Britta Velten
| Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: RELEASE_3_20 |
| git_last_commit: 04d5a90 |
| git_last_commit_date: 2024-10-29 10:33:50 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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 899/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.22.0 (landing page) Britta Velten
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | 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. |
| Package: graper |
| Version: 1.22.0 |
| 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_1.22.0.tar.gz |
| StartedAt: 2024-11-20 04:01:05 -0500 (Wed, 20 Nov 2024) |
| EndedAt: 2024-11-20 04:02:26 -0500 (Wed, 20 Nov 2024) |
| EllapsedTime: 80.9 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_1.22.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/graper.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.22.0’
* 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 13.2.0-23ubuntu4) 13.2.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 6.0Mb
sub-directories of 1Mb or more:
libs 5.8Mb
* 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
‘/media/volume/teran2_disk/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 ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘graper’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/media/volume/teran2_disk/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'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/media/volume/teran2_disk/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 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11,
from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
from /media/volume/teran2_disk/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:
/media/volume/teran2_disk/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 /media/volume/teran2_disk/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
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=-888.055
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-600.107
ELB improved by 287.948
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-540.22
ELB improved by 59.8863
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-494.545
ELB improved by 45.6756
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.479
ELB improved by 23.066
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.111
ELB improved by 10.3675
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.725
ELB improved by 7.38624
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.031
ELB improved by 7.6942
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.477
ELB improved by 8.55415
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.035
ELB improved by 8.44205
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.301
ELB improved by 6.73418
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.872
ELB improved by 4.4284
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.15
ELB improved by 2.72244
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.27
ELB improved by 1.87969
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.734
ELB improved by 1.53621
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.383
ELB improved by 1.35131
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.163
ELB improved by 1.21952
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.045
ELB improved by 1.11757
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.1
ELB improved by 0.944981
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.331
ELB improved by 0.769841
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.669
ELB improved by 0.661301
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.072
ELB improved by 0.59747
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.511
ELB improved by 0.560986
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.965
ELB improved by 0.545653
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.421
ELB improved by 0.544588
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.869
ELB improved by 0.551296
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.307
ELB improved by 0.562036
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.732
ELB improved by 0.575345
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.141
ELB improved by 0.591183
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.53
ELB improved by 0.610937
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.891
ELB improved by 0.638969
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.203
ELB improved by 0.687942
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.407
ELB improved by 0.796142
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.339
ELB improved by 1.06746
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.778
ELB improved by 1.56111
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.891
ELB improved by 1.88681
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.891
ELB improved by 2.00046
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.028
ELB improved by 1.86265
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.298
ELB improved by 1.73017
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.45
ELB improved by 1.84837
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.976
ELB improved by 1.47391
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.021
ELB improved by 0.954584
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.409
ELB improved by 0.61257
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.987
ELB improved by 0.421815
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.681
ELB improved by 0.305924
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.457
ELB improved by 0.223469
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.294
ELB improved by 0.163255
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.173
ELB improved by 0.121664
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.079
ELB improved by 0.0939149
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.003
ELB improved by 0.0751407
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.942
ELB improved by 0.0618709
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.89
ELB improved by 0.0520164
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.845
ELB improved by 0.0443831
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.807
ELB improved by 0.0382796
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.774
ELB improved by 0.0332872
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.745
ELB improved by 0.0291377
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.719
ELB improved by 0.0256491
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.696
ELB improved by 0.0226918
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.676
ELB improved by 0.0201691
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.658
ELB improved by 0.0180066
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.642
ELB improved by 0.0161455
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.627
ELB improved by 0.0145386
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.614
ELB improved by 0.013147
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.602
ELB improved by 0.0119386
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.591
ELB improved by 0.0108867
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.581
ELB improved by 0.00996878
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-842.315
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-534.819
ELB improved by 307.495
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-477.615
ELB improved by 57.2044
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.01
ELB improved by 26.6047
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.974
ELB improved by 9.03658
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.819
ELB improved by 4.15491
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.15
ELB improved by 2.66839
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.037
ELB improved by 2.11322
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.098
ELB improved by 1.93931
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.151
ELB improved by 1.94644
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.097
ELB improved by 2.05413
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.887
ELB improved by 2.2108
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.536
ELB improved by 2.35091
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.148
ELB improved by 2.38783
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.89
ELB improved by 2.25826
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.902
ELB improved by 1.98768
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.216
ELB improved by 1.68577
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.759
ELB improved by 1.45709
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.42
ELB improved by 1.33853
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.102
ELB improved by 1.31877
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.726
ELB improved by 1.37584
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.247
ELB improved by 1.47879
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.668
