Britta Velten
| Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 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 2024-06-14 14:37 -0400 (Fri, 14 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 |
| 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 | | ||||||||
|
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: 2024-06-12 23:44:38 -0400 (Wed, 12 Jun 2024) |
| EndedAt: 2024-06-12 23:45:59 -0400 (Wed, 12 Jun 2024) |
| EllapsedTime: 81.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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 4.4.0 (2024-04-24)
* 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 4.4.0 (2024-04-24) -- "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=-857.676
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-571.976
ELB improved by 285.699
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-511.656
ELB improved by 60.3201
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.659
ELB improved by 37.9976
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.356
ELB improved by 16.3023
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.046
ELB improved by 7.31012
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.964
ELB improved by 5.08244
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.214
ELB improved by 4.75011
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.343
ELB improved by 4.87061
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.5
ELB improved by 4.84316
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.189
ELB improved by 4.31071
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.892
ELB improved by 3.29738
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.666
ELB improved by 2.22605
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.206
ELB improved by 1.45943
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.203
ELB improved by 1.00331
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.482
ELB improved by 0.720935
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.949
ELB improved by 0.532498
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.54
ELB improved by 0.409924
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.207
ELB improved by 0.333015
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.922
ELB improved by 0.284696
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.668
ELB improved by 0.25375
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.435
ELB improved by 0.233562
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.214
ELB improved by 0.22025
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.003
ELB improved by 0.211464
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.797
ELB improved by 0.205721
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.595
ELB improved by 0.202044
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.395
ELB improved by 0.199779
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.197
ELB improved by 0.198482
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.999
ELB improved by 0.197874
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.801
ELB improved by 0.1978
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.603
ELB improved by 0.198219
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.404
ELB improved by 0.199179
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.203
ELB improved by 0.200805
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413
ELB improved by 0.203278
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.793
ELB improved by 0.206815
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.581
ELB improved by 0.211647
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.363
ELB improved by 0.217995
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.137
ELB improved by 0.226054
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.901
ELB improved by 0.235964
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.653
ELB improved by 0.247785
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.392
ELB improved by 0.261461
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.115
ELB improved by 0.27676
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.822
ELB improved by 0.29317
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.512
ELB improved by 0.309738
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.187
ELB improved by 0.32482
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.852
ELB improved by 0.335863
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.512
ELB improved by 0.339595
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.179
ELB improved by 0.333091
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.863
ELB improved by 0.315465
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.575
ELB improved by 0.288622
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.319
ELB improved by 0.256185
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.097
ELB improved by 0.221812
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.909
ELB improved by 0.188298
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.751
ELB improved by 0.157441
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.621
ELB improved by 0.130196
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.514
ELB improved by 0.10688
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.427
ELB improved by 0.0873831
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.355
ELB improved by 0.0713468
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.297
ELB improved by 0.0583061
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.249
ELB improved by 0.0477791
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.21
ELB improved by 0.0393174
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.177
ELB improved by 0.0325288
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.15
ELB improved by 0.0270834
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.128
ELB improved by 0.02271
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.108
ELB improved by 0.0191895
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.092
ELB improved by 0.0163467
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.078
ELB improved by 0.0140423
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.066
ELB improved by 0.0121659
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.055
ELB improved by 0.0106306
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.046
ELB improved by 0.00936736
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-855.156
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-567.291
ELB improved by 287.865
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-506.824
ELB improved by 60.4669
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.336
ELB improved by 42.4885
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.48
ELB improved by 19.8557
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.82
ELB improved by 7.66
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.859
ELB improved by 3.96079
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.197
ELB improved by 2.66244
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.143
ELB improved by 2.05356
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.417
ELB improved by 1.72602
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.905
ELB improved by 1.51228
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.555
ELB improved by 1.34994
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.34
ELB improved by 1.21479
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.243
ELB improved by 1.097
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.251
ELB improved by 0.992399
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.352
ELB improved by 0.898693
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.538
ELB improved by 0.814026
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.801
ELB improved by 0.736594
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.137
ELB improved by 0.664722
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.54
ELB improved by 0.597049
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.007
ELB improved by 0.532691
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.536
ELB improved by 0.471337
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.122
ELB improved by 0.413253
