Britta Velten
| Snapshot Date: 2026-02-23 13:40 -0500 (Mon, 23 Feb 2026) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: 95474d7 |
| git_last_commit_date: 2025-10-29 10:49:21 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-24 11:32 -0500 (Tue, 24 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4872 |
| 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 926/2354 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.27.0 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for graper in R Universe. | ||||||||||||||
|
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: 1.27.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings graper_1.27.0.tar.gz |
| StartedAt: 2026-02-24 00:20:49 -0500 (Tue, 24 Feb 2026) |
| EndedAt: 2026-02-24 00:22:20 -0500 (Tue, 24 Feb 2026) |
| EllapsedTime: 91.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings graper_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.27.0’
* 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 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 ... INFO
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: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.27.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c fit_graper.cpp -o fit_graper.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -llapack -L/home/biocbuild/bbs-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.23-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 Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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=-858.478
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-557.269
ELB improved by 301.209
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-498.492
ELB improved by 58.7766
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.189
ELB improved by 35.3031
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.356
ELB improved by 15.8334
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.288
ELB improved by 7.06779
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.881
ELB improved by 4.40727
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.189
ELB improved by 3.69156
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.737
ELB improved by 3.45255
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.337
ELB improved by 3.39973
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.906
ELB improved by 3.43139
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.457
ELB improved by 3.44886
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.152
ELB improved by 3.30444
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.282
ELB improved by 2.87017
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.088
ELB improved by 2.19447
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.588
ELB improved by 1.49929
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.621
ELB improved by 0.967838
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.99
ELB improved by 0.630843
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.555
ELB improved by 0.434319
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.235
ELB improved by 0.320083
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.985
ELB improved by 0.250516
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.78
ELB improved by 0.205163
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.606
ELB improved by 0.173463
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.456
ELB improved by 0.14994
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.325
ELB improved by 0.131669
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.208
ELB improved by 0.117007
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.103
ELB improved by 0.104976
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.008
ELB improved by 0.0949504
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.921
ELB improved by 0.0864983
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.842
ELB improved by 0.0793071
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.769
ELB improved by 0.0731405
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.701
ELB improved by 0.0678156
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.638
ELB improved by 0.0631887
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.579
ELB improved by 0.0591452
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.523
ELB improved by 0.055593
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.47
ELB improved by 0.0524571
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.421
ELB improved by 0.0496759
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.374
ELB improved by 0.0471986
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.329
ELB improved by 0.0449823
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.286
ELB improved by 0.0429915
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.244
ELB improved by 0.0411959
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.205
ELB improved by 0.0395698
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.167
ELB improved by 0.0380916
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.13
ELB improved by 0.036743
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.095
ELB improved by 0.0355085
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.06
ELB improved by 0.034375
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.027
ELB improved by 0.0333318
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.994
ELB improved by 0.0323701
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.963
ELB improved by 0.0314828
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.932
ELB improved by 0.0306646
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.902
ELB improved by 0.0299115
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.873
ELB improved by 0.0292207
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.845
ELB improved by 0.0285911
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.817
ELB improved by 0.0280223
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.789
ELB improved by 0.0275153
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.762
ELB improved by 0.0270718
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.735
ELB improved by 0.0266949
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.709
ELB improved by 0.0263885
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.683
ELB improved by 0.0261573
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.657
ELB improved by 0.0260073
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.631
ELB improved by 0.0259452
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.605
ELB improved by 0.0259788
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.579
ELB improved by 0.0261168
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.552
ELB improved by 0.0263688
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.526
ELB improved by 0.0267452
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.498
ELB improved by 0.0272573
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.47
ELB improved by 0.0279166
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.442
ELB improved by 0.0287355
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.412
ELB improved by 0.0297271
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.381
ELB improved by 0.0309058
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.349
ELB improved by 0.0322889
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.315
ELB improved by 0.0338983
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.279
ELB improved by 0.0357639
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.241
ELB improved by 0.0379275
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.201
ELB improved by 0.0404471
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.157
ELB improved by 0.0434026
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.11
ELB improved by 0.0469008
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.059
ELB improved by 0.0510824
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.003
ELB improved by 0.0561292
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.941
ELB improved by 0.0622763
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.871
ELB improved by 0.069828
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.792
ELB improved by 0.0791816
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.701
ELB improved by 0.0908626
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.595
ELB improved by 0.105577
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.471
ELB improved by 0.124292
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.323
ELB improved by 0.148364
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.143
ELB improved by 0.179743
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.922
ELB improved by 0.221268
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.645
ELB improved by 0.276917
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.294
ELB improved by 0.35133
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.847
ELB improved by 0.446581
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.292
ELB improved by 0.554701
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.638
ELB improved by 0.654387
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.913
