Britta Velten
| Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: RELEASE_3_19 |
| git_last_commit: a4dfa52 |
| git_last_commit_date: 2024-04-30 11:11:42 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-21 17:38 -0400 (Fri, 21 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4758 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4492 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4506 |
| kjohnson1 | macOS 13.6.6 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 | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | 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: 2024-06-19 23:50:36 -0400 (Wed, 19 Jun 2024) |
| EndedAt: 2024-06-19 23:51:58 -0400 (Wed, 19 Jun 2024) |
| EllapsedTime: 81.3 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=-860.179
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-561.919
ELB improved by 298.26
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-504.869
ELB improved by 57.0502
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.135
ELB improved by 36.7338
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.2
ELB improved by 16.9356
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.74
ELB improved by 7.45986
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.235
ELB improved by 4.50468
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.232
ELB improved by 4.00305
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.995
ELB improved by 4.23701
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.237
ELB improved by 4.75823
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.943
ELB improved by 5.29423
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.445
ELB improved by 5.49725
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.373
ELB improved by 5.072
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.347
ELB improved by 4.02643
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.562
ELB improved by 2.78454
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.753
ELB improved by 1.80944
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.554
ELB improved by 1.19928
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.69
ELB improved by 0.86344
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.001
ELB improved by 0.688994
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.403
ELB improved by 0.598414
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.852
ELB improved by 0.550598
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.327
ELB improved by 0.524726
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.818
ELB improved by 0.509434
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.32
ELB improved by 0.497882
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.834
ELB improved by 0.485802
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.364
ELB improved by 0.470744
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.912
ELB improved by 0.451712
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.483
ELB improved by 0.428811
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.08
ELB improved by 0.402858
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.705
ELB improved by 0.374995
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.359
ELB improved by 0.346402
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.041
ELB improved by 0.318134
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.75
ELB improved by 0.291048
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.484
ELB improved by 0.265806
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.241
ELB improved by 0.242894
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.018
ELB improved by 0.222675
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.813
ELB improved by 0.20546
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.621
ELB improved by 0.19164
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.439
ELB improved by 0.181927
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.261
ELB improved by 0.177895
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.078
ELB improved by 0.183396
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.869
ELB improved by 0.208615
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.588
ELB improved by 0.281189
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.128
ELB improved by 0.459981
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.357
ELB improved by 0.771638
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.176
ELB improved by 1.18059
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.647
ELB improved by 1.52911
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.259
ELB improved by 1.38817
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.116
ELB improved by 1.1426
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.173
ELB improved by 0.942722
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.42
ELB improved by 0.753372
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.846
ELB improved by 0.573681
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.428
ELB improved by 0.418654
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.129
ELB improved by 0.298403
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.917
ELB improved by 0.212294
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.764
ELB improved by 0.153071
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.651
ELB improved by 0.112525
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.567
ELB improved by 0.0842938
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.503
ELB improved by 0.0641765
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.453
ELB improved by 0.0495444
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.415
ELB improved by 0.0387392
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.384
ELB improved by 0.030676
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.359
ELB improved by 0.0246139
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.339
ELB improved by 0.0200285
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.323
ELB improved by 0.0165385
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.309
ELB improved by 0.0138627
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.297
ELB improved by 0.0117927
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.287
ELB improved by 0.0101744
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.278
ELB improved by 0.00889404
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-860.772
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-579.591
ELB improved by 281.181
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-520.423
ELB improved by 59.1681
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-479.373
ELB improved by 41.0496
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.227
ELB improved by 18.1459
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.35
ELB improved by 7.87663
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.273
ELB improved by 5.07699
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.755
ELB improved by 4.5184
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.25
ELB improved by 4.50531
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.726
ELB improved by 4.5242
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.436
ELB improved by 4.28986
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.774
ELB improved by 3.66128
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.995
ELB improved by 2.77971
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.046
ELB improved by 1.94831
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.704
ELB improved by 1.34262
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.75
ELB improved by 0.953804
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.038