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.763
ELB improved by 0.359136
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.453
ELB improved by 0.309834
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.187
ELB improved by 0.266034
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.959
ELB improved by 0.228039
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.764
ELB improved by 0.195726
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.595
ELB improved by 0.168642
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.449
ELB improved by 0.14617
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.321
ELB improved by 0.127665
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.209
ELB improved by 0.112535
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.108
ELB improved by 0.100265
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.018
ELB improved by 0.0904127
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.935
ELB improved by 0.0825978
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.859
ELB improved by 0.0764955
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.787
ELB improved by 0.0718316
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.719
ELB improved by 0.0683788
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.653
ELB improved by 0.0659521
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.588
ELB improved by 0.0644035
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.525
ELB improved by 0.0636156
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.461
ELB improved by 0.063496
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.397
ELB improved by 0.0639715
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.332
ELB improved by 0.0649827
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.266
ELB improved by 0.0664787
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.197
ELB improved by 0.0684129
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.127
ELB improved by 0.0707373
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.053
ELB improved by 0.0733984
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.977
ELB improved by 0.0763325
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.897
ELB improved by 0.0794618
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.815
ELB improved by 0.0826913
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.729
ELB improved by 0.085908
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.64
ELB improved by 0.0889828
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.548
ELB improved by 0.0917768
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.454
ELB improved by 0.0941515
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.358
ELB improved by 0.095985
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.261
ELB improved by 0.0971916
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.163
ELB improved by 0.0977434
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.065
ELB improved by 0.0976911
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.968
ELB improved by 0.0971811
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.872
ELB improved by 0.0964675
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.776
ELB improved by 0.0959221
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.68
ELB improved by 0.0960453
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.582
ELB improved by 0.0974916
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.481
ELB improved by 0.101119
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.373
ELB improved by 0.108084
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.253
ELB improved by 0.119987
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.114
ELB improved by 0.139107
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.945
ELB improved by 0.168722
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.732
ELB improved by 0.213601
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.451
ELB improved by 0.280343
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.076
ELB improved by 0.374677
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.588
ELB improved by 0.488154
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408
ELB improved by 0.588708
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.339
ELB improved by 0.660374
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.614
ELB improved by 0.72509
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.798
ELB improved by 0.816112
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.796
ELB improved by 1.0025
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.382
ELB improved by 1.4138
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.517
ELB improved by 1.86446
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.743
ELB improved by 1.7747
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.34
ELB improved by 1.40217
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.222
ELB improved by 1.11841
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.262
ELB improved by 0.959747
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.53
ELB improved by 0.732649
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.08
ELB improved by 0.449472
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.82
ELB improved by 0.259831
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.664
ELB improved by 0.155827
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.566
ELB improved by 0.0986513
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.5
ELB improved by 0.0661976
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.452
ELB improved by 0.0471456
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.417
ELB improved by 0.035546
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.389
ELB improved by 0.0281892
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.365
ELB improved by 0.0233071
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.346
ELB improved by 0.0199083
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.328
ELB improved by 0.0174274
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.313
ELB improved by 0.0155355
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.299
ELB improved by 0.0140373
iteration 99
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.286
ELB improved by 0.0128137
iteration 100
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.274
ELB improved by 0.0117906
iteration 101
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.263
ELB improved by 0.01092
iteration 102
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.253
ELB improved by 0.0101704
iteration 103
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.243
ELB improved by 0.00952004
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-895.775
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-600.821
ELB improved by 294.954
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-540.135
ELB improved by 60.6862
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-499.515
ELB improved by 40.6194
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-477.962
ELB improved by 21.5527
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.58
ELB improved by 11.3822
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.043
ELB improved by 7.53765
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.506
ELB improved by 6.53698
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.941
ELB improved by 6.56476
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.917
ELB improved by 7.02351
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.72
ELB improved by 7.19734
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.216
ELB improved by 6.50386
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.102
ELB improved by 5.11417
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.378
ELB improved by 3.72436
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.607
ELB improved by 2.77079
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.383
ELB improved by 2.2238
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.556
ELB improved by 1.82676
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.151
ELB improved by 1.40552
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.132
ELB improved by 1.01842
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.428