ELB improved by 1.57913
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.025
ELB improved by 1.6428
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.354
ELB improved by 1.67111
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.679
ELB improved by 1.67487
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.023
ELB improved by 1.65602
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.417
ELB improved by 1.60574
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.907
ELB improved by 1.51033
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.545
ELB improved by 1.3616
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.38
ELB improved by 1.16595
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.433
ELB improved by 0.946835
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.697
ELB improved by 0.736057
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.139
ELB improved by 0.557756
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.72
ELB improved by 0.419261
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.404
ELB improved by 0.315379
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.167
ELB improved by 0.237666
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.987
ELB improved by 0.179599
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.85
ELB improved by 0.136777
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.744
ELB improved by 0.105673
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.661
ELB improved by 0.0832072
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.594
ELB improved by 0.0668876
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.54
ELB improved by 0.0548762
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.494
ELB improved by 0.0458853
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.455
ELB improved by 0.0390285
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.421
ELB improved by 0.0336959
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.391
ELB improved by 0.0294661
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.365
ELB improved by 0.0260461
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.342
ELB improved by 0.0232305
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.321
ELB improved by 0.0208742
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.302
ELB improved by 0.0188734
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.285
ELB improved by 0.0171531
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.27
ELB improved by 0.0156581
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.255
ELB improved by 0.0143472
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.242
ELB improved by 0.0131893
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.23
ELB improved by 0.0121601
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.219
ELB improved by 0.0112408
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.208
ELB improved by 0.0104162
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.199
ELB improved by 0.00967377
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-872.569
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-578.147
ELB improved by 294.422
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-517.054
ELB improved by 61.0927
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-479.46
ELB improved by 37.5941
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.727
ELB improved by 15.7336
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.39
ELB improved by 6.33661
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.444
ELB improved by 3.94616
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.965
ELB improved by 3.47825
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.459
ELB improved by 3.50617
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.739
ELB improved by 3.72041
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.812
ELB improved by 3.92668
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.906
ELB improved by 3.9061
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.474
ELB improved by 3.43224
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.866
ELB improved by 2.60764
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.057
ELB improved by 1.80966
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.81
ELB improved by 1.24639
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.9
ELB improved by 0.909911
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.17
ELB improved by 0.730194
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.523
ELB improved by 0.646946
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.906
ELB improved by 0.617557
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.292
ELB improved by 0.613146
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.677
ELB improved by 0.615003
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.065
ELB improved by 0.612794
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.461
ELB improved by 0.603887
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.869
ELB improved by 0.591317
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.29
ELB improved by 0.579
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.721
ELB improved by 0.569203
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.158
ELB improved by 0.563021
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.597
ELB improved by 0.560911
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.035
ELB improved by 0.562616
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.468
ELB improved by 0.566964
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.896
ELB improved by 0.571774
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.322
ELB improved by 0.573975
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.752
ELB improved by 0.570019
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.195
ELB improved by 0.556613
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.664
ELB improved by 0.531607
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.169
ELB improved by 0.494678
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.722
ELB improved by 0.447509
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.328
ELB improved by 0.393434
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.991
ELB improved by 0.336786
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.709
ELB improved by 0.282046
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.476
ELB improved by 0.232847
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.285
ELB improved by 0.19119
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.128
ELB improved by 0.157349
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.997
ELB improved by 0.130401
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.889
ELB improved by 0.108929
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.797
ELB improved by 0.0915605
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.72
ELB improved by 0.077229
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.655
ELB improved by 0.0652193
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.599
ELB improved by 0.0550914
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.553
ELB improved by 0.0465651
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.513
ELB improved by 0.0394286
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.48
ELB improved by 0.0334919
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.451
ELB improved by 0.0285753
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.427
ELB improved by 0.0245122
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.406
ELB improved by 0.0211548
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.387
ELB improved by 0.0183762
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.371
ELB improved by 0.0160706
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.357
ELB improved by 0.0141506
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.345
ELB improved by 0.0125449
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.333
ELB improved by 0.0111959
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.323
ELB improved by 0.0100566
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.314
ELB improved by 0.0090892
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-856.178
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-572.724
ELB improved by 283.454
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-512.515
ELB improved by 60.2089
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.39
ELB improved by 39.1253
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.551
ELB improved by 18.8389
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.051
ELB improved by 7.49966
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.715
ELB improved by 3.336
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.848
ELB improved by 1.86767
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.589
ELB improved by 1.25915
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.624
ELB improved by 0.964516
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.817
ELB improved by 0.806608
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.104