ELB improved by 0.711654
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.476
ELB improved by 0.562671
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418
ELB improved by 0.475845
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.572
ELB improved by 0.427915
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.178
ELB improved by 0.393899
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.827
ELB improved by 0.351376
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.531
ELB improved by 0.296119
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.286
ELB improved by 0.244278
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.077
ELB improved by 0.209554
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.884
ELB improved by 0.192388
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.696
ELB improved by 0.188321
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.503
ELB improved by 0.193315
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.3
ELB improved by 0.202283
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.094
ELB improved by 0.206014
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.901
ELB improved by 0.193339
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.739
ELB improved by 0.162076
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.615
ELB improved by 0.123928
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.523
ELB improved by 0.0919151
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.453
ELB improved by 0.0700914
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.397
ELB improved by 0.0562799
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.349
ELB improved by 0.0473118
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.308
ELB improved by 0.0410152
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.272
ELB improved by 0.0362148
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.24
ELB improved by 0.0323251
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.211
ELB improved by 0.0290525
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.185
ELB improved by 0.0262381
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.161
ELB improved by 0.0237863
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.139
ELB improved by 0.0216324
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.119
ELB improved by 0.0197292
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.101
ELB improved by 0.0180399
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.085
ELB improved by 0.0165348
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.07
ELB improved by 0.0151896
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.056
ELB improved by 0.0139838
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.043
ELB improved by 0.0129001
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.031
ELB improved by 0.0119239
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.02
ELB improved by 0.0110426
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.01
ELB improved by 0.0102453
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414
ELB improved by 0.00952258
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-861.131
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-581.519
ELB improved by 279.612
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-523.324
ELB improved by 58.1946
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-481.649
ELB improved by 41.6755
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.149
ELB improved by 22.4996
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.27
ELB improved by 9.8793
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.088
ELB improved by 5.1814
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.087
ELB improved by 4.00115
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.202
ELB improved by 3.88527
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.015
ELB improved by 4.18663
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.31
ELB improved by 4.70559
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.14
ELB improved by 5.16992
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.994
ELB improved by 5.14578
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.582
ELB improved by 4.41211
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.253
ELB improved by 3.32914
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.907
ELB improved by 2.34574
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.337
ELB improved by 1.57014
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.314
ELB improved by 1.02302
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.629
ELB improved by 0.684899
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.143
ELB improved by 0.486141
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.777
ELB improved by 0.366192
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.487
ELB improved by 0.289861
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.247
ELB improved by 0.239667
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.041
ELB improved by 0.206555
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.856
ELB improved by 0.184865
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.685
ELB improved by 0.170866
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.523
ELB improved by 0.162261
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.365
ELB improved by 0.157601
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.209
ELB improved by 0.155613
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.055
ELB improved by 0.154677
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.902
ELB improved by 0.15293
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.753
ELB improved by 0.14929
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.608
ELB improved by 0.144396
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.468
ELB improved by 0.139944
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.331
ELB improved by 0.137174
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.195
ELB improved by 0.136327
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.058
ELB improved by 0.137096
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.918
ELB improved by 0.139104
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.776
ELB improved by 0.142075
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.631
ELB improved by 0.145828
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.48
ELB improved by 0.15023
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.325
ELB improved by 0.15517
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.165
ELB improved by 0.160568
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.998
ELB improved by 0.16641
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.825
ELB improved by 0.172777
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.646
ELB improved by 0.179862
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.458
ELB improved by 0.187942
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.26
ELB improved by 0.197333
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.052
ELB improved by 0.208351
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.831
ELB improved by 0.221293
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.594
ELB improved by 0.236477
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.34
ELB improved by 0.25434
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.064
ELB improved by 0.275706
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.762
ELB improved by 0.302346
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.424
ELB improved by 0.338156
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.033
ELB improved by 0.390965
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.561
