Britta Velten
| Snapshot Date: 2024-12-12 13:40 -0500 (Thu, 12 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: 91803f0 |
| git_last_commit_date: 2024-10-29 10:33:50 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-13 11:46 -0500 (Fri, 13 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4752 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4464 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4416 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4371 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4318 |
| 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 893/2273 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.23.0 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: graper |
| Version: 1.23.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings graper_1.23.0.tar.gz |
| StartedAt: 2024-12-13 11:55:08 -0000 (Fri, 13 Dec 2024) |
| EndedAt: 2024-12-13 11:56:14 -0000 (Fri, 13 Dec 2024) |
| EllapsedTime: 65.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings graper_1.23.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/graper.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.23.0’
* 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: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
installed size is 6.1Mb
sub-directories of 1Mb or more:
libs 5.9Mb
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL graper
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘graper’ ...
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++11
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c fit_graper.cpp -o fit_graper.o
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/R/R-4.5.0-devel_2024-11-24/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)"
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -lopenblas -lgfortran -lm -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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=-847.993
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-575.033
ELB improved by 272.96
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-516.819
ELB improved by 58.2133
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-475.074
ELB improved by 41.7455
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.294
ELB improved by 20.7797
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.402
ELB improved by 8.89227
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.605
ELB improved by 5.79686
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.385
ELB improved by 5.22047
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.217
ELB improved by 5.16802
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.045
ELB improved by 5.17171
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.116
ELB improved by 4.92847
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.798
ELB improved by 4.31876
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.339
ELB improved by 3.45826
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.767
ELB improved by 2.57217
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.886
ELB improved by 1.88105
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.414
ELB improved by 1.47242
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.141
ELB improved by 1.27319
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.978
ELB improved by 1.16265
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.906
ELB improved by 1.07204
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.919
ELB improved by 0.987061
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.031
ELB improved by 0.888199
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.285
ELB improved by 0.745767
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.714
ELB improved by 0.570633
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.294
ELB improved by 0.420669
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.972
ELB improved by 0.32174
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.711
ELB improved by 0.260463
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.491
ELB improved by 0.220635
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.297
ELB improved by 0.19346
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.122
ELB improved by 0.175354
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.956
ELB improved by 0.165688
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.79
ELB improved by 0.165769
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.613
ELB improved by 0.177449
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.415
ELB improved by 0.197825
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.205
ELB improved by 0.210014
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.014
ELB improved by 0.191147
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.868
ELB improved by 0.146214
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.764
ELB improved by 0.103333
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.689
ELB improved by 0.0757426
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.629
ELB improved by 0.0600409
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.578
ELB improved by 0.0505674
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.534
ELB improved by 0.0440802
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.495
ELB improved by 0.0391278
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.46
ELB improved by 0.0350813
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.428
ELB improved by 0.0316473
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.4
ELB improved by 0.0286717
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.373
ELB improved by 0.0260621
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.35
ELB improved by 0.0237564
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.328
ELB improved by 0.0217088
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.308
ELB improved by 0.0198839
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.29
ELB improved by 0.0182526
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.273
ELB improved by 0.0167908
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.258
ELB improved by 0.015478
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.243
ELB improved by 0.0142966
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.23
ELB improved by 0.0132316
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.218
ELB improved by 0.0122697
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.206
ELB improved by 0.0113995
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.196
ELB improved by 0.0106111
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.186
ELB improved by 0.00989562
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-892.334
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-613.861
ELB improved by 278.473
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-554.14
ELB improved by 59.7208
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-506.782
ELB improved by 47.3581
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-480.377
ELB improved by 26.4051
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.028
ELB improved by 11.3488
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.183
ELB improved by 5.84508
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.1
ELB improved by 4.08235
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.456
ELB improved by 3.64487
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.755
ELB improved by 3.70022
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.788
ELB improved by 3.9677
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.458
ELB improved by 4.32977
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.848
ELB improved by 4.61015
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.375
ELB improved by 4.47268
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.622
ELB improved by 3.75283
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.843
ELB improved by 2.77887
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.893
ELB improved by 1.95012
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.496
ELB improved by 1.39708
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.435