ELB improved by 0.713919
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.449
ELB improved by 0.654715
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.834
ELB improved by 0.614604
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.247
ELB improved by 0.586895
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.679
ELB improved by 0.568387
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.121
ELB improved by 0.557478
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.568
ELB improved by 0.553244
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.013
ELB improved by 0.554914
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.452
ELB improved by 0.561504
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.88
ELB improved by 0.5715
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.298
ELB improved by 0.582601
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.706
ELB improved by 0.591661
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.111
ELB improved by 0.595127
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.521
ELB improved by 0.590165
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.945
ELB improved by 0.576197
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.389
ELB improved by 0.555755
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.855
ELB improved by 0.533639
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.34
ELB improved by 0.514663
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.839
ELB improved by 0.501505
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.345
ELB improved by 0.493849
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.856
ELB improved by 0.4889
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.374
ELB improved by 0.482707
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.902
ELB improved by 0.471658
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.448
ELB improved by 0.453675
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.019
ELB improved by 0.428698
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.621
ELB improved by 0.398362
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.256
ELB improved by 0.365144
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.925
ELB improved by 0.331477
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.625
ELB improved by 0.299217
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.356
ELB improved by 0.269498
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.113
ELB improved by 0.242842
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.894
ELB improved by 0.219347
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.695
ELB improved by 0.198869
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.514
ELB improved by 0.181158
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.348
ELB improved by 0.16594
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.195
ELB improved by 0.152972
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.053
ELB improved by 0.142078
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.919
ELB improved by 0.133172
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.793
ELB improved by 0.126306
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.671
ELB improved by 0.12174
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.551
ELB improved by 0.120077
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.429
ELB improved by 0.122478
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.298
ELB improved by 0.130899
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.15
ELB improved by 0.147871
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.976
ELB improved by 0.174363
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.77
ELB improved by 0.205297
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.539
ELB improved by 0.23167
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.28
ELB improved by 0.258703
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.966
ELB improved by 0.314049
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.555
ELB improved by 0.410585
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.082
ELB improved by 0.473148
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.647
ELB improved by 0.435287
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.286
ELB improved by 0.361376
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.984
ELB improved by 0.30107
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.726
ELB improved by 0.258784
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.497
ELB improved by 0.228908
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.29
ELB improved by 0.206388
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.102
ELB improved by 0.188294
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.928
ELB improved by 0.173657
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.766
ELB improved by 0.162833
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.609
ELB improved by 0.156501
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.455
ELB improved by 0.153975
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.304
ELB improved by 0.151138
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.163
ELB improved by 0.141246
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.041
ELB improved by 0.121372
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.945
ELB improved by 0.0964674
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.871
ELB improved by 0.0736154
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.815
ELB improved by 0.0561464
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.771
ELB improved by 0.043976
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.735
ELB improved by 0.0358599
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.705
ELB improved by 0.0306134
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.677
ELB improved by 0.0274306
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.651
ELB improved by 0.0258775
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.626
ELB improved by 0.0258334
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.598
ELB improved by 0.0274602
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.567
ELB improved by 0.0311823
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.529
ELB improved by 0.0375725
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.482
ELB improved by 0.0468838
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.425
ELB improved by 0.057965
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.357
ELB improved by 0.0672549
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.287
ELB improved by 0.0703479
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.221
ELB improved by 0.0663454
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.161
ELB improved by 0.0590774
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.108
ELB improved by 0.0536046
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.053
ELB improved by 0.0544531
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.985
ELB improved by 0.0681666
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.877
ELB improved by 0.107908
iteration 99
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.691
ELB improved by 0.186573
iteration 100
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.427
ELB improved by 0.264148
iteration 101
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.169
ELB improved by 0.257258
iteration 102
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.978
ELB improved by 0.191788
iteration 103
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.846
ELB improved by 0.131252
iteration 104
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.757
ELB improved by 0.0895891
iteration 105
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.694
ELB improved by 0.0628078
iteration 106
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.648
ELB improved by 0.0457415
iteration 107
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.614
ELB improved by 0.0346063
iteration 108
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.587
ELB improved by 0.0270149
iteration 109
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.565
ELB improved by 0.0215736
iteration 110
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.547
ELB improved by 0.017502
iteration 111
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.533
ELB improved by 0.0143663
iteration 112
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.521
ELB improved by 0.0119158
iteration 113
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.511
ELB improved by 0.00999191
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
1.509 0.337 2.039
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.029 | 0.008 | 0.037 | |
| getPIPs | 0.030 | 0.004 | 0.034 | |
| graper | 0.052 | 0.004 | 0.058 | |
| makeExampleData | 0.007 | 0.000 | 0.006 | |
| makeExampleDataWithUnequalGroups | 0.006 | 0.002 | 0.008 | |
| plotELBO | 0.137 | 0.013 | 0.150 | |
| plotGroupPenalties | 0.536 | 0.002 | 0.538 | |
| plotPosterior | 0.686 | 0.016 | 1.032 | |
| predict.graper | 1.264 | 0.018 | 1.503 | |
| print.graper | 0.032 | 0.005 | 0.038 | |