Britta Velten
| Snapshot Date: 2024-05-30 18:28:32 -0400 (Thu, 30 May 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 2024-05-31 17:02:59 -0400 (Fri, 31 May 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" | 4753 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
| 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 | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: graper |
| Version: 1.20.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings graper_1.20.0.tar.gz |
| StartedAt: 2024-05-31 04:19:58 -0400 (Fri, 31 May 2024) |
| EndedAt: 2024-05-31 04:21:20 -0400 (Fri, 31 May 2024) |
| EllapsedTime: 82.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings graper_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/graper.Rcheck’
* using R version 4.4.0 (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=-842.062
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-593.882
ELB improved by 248.18
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-536.859
ELB improved by 57.0235
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-492.628
ELB improved by 44.2314
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.806
ELB improved by 23.8218
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.688
ELB improved by 10.1179
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.737
ELB improved by 5.95092
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.619
ELB improved by 5.11799
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.606
ELB improved by 5.01336
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.731
ELB improved by 4.87487
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.388
ELB improved by 4.34271
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.917
ELB improved by 3.47108
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.361
ELB improved by 2.55582
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.534
ELB improved by 1.8268
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.184
ELB improved by 1.35028
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.108
ELB improved by 1.07649
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.174
ELB improved by 0.93383
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.303
ELB improved by 0.87062
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.447
ELB improved by 0.855842
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.576
ELB improved by 0.87135
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.67
ELB improved by 0.906084
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.717
ELB improved by 0.953252
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.707
ELB improved by 1.00954
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.632
ELB improved by 1.07495
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.48
ELB improved by 1.15168
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.239
ELB improved by 1.24145
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.897
ELB improved by 1.34163
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.455
ELB improved by 1.44231
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.93
ELB improved by 1.52542
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.364
ELB improved by 1.56558
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.829
ELB improved by 1.53531
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.409
ELB improved by 1.41997
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.172
ELB improved by 1.23701
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.132
ELB improved by 1.03953
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.241
ELB improved by 0.891108
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.413
ELB improved by 0.828085
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.592
ELB improved by 0.821108
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.854
ELB improved by 0.737906
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.325
ELB improved by 0.528855
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.985
ELB improved by 0.340419
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.751
ELB improved by 0.234045
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.566
ELB improved by 0.184849
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.396
ELB improved by 0.170202
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.216
ELB improved by 0.179705
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.012
ELB improved by 0.204303
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.788
ELB improved by 0.224103
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.576
ELB improved by 0.211405
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.414
ELB improved by 0.161674
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.311
ELB improved by 0.103477
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.249
ELB improved by 0.0621087
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.209
ELB improved by 0.0398359
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.18
ELB improved by 0.0289398
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.157
ELB improved by 0.023291
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.137
ELB improved by 0.0198893
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.119
ELB improved by 0.0174952
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.104
ELB improved by 0.0156171
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.09
ELB improved by 0.0140533
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.077
ELB improved by 0.012712
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.065
ELB improved by 0.011545
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.055
ELB improved by 0.0105219
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.045
ELB improved by 0.00962113
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-870.603
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-556.493
ELB improved by 314.11
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-501.316
ELB improved by 55.1778
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.991
ELB improved by 29.3249
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.458
ELB improved by 12.5329
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.306
ELB improved by 6.15219
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.657
ELB improved by 4.649
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.148
ELB improved by 4.50826
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.319
ELB improved by 4.82928
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.923
ELB improved by 5.39618
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.946
ELB improved by 5.97685
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.788
ELB improved by 6.15771
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.176
ELB improved by 5.61196
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.604
ELB improved by 4.57268
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.945
ELB improved by 3.6588
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.884
ELB improved by 3.06096
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.523
ELB improved by 2.36047
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.849
ELB improved by 1.67425
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.693
ELB improved by 1.15636
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.894
ELB improved by 0.798788
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.317
ELB improved by 0.576794
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.879
ELB improved by 0.437867
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.534
ELB improved by 0.345018
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.255
ELB improved by 0.279004
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.026
ELB improved by 0.229882
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.833
ELB improved by 0.192141
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.671
ELB improved by 0.162463
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.532
ELB improved by 0.13871
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.413
ELB improved by 0.119423
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.309
ELB improved by 0.103571
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.219
ELB improved by 0.0904059
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.139
ELB improved by 0.0793701
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.069
ELB improved by 0.0700427
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.007
ELB improved by 0.062101
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.952
ELB improved by 0.0552941
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.903
ELB improved by 0.0494246
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.858
ELB improved by 0.0443358
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.818
ELB improved by 0.0399019
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.782
ELB improved by 0.0360211
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.75
ELB improved by 0.0326101
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.72
ELB improved by 0.0296007
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.693
ELB improved by 0.0269363
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.669
ELB improved by 0.0245695
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.646
ELB improved by 0.0224608
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.626
ELB improved by 0.0205769
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.607
ELB improved by 0.0188894
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.589
ELB improved by 0.0173741
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.573
ELB improved by 0.0160105
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.559
ELB improved by 0.0147806
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.545
ELB improved by 0.0136692
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.532
ELB improved by 0.012663
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.52
ELB improved by 0.0117504
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.51
ELB improved by 0.0109213
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.499
ELB improved by 0.0101669
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.49
ELB improved by 0.00947932
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-851.415
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-569.408