ELB improved by 1.06143
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.587
ELB improved by 0.847839
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.888
ELB improved by 0.698781
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.291
ELB improved by 0.597601
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.753
ELB improved by 0.53718
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.246
ELB improved by 0.507352
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.747
ELB improved by 0.498725
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.242
ELB improved by 0.504858
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.72
ELB improved by 0.52202
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.171
ELB improved by 0.548939
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.585
ELB improved by 0.585934
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.954
ELB improved by 0.631384
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.278
ELB improved by 0.676426
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.571
ELB improved by 0.706836
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.855
ELB improved by 0.715733
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.148
ELB improved by 0.706725
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.465
ELB improved by 0.683712
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.818
ELB improved by 0.647179
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.22
ELB improved by 0.597555
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.682
ELB improved by 0.537561
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.211
ELB improved by 0.471872
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.805
ELB improved by 0.405728
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.461
ELB improved by 0.343669
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.172
ELB improved by 0.288731
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.93
ELB improved by 0.242183
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.727
ELB improved by 0.203673
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.555
ELB improved by 0.171645
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.411
ELB improved by 0.144035
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.292
ELB improved by 0.119251
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.195
ELB improved by 0.0969202
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.117
ELB improved by 0.0776323
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.055
ELB improved by 0.0619588
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.005
ELB improved by 0.0498454
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.965
ELB improved by 0.0407349
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.931
ELB improved by 0.0339327
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.902
ELB improved by 0.0288326
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.877
ELB improved by 0.0249762
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.855
ELB improved by 0.0220361
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.835
ELB improved by 0.0197835
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.817
ELB improved by 0.0180605
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.8
ELB improved by 0.0167609
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.784
ELB improved by 0.0158172
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.769
ELB improved by 0.0151924
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.754
ELB improved by 0.0148762
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.739
ELB improved by 0.0148826
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.724
ELB improved by 0.0152511
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.708
ELB improved by 0.0160467
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.691
ELB improved by 0.0173586
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.671
ELB improved by 0.0192908
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.649
ELB improved by 0.0219348
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.624
ELB improved by 0.0253099
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.595
ELB improved by 0.02926
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.562
ELB improved by 0.0333203
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.525
ELB improved by 0.0366351
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.487
ELB improved by 0.0380938
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.45
ELB improved by 0.036822
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.417
ELB improved by 0.0328176
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.39
ELB improved by 0.0271187
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.369
ELB improved by 0.0211967
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.353
ELB improved by 0.0161433
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.34
ELB improved by 0.0123571
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.331
ELB improved by 0.00973666
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-854.324
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-582.18
ELB improved by 272.144
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-523.143
ELB improved by 59.0372
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-483.513
ELB improved by 39.6298
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.828
ELB improved by 18.6846
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.86
ELB improved by 8.9679
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.935
ELB improved by 5.92489
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.607
ELB improved by 5.32818
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.153
ELB improved by 5.4539
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.617
ELB improved by 5.53672
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.527
ELB improved by 5.08966
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.445
ELB improved by 4.08171
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.488
ELB improved by 2.95743
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.391
ELB improved by 2.09679
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.867
ELB improved by 1.52349
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.747
ELB improved by 1.12005
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.908
ELB improved by 0.83971
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.24
ELB improved by 0.667283
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.667
ELB improved by 0.573253
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.141
ELB improved by 0.526198
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.651
ELB improved by 0.489862
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.22
ELB improved by 0.431025
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.868
ELB improved by 0.352539
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.586
ELB improved by 0.281476
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.356
ELB improved by 0.23022
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.16
ELB improved by 0.195732
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.988
ELB improved by 0.172184
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.832
ELB improved by 0.155482
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.689
ELB improved by 0.143273
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.555
ELB improved by 0.134249
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.427
ELB improved by 0.127653
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.304
ELB improved by 0.123023
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.184
ELB improved by 0.120055
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.066
ELB improved by 0.118542
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.947
ELB improved by 0.118338
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.828
ELB improved by 0.119343
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.706
ELB improved by 0.121485
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.582