ELB improved by 0.471809
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.982
ELB improved by 0.578366
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.313
ELB improved by 0.669671
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.593
ELB improved by 0.72019
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.829
ELB improved by 0.763278
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.031
ELB improved by 0.798663
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.261
ELB improved by 0.769906
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.591
ELB improved by 0.669945
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.052
ELB improved by 0.539264
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.642
ELB improved by 0.409355
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.336
ELB improved by 0.305809
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.112
ELB improved by 0.224483
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.955
ELB improved by 0.156824
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.849
ELB improved by 0.106358
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.775
ELB improved by 0.0734735
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.722
ELB improved by 0.0529326
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.683
ELB improved by 0.0397356
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.652
ELB improved by 0.0308574
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.627
ELB improved by 0.0246405
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.607
ELB improved by 0.0201466
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.59
ELB improved by 0.0168129
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.576
ELB improved by 0.0142843
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.564
ELB improved by 0.0123287
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.553
ELB improved by 0.0107899
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.543
ELB improved by 0.00955984
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-863.484
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-589.202
ELB improved by 274.282
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-528.898
ELB improved by 60.3037
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-484.881
ELB improved by 44.0175
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.22
ELB improved by 22.6612
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.327
ELB improved by 9.89296
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.437
ELB improved by 5.88986
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.447
ELB improved by 4.98999
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.576
ELB improved by 4.87116
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.639
ELB improved by 4.93648
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.637
ELB improved by 5.00168
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.582
ELB improved by 5.0554
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.715
ELB improved by 4.86751
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.644
ELB improved by 4.07048
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.653
ELB improved by 2.99095
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.549
ELB improved by 2.10406
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.04
ELB improved by 1.50884
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.917
ELB improved by 1.12294
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.033
ELB improved by 0.884313
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.282
ELB improved by 0.750841
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.601
ELB improved by 0.681276
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.955
ELB improved by 0.645393
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.327
ELB improved by 0.627974
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.703
ELB improved by 0.624452
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.069
ELB improved by 0.633996
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.416
ELB improved by 0.652668
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.748
ELB improved by 0.66885
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.076
ELB improved by 0.671542
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.41
ELB improved by 0.665635
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.745
ELB improved by 0.665076
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.068
ELB improved by 0.677115
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.367
ELB improved by 0.701177
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.634
ELB improved by 0.732774
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.869
ELB improved by 0.764975
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.08
ELB improved by 0.789107
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.284
ELB improved by 0.796374
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.504
ELB improved by 0.780171
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.766
ELB improved by 0.73792
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.094
ELB improved by 0.671924
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.504
ELB improved by 0.589384
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.004
ELB improved by 0.500415
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.59
ELB improved by 0.41367
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.257
ELB improved by 0.33374
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.994
ELB improved by 0.262992
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.79
ELB improved by 0.203615
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.633
ELB improved by 0.15669
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.512
ELB improved by 0.121203
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.417
ELB improved by 0.0948597
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.342
ELB improved by 0.0752851
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.281
ELB improved by 0.0605856
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.232
ELB improved by 0.0493978
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.191
ELB improved by 0.0407691
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.157
ELB improved by 0.0340322
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.128
ELB improved by 0.028713
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.104
ELB improved by 0.0244695
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.083
ELB improved by 0.0210512
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.065
ELB improved by 0.0182728
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.049
ELB improved by 0.015995
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.034
ELB improved by 0.0141127
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.022
ELB improved by 0.0125452
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.011
ELB improved by 0.0112307
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.001
ELB improved by 0.0101208
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.991
ELB improved by 0.00917785
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
1.952 0.194 2.135
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.070 | 0.011 | 0.082 | |
| getPIPs | 0.060 | 0.004 | 0.065 | |
| graper | 0.086 | 0.021 | 0.105 | |
| makeExampleData | 0.007 | 0.003 | 0.011 | |
| makeExampleDataWithUnequalGroups | 0.005 | 0.007 | 0.013 | |
| plotELBO | 0.224 | 0.036 | 0.260 | |
| plotGroupPenalties | 0.857 | 0.080 | 0.936 | |
| plotPosterior | 0.468 | 0.012 | 0.479 | |
| predict.graper | 2.058 | 0.069 | 2.126 | |
| print.graper | 0.050 | 0.014 | 0.065 | |