ELB improved by 0.725328
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.153
ELB improved by 0.760045
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.396
ELB improved by 0.75686
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.678
ELB improved by 0.71724
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.035
ELB improved by 0.643828
iteration 99
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.494
ELB improved by 0.54061
iteration 100
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.07
ELB improved by 0.423682
iteration 101
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.755
ELB improved by 0.31504
iteration 102
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.529
ELB improved by 0.226699
iteration 103
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.368
ELB improved by 0.160283
iteration 104
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.256
ELB improved by 0.112594
iteration 105
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.176
ELB improved by 0.0791717
iteration 106
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.121
ELB improved by 0.0559771
iteration 107
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.081
ELB improved by 0.0399012
iteration 108
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.052
ELB improved by 0.0287231
iteration 109
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.031
ELB improved by 0.0209077
iteration 110
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.016
ELB improved by 0.0154069
iteration 111
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.004
ELB improved by 0.0115072
iteration 112
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.995
ELB improved by 0.00872202
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-893.154
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-571.716
ELB improved by 321.438
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-511.937
ELB improved by 59.7793
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-476.481
ELB improved by 35.456
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.8
ELB improved by 12.6809
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.979
ELB improved by 4.82101
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.846
ELB improved by 3.13282
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.216
ELB improved by 2.63029
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.713
ELB improved by 2.503
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.142
ELB improved by 2.57071
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.365
ELB improved by 2.7768
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.269
ELB improved by 3.09623
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.801
ELB improved by 3.46805
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.073
ELB improved by 3.72798
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.443
ELB improved by 3.63018
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.379
ELB improved by 3.06386
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.132
ELB improved by 2.24712
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.596
ELB improved by 1.53555
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.509
ELB improved by 1.08677
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.658
ELB improved by 0.85156
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.915
ELB improved by 0.742402
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.208
ELB improved by 0.70732
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.481
ELB improved by 0.727003
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.684
ELB improved by 0.797474
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.785
ELB improved by 0.89894
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.821
ELB improved by 0.963156
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.875
ELB improved by 0.946096
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.99
ELB improved by 0.885135
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.178
ELB improved by 0.811802
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.442
ELB improved by 0.736928
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.773
ELB improved by 0.668042
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.163
ELB improved by 0.610982
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.591
ELB improved by 0.571017
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.035
ELB improved by 0.556691
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.447
ELB improved by 0.587375
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.749
ELB improved by 0.698014
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.886
ELB improved by 0.86316
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.024
ELB improved by 0.862667
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.336
ELB improved by 0.687372
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.81
ELB improved by 0.525944
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.402
ELB improved by 0.407795
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.081
ELB improved by 0.321056
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.823
ELB improved by 0.25845
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.609
ELB improved by 0.214369
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.425
ELB improved by 0.183753
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.263
ELB improved by 0.162024
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.118
ELB improved by 0.145158
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.987
ELB improved by 0.130173
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.872
ELB improved by 0.115722
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.77
ELB improved by 0.101993
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.68
ELB improved by 0.0898484
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.6
ELB improved by 0.0800762
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.527
ELB improved by 0.0731725
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.457
ELB improved by 0.0694648
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.388
ELB improved by 0.0692675
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.315
ELB improved by 0.0728101
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.236
ELB improved by 0.0795736
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.149
ELB improved by 0.0868883
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.059
ELB improved by 0.0894467
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.976
ELB improved by 0.0832005
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.905
ELB improved by 0.0708335
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.846
ELB improved by 0.0595216
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.791
ELB improved by 0.0545469
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.733
ELB improved by 0.0582468
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.661
ELB improved by 0.071742
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.569
ELB improved by 0.0926293
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.461
ELB improved by 0.107382
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.364
ELB improved by 0.097379
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.296
ELB improved by 0.0678904
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.255
ELB improved by 0.0409399
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.23
ELB improved by 0.0247876
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.214
ELB improved by 0.0164675
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.201
ELB improved by 0.0122364
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.191
ELB improved by 0.00996941
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-857.917
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-594.768
ELB improved by 263.149
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-532.637
ELB improved by 62.1316
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-487.936
ELB improved by 44.7002
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.104
ELB improved by 22.8321
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.219
ELB improved by 9.88522
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.96
ELB improved by 5.25875
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.848
ELB improved by 4.11192
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.111
ELB improved by 3.73695
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.561
ELB improved by 3.55074
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.16
ELB improved by 3.4006
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.964
ELB improved by 3.19658
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.105
ELB improved by 2.8583
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.717
ELB improved by 2.38858
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.852
ELB improved by 1.86488
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.481
ELB improved by 1.37063
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.515
ELB improved by 0.965655
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.841
