improved by 0.0677654
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.039
ELB improved by 0.0613226
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.983
ELB improved by 0.0556746
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.932
ELB improved by 0.0506952
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.886
ELB improved by 0.0462841
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.844
ELB improved by 0.0423602
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.805
ELB improved by 0.0388568
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.769
ELB improved by 0.0357182
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.736
ELB improved by 0.0328981
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.706
ELB improved by 0.0303569
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.678
ELB improved by 0.0280612
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.652
ELB improved by 0.0259823
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.628
ELB improved by 0.0240954
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.605
ELB improved by 0.0223794
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.585
ELB improved by 0.0208156
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.565
ELB improved by 0.0193879
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.547
ELB improved by 0.0180823
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.53
ELB improved by 0.0168863
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.514
ELB improved by 0.0157891
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.5
ELB improved by 0.0147809
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.486
ELB improved by 0.0138534
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.473
ELB improved by 0.0129989
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.461
ELB improved by 0.0122107
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.449
ELB improved by 0.0114828
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.438
ELB improved by 0.0108098
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.428
ELB improved by 0.010187
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.418
ELB improved by 0.00960982
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-881.16
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-565.35
ELB improved by 315.81
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-505.645
ELB improved by 59.7055
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.687
ELB improved by 33.9574
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.474
ELB improved by 14.2136
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.917
ELB improved by 6.55622
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.249
ELB improved by 4.66843
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.984
ELB improved by 4.26454
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.729
ELB improved by 4.25595
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.397
ELB improved by 4.33121
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.134
ELB improved by 4.263
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.264
ELB improved by 3.87052
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.104
ELB improved by 3.15995
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.782
ELB improved by 2.32226
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.21
ELB improved by 1.57132
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.187
ELB improved by 1.0235
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.512
ELB improved by 0.675193
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.043
ELB improved by 0.46831
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.696
ELB improved by 0.347214
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.421
ELB improved by 0.274784
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.192
ELB improved by 0.229635
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.992
ELB improved by 0.20014
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.811
ELB improved by 0.180004
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.646
ELB improved by 0.165712
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.491
ELB improved by 0.155217
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.343
ELB improved by 0.147274
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.202
ELB improved by 0.141085
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.066
ELB improved by 0.136116
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.934
ELB improved by 0.13198
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.806
ELB improved by 0.128384
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.681
ELB improved by 0.125098
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.559
ELB improved by 0.12195
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.44
ELB improved by 0.118822
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.324
ELB improved by 0.115658
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.212
ELB improved by 0.112461
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.102
ELB improved by 0.109284
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.996
ELB improved by 0.106225
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.893
ELB improved by 0.103432
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.792
ELB improved by 0.101114
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.692
ELB improved by 0.0995867
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.593
ELB improved by 0.0993463
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.492
ELB improved by 0.101196
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.385
ELB improved by 0.106392
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.269
ELB improved by 0.11664
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.135
ELB improved by 0.133448
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.978
ELB improved by 0.156595
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.794
ELB improved by 0.184018
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.578
ELB improved by 0.21671
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.316
ELB improved by 0.261627
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.001
ELB improved by 0.315029
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.666
ELB improved by 0.335342
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.372
ELB improved by 0.293299
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.137
ELB improved by 0.234996
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.94
ELB improved by 0.197817
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.759
ELB improved by 0.180236
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.586
ELB improved by 0.173636
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.413
ELB improved by 0.172775
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.238
ELB improved by 0.175184
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.058
ELB improved by 0.179965
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.871
ELB improved by 0.187208
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.673
ELB improved by 0.197715
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.46
ELB improved by 0.21244
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.23
ELB improved by 0.230721
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.983
ELB improved by 0.246934
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.733
ELB improved by 0.250188
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.499
ELB improved by 0.234098
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.293
ELB improved by 0.205117
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.119
ELB improved by 0.173961
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.973
ELB improved by 0.146276
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.85
ELB improved by 0.12326
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.745
ELB improved by 0.104488
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.656
ELB improved by 0.0891798
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.58
ELB improved by 0.0765695
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.514
ELB improved by 0.0660127
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.457
ELB improved by 0.0570191
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.407
ELB improved by 0.0492512
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.365
ELB improved by 0.0424954
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.328
ELB improved by 0.0366204
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.297
ELB improved by 0.0315355
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.27
ELB improved by 0.0271634
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.246
ELB improved by 0.023428
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.226
ELB improved by 0.0202525
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.208
ELB improved by 0.0175617
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.193
ELB improved by 0.0152858
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.18
ELB improved by 0.0133617
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.168
ELB improved by 0.0117342
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.158
ELB improved by 0.0103559
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.148
ELB improved by 0.00918651
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
1.962 0.145 2.097
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.057 | 0.000 | 0.058 | |
| getPIPs | 0.053 | 0.001 | 0.054 | |
| graper | 0.079 | 0.009 | 0.087 | |
| makeExampleData | 0.01 | 0.00 | 0.01 | |
| makeExampleDataWithUnequalGroups | 0.012 | 0.000 | 0.012 | |
| plotELBO | 0.218 | 0.032 | 0.251 | |
| plotGroupPenalties | 0.858 | 0.047 | 0.905 | |
| plotPosterior | 0.468 | 0.016 | 0.484 | |
| predict.graper | 2.052 | 0.016 | 2.069 | |
| print.graper | 0.047 | 0.008 | 0.055 | |