ELB improved by 0.704722
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.944
ELB improved by 0.483353
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.596
ELB improved by 0.348251
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.33
ELB improved by 0.265946
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.118
ELB improved by 0.211678
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.945
ELB improved by 0.173062
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.801
ELB improved by 0.144107
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.68
ELB improved by 0.121652
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.576
ELB improved by 0.103837
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.486
ELB improved by 0.089469
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.409
ELB improved by 0.0777272
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.341
ELB improved by 0.0680256
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.281
ELB improved by 0.0599326
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.227
ELB improved by 0.0531241
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.18
ELB improved by 0.0473529
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.138
ELB improved by 0.0424274
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.1
ELB improved by 0.0381978
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.065
ELB improved by 0.0345455
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.034
ELB improved by 0.0313757
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.005
ELB improved by 0.0286118
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.979
ELB improved by 0.0261916
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.955
ELB improved by 0.0240641
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.933
ELB improved by 0.0221872
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.912
ELB improved by 0.0205257
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.893
ELB improved by 0.0190504
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.875
ELB improved by 0.0177366
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.859
ELB improved by 0.0165636
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.843
ELB improved by 0.0155134
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.829
ELB improved by 0.014571
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.815
ELB improved by 0.0137233
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.802
ELB improved by 0.0129592
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.79
ELB improved by 0.0122689
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.778
ELB improved by 0.011644
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.767
ELB improved by 0.0110773
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.756
ELB improved by 0.0105622
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.746
ELB improved by 0.0100932
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.737
ELB improved by 0.00966537
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-859.025
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-569.208
ELB improved by 289.817
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-506.499
ELB improved by 62.7083
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.722
ELB improved by 37.7775
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.449
ELB improved by 16.2725
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.658
ELB improved by 6.79111
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.9
ELB improved by 3.75846
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.11
ELB improved by 2.78955
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.739
ELB improved by 2.37127
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.632
ELB improved by 2.10666
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.76
ELB improved by 1.8721
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.133
ELB improved by 1.62699
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.764
ELB improved by 1.36926
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.649
ELB improved by 1.11502
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.764
ELB improved by 0.884691
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.071
ELB improved by 0.692828
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.528
ELB improved by 0.543747
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.094
ELB improved by 0.433236
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.741
ELB improved by 0.35305
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.447
ELB improved by 0.294615
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.196
ELB improved by 0.250777
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.98
ELB improved by 0.216192
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.793
ELB improved by 0.187279
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.631
ELB improved by 0.162076
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.491
ELB improved by 0.139884
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.37
ELB improved by 0.120646
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.266
ELB improved by 0.104362
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.175
ELB improved by 0.0908262
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.095
ELB improved by 0.079657
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.025
ELB improved by 0.0704128
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.962
ELB improved by 0.0626872
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.906
ELB improved by 0.0561488
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.855
ELB improved by 0.0505444
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.81
ELB improved by 0.0456878
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.768
ELB improved by 0.0414433
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.73
ELB improved by 0.0377115
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.696
ELB improved by 0.0344175
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.665
ELB improved by 0.0315027
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.636
ELB improved by 0.0289194
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.609
ELB improved by 0.026627
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.584
ELB improved by 0.0245904
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.562
ELB improved by 0.0227784
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.541
ELB improved by 0.0211635
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.521
ELB improved by 0.0197211
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.502
ELB improved by 0.0184293
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.485
ELB improved by 0.0172692
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.469
ELB improved by 0.0162238
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.454
ELB improved by 0.0152788
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.439
ELB improved by 0.0144214
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.426
ELB improved by 0.0136406
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.413
ELB improved by 0.0129272
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.4
ELB improved by 0.0122731
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.389
ELB improved by 0.0116712
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.378
ELB improved by 0.0111158
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.367
ELB improved by 0.0106015
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.357
ELB improved by 0.0101241
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.347
ELB improved by 0.00967969
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.126 0.188 2.304
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.065 | 0.003 | 0.068 | |
| getPIPs | 0.043 | 0.020 | 0.063 | |
| graper | 0.078 | 0.028 | 0.105 | |
| makeExampleData | 0.011 | 0.000 | 0.012 | |
| makeExampleDataWithUnequalGroups | 0.013 | 0.000 | 0.013 | |
| plotELBO | 0.216 | 0.040 | 0.255 | |
| plotGroupPenalties | 0.852 | 0.068 | 0.920 | |
| plotPosterior | 0.440 | 0.027 | 0.467 | |
| predict.graper | 2.072 | 0.052 | 2.124 | |
| print.graper | 0.052 | 0.011 | 0.064 | |