ELB improved by 282.007
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-512.055
ELB improved by 57.3531
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.643
ELB improved by 38.4125
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.328
ELB improved by 17.3142
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.774
ELB improved by 7.55463
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.578
ELB improved by 5.19576
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.878
ELB improved by 4.70003
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.267
ELB improved by 4.61054
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.608
ELB improved by 4.65993
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.924
ELB improved by 4.68356
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.429
ELB improved by 4.49516
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.489
ELB improved by 3.93947
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.412
ELB improved by 3.07686
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.221
ELB improved by 2.19109
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.721
ELB improved by 1.50028
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.698
ELB improved by 1.02317
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.99
ELB improved by 0.708101
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.483
ELB improved by 0.506769
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.104
ELB improved by 0.378697
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.81
ELB improved by 0.29466
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.573
ELB improved by 0.236794
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.378
ELB improved by 0.195036
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.214
ELB improved by 0.163716
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.075
ELB improved by 0.139488
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.954
ELB improved by 0.120264
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.85
ELB improved by 0.10468
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.758
ELB improved by 0.0918165
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.677
ELB improved by 0.0810374
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.605
ELB improved by 0.0718931
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.541
ELB improved by 0.0640581
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.484
ELB improved by 0.0572918
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.432
ELB improved by 0.0514113
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.386
ELB improved by 0.0462749
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.344
ELB improved by 0.0417697
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.306
ELB improved by 0.0378045
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.272
ELB improved by 0.0343039
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.241
ELB improved by 0.031205
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.212
ELB improved by 0.0284547
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.186
ELB improved by 0.0260079
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.163
ELB improved by 0.0238261
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.141
ELB improved by 0.0218762
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.121
ELB improved by 0.0201298
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.102
ELB improved by 0.0185624
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.085
ELB improved by 0.0171527
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.069
ELB improved by 0.0158825
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.054
ELB improved by 0.0147359
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.041
ELB improved by 0.0136989
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.028
ELB improved by 0.0127596
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.016
ELB improved by 0.0119074
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.005
ELB improved by 0.011133
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.994
ELB improved by 0.0104285
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.985
ELB improved by 0.00978661
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-857.379
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-581.245
ELB improved by 276.133
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-520.742
ELB improved by 60.5031
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-477.897
ELB improved by 42.845
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.056
ELB improved by 18.8413
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.175
ELB improved by 7.88138
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.056
ELB improved by 5.11897
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.368
ELB improved by 4.68789
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.384
ELB improved by 4.98423
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.972
ELB improved by 5.41181
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.578
ELB improved by 5.39415
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.999
ELB improved by 4.5784
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.671
ELB improved by 3.32857
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.364
ELB improved by 2.30669
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.631
ELB improved by 1.73273
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.152
ELB improved by 1.47921
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.76
ELB improved by 1.39199
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.4
ELB improved by 1.36038
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.077
ELB improved by 1.32216
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.803
ELB improved by 1.27411
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.575
ELB improved by 1.2285
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.384
ELB improved by 1.19099
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.219
ELB improved by 1.16513
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.066
ELB improved by 1.15236
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.917
ELB improved by 1.14932
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.769
ELB improved by 1.14753
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.633
ELB improved by 1.13698
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.522
ELB improved by 1.11018
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.459
ELB improved by 1.06289
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.466
ELB improved by 0.993181
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.564
ELB improved by 0.901848
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.771
ELB improved by 0.793299
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.096
ELB improved by 0.674944
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.54
ELB improved by 0.555863
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.095
ELB improved by 0.445391
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.744
ELB improved by 0.350928
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.468
ELB improved by 0.276009
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.248
ELB improved by 0.220229
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.067
ELB improved by 0.18095
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.911
ELB improved by 0.155533
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.768
ELB improved by 0.14337
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.62
ELB improved by 0.148182
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.44
ELB improved by 0.180056
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.195
ELB improved by 0.244985
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.894
ELB improved by 0.300852
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.61
ELB improved by 0.283656
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.385
ELB improved by 0.225128
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.214
ELB improved by 0.171121
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.083
ELB improved by 0.130471
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.979
ELB improved by 0.103963
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.89
ELB improved by 0.0891781
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.808
ELB improved by 0.0820343
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.729
ELB improved by 0.0788539
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.653
ELB improved by 0.0768358
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.579
ELB improved by 0.074053
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.509
ELB improved by 0.0697247
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.444
ELB improved by 0.0644107
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.385
ELB improved by 0.0594901
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.329
ELB improved by 0.0561187
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.274
ELB improved by 0.0544466
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.221
ELB improved by 0.0534543
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.169
ELB improved by 0.0513982
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.123
ELB improved by 0.0468352
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.083
ELB improved by 0.0396893
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.052
ELB improved by 0.0312999
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.028
ELB improved by 0.0233571
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.011
ELB improved by 0.016908
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.999
ELB improved by 0.0121854
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.99
ELB improved by 0.00894225
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.039 0.171 2.196
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.047 | 0.020 | 0.068 | |
| getPIPs | 0.052 | 0.012 | 0.064 | |
| graper | 0.081 | 0.028 | 0.109 | |
| makeExampleData | 0.008 | 0.003 | 0.011 | |
| makeExampleDataWithUnequalGroups | 0.002 | 0.011 | 0.013 | |
| plotELBO | 0.24 | 0.02 | 0.26 | |
| plotGroupPenalties | 0.856 | 0.048 | 0.904 | |
| plotPosterior | 0.456 | 0.028 | 0.483 | |
| predict.graper | 2.087 | 0.027 | 2.114 | |
| print.graper | 0.041 | 0.025 | 0.064 | |