ELB improved by 0.124718
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.453
ELB improved by 0.129013
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.318
ELB improved by 0.134357
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.178
ELB improved by 0.140751
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.029
ELB improved by 0.148207
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.873
ELB improved by 0.156756
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.706
ELB improved by 0.166443
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.529
ELB improved by 0.177337
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.339
ELB improved by 0.189529
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.136
ELB improved by 0.203127
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.918
ELB improved by 0.21824
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.683
ELB improved by 0.234946
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.43
ELB improved by 0.253225
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.157
ELB improved by 0.272855
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.864
ELB improved by 0.29327
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.55
ELB improved by 0.313373
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.219
ELB improved by 0.331392
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.874
ELB improved by 0.344858
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.523
ELB improved by 0.350911
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.176
ELB improved by 0.346983
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.844
ELB improved by 0.331718
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.539
ELB improved by 0.305684
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.267
ELB improved by 0.271408
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.035
ELB improved by 0.232684
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.841
ELB improved by 0.193475
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.684
ELB improved by 0.156973
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.559
ELB improved by 0.12513
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.46
ELB improved by 0.0986849
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.383
ELB improved by 0.0774933
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.322
ELB improved by 0.0609202
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.274
ELB improved by 0.0481524
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.235
ELB improved by 0.0383907
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.205
ELB improved by 0.0309419
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.179
ELB improved by 0.0252454
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.158
ELB improved by 0.0208664
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.141
ELB improved by 0.0174759
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.126
ELB improved by 0.0148286
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.113
ELB improved by 0.0127428
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.102
ELB improved by 0.0110837
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.093
ELB improved by 0.00975144
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-852.814
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-585.392
ELB improved by 267.422
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-523.451
ELB improved by 61.9413
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-479.238
ELB improved by 44.2134
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.77
ELB improved by 20.4676
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.788
ELB improved by 8.98192
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.325
ELB improved by 6.46355
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.886
ELB improved by 6.43813
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.074
ELB improved by 6.81231
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.453
ELB improved by 6.62105
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.869
ELB improved by 5.58363
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.667
ELB improved by 4.20268
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.618
ELB improved by 3.04846
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.348
ELB improved by 2.2704
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.518
ELB improved by 1.82966
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.848
ELB improved by 1.66996
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.156
ELB improved by 1.69193
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.411
ELB improved by 1.74578
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.651
ELB improved by 1.75951
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.881
ELB improved by 1.76998
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.087
ELB improved by 1.79404
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.268
ELB improved by 1.8195
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.428
ELB improved by 1.83955
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.572
ELB improved by 1.85554
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.701
ELB improved by 1.87165
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.808
ELB improved by 1.89251
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.889
ELB improved by 1.91977
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.949
ELB improved by 1.93949
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.047
ELB improved by 1.90243
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.311
ELB improved by 1.73607
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.886
ELB improved by 1.4249
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.833
ELB improved by 1.05269
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.113
ELB improved by 0.719945
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.64
ELB improved by 0.47297
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.33
ELB improved by 0.309591
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.122
ELB improved by 0.208162
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.976
ELB improved by 0.146348
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.868
ELB improved by 0.10791
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.785
ELB improved by 0.0828848
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.719
ELB improved by 0.065665
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.666
ELB improved by 0.0531922
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.622
ELB improved by 0.0437811
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.586
ELB improved by 0.0364667
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.555
ELB improved by 0.030664
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.529
ELB improved by 0.0259959
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.507
ELB improved by 0.0222041
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.488
ELB improved by 0.0191028
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.471
ELB improved by 0.0165529
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.457
ELB improved by 0.0144474
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.444
ELB improved by 0.0127024
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.433
ELB improved by 0.011251
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.423
ELB improved by 0.0100396
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.414
ELB improved by 0.00902509
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.695 0.126 2.812
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.054 | 0.001 | 0.054 | |
| getPIPs | 0.049 | 0.000 | 0.050 | |
| graper | 0.068 | 0.008 | 0.076 | |
| makeExampleData | 0.009 | 0.000 | 0.009 | |
| makeExampleDataWithUnequalGroups | 0.029 | 0.000 | 0.029 | |
| plotELBO | 0.250 | 0.004 | 0.255 | |
| plotGroupPenalties | 0.960 | 0.008 | 0.970 | |
| plotPosterior | 0.747 | 0.000 | 0.749 | |
| predict.graper | 1.007 | 0.008 | 1.017 | |
| print.graper | 0.040 | 0.008 | 0.049 | |