ELB improved by 0.674052
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.358
ELB improved by 0.482952
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.996
ELB improved by 0.362204
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.712
ELB improved by 0.284547
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.48
ELB improved by 0.232076
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.285
ELB improved by 0.194512
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.119
ELB improved by 0.166189
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.975
ELB improved by 0.143948
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.849
ELB improved by 0.125953
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.738
ELB improved by 0.111079
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.639
ELB improved by 0.098589
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.551
ELB improved by 0.0879778
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.473
ELB improved by 0.0788784
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.401
ELB improved by 0.071016
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.337
ELB improved by 0.0641786
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.279
ELB improved by 0.0581988
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.226
ELB improved by 0.052943
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.178
ELB improved by 0.0483025
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.134
ELB improved by 0.0441885
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.093
ELB improved by 0.0405275
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.056
ELB improved by 0.0372583
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.022
ELB improved by 0.0343298
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.99
ELB improved by 0.0316987
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.961
ELB improved by 0.0293284
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.933
ELB improved by 0.0271877
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.908
ELB improved by 0.0252498
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.885
ELB improved by 0.0234917
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.863
ELB improved by 0.0218935
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.842
ELB improved by 0.0204379
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.823
ELB improved by 0.0191098
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.805
ELB improved by 0.0178962
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.788
ELB improved by 0.0167854
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.773
ELB improved by 0.0157673
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.758
ELB improved by 0.0148329
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.744
ELB improved by 0.0139742
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.731
ELB improved by 0.0131842
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.718
ELB improved by 0.0124566
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.706
ELB improved by 0.0117857
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.695
ELB improved by 0.0111665
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.685
ELB improved by 0.0105946
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.675
ELB improved by 0.0100658
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.665
ELB improved by 0.00957654
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-853.386
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-566.53
ELB improved by 286.855
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-505.083
ELB improved by 61.4477
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.786
ELB improved by 39.2966
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.665
ELB improved by 17.1209
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.405
ELB improved by 7.25993
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.885
ELB improved by 4.52029
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.084
ELB improved by 3.80077
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.396
ELB improved by 3.68798
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.57
ELB improved by 3.82572
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.574
ELB improved by 3.99618
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.548
ELB improved by 4.0261
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.748
ELB improved by 3.79969
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.423
ELB improved by 3.32529
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.734
ELB improved by 2.68859
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.773
ELB improved by 1.96105
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.411
ELB improved by 1.36234
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.418
ELB improved by 0.993502
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.642
ELB improved by 0.775155
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.008
ELB improved by 0.634832
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.466
ELB improved by 0.541415
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.986
ELB improved by 0.479787
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.547
ELB improved by 0.439316
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.135
ELB improved by 0.412336
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.741
ELB improved by 0.394128
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.358
ELB improved by 0.382588
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.98
ELB improved by 0.377906
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.597
ELB improved by 0.382907
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.193
ELB improved by 0.404616
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.735
ELB improved by 0.457138
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.176
ELB improved by 0.55925
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.477
ELB improved by 0.699471
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.673
ELB improved by 0.803802
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.805
ELB improved by 0.867869
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.824
ELB improved by 0.98087
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.667
ELB improved by 1.15747
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.333
ELB improved by 1.3333
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.831
ELB improved by 1.5022
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.128
ELB improved by 1.70333
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.257
ELB improved by 1.87073
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.516
ELB improved by 1.74135
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.188
ELB improved by 1.32782
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.261
ELB improved by 0.9275
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.618
ELB improved by 0.642149
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.165
ELB improved by 0.453093
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.841
ELB improved by 0.324706
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.607
ELB improved by 0.233995
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.437
ELB improved by 0.169596
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.312
ELB improved by 0.124539
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.219
ELB improved by 0.0932379
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.148
ELB improved by 0.0713294
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.092
ELB improved by 0.055733
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.048
ELB improved by 0.0444087
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.012
ELB improved by 0.0360318
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.982
ELB improved by 0.0297344
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.957
ELB improved by 0.0249342
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.936
ELB improved by 0.0212303
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.917
ELB improved by 0.018341
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.901
ELB improved by 0.0160646
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.887
ELB improved by 0.0142553
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.874
ELB improved by 0.0128066
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.863
ELB improved by 0.0116397
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.852
ELB improved by 0.010696
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.842
ELB improved by 0.00993101
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.464 0.214 2.664
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.047 | 0.018 | 0.066 | |
| getPIPs | 0.043 | 0.018 | 0.061 | |
| graper | 0.081 | 0.019 | 0.101 | |
| makeExampleData | 0.009 | 0.002 | 0.011 | |
| makeExampleDataWithUnequalGroups | 0.010 | 0.003 | 0.012 | |
| plotELBO | 0.326 | 0.021 | 0.347 | |
| plotGroupPenalties | 1.099 | 0.048 | 1.148 | |
| plotPosterior | 0.639 | 0.020 | 0.660 | |
| predict.graper | 2.050 | 0.079 | 2.129 | |
| print.graper | 0.049 | 0.015 | 0.064 | |