Britta Velten
| Snapshot Date: 2026-01-05 13:40 -0500 (Mon, 05 Jan 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 Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-06 11:34 -0500 (Tue, 06 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" | 4815 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4593 |
| 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 915/2332 | 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 | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: graper |
| Version: 1.27.0 |
| 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: 2026-01-06 00:05:09 -0500 (Tue, 06 Jan 2026) |
| EndedAt: 2026-01-06 00:06:42 -0500 (Tue, 06 Jan 2026) |
| EllapsedTime: 93.2 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) (2025-12-22 r89219)
* 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) (2025-12-22 r89219) -- "Unsuffered Consequences"
Copyright (C) 2025 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=-840.511
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-588.869
ELB improved by 251.641
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-528.615
ELB improved by 60.2541
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-479.661
ELB improved by 48.954
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.984
ELB improved by 26.677
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.109
ELB improved by 9.87569
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.277
ELB improved by 4.83182
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.468
ELB improved by 3.80893
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.627
ELB improved by 3.84118
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.226
ELB improved by 4.4004
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.905
ELB improved by 5.3213
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.562
ELB improved by 6.34258
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.77
ELB improved by 6.79241
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.814
ELB improved by 5.95568
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.656
ELB improved by 4.1586
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.992
ELB improved by 2.66343
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.104
ELB improved by 1.88862
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.743
ELB improved by 1.36041
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.842
ELB improved by 0.901268
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.242
ELB improved by 0.599924
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.802
ELB improved by 0.439622
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.444
ELB improved by 0.358823
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.122
ELB improved by 0.321191
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.811
ELB improved by 0.311695
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.483
ELB improved by 0.327812
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.106
ELB improved by 0.376898
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.631
ELB improved by 0.474883
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.997
ELB improved by 0.634047
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.158
ELB improved by 0.838685
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.137
ELB improved by 1.02097
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.015
ELB improved by 1.12194
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.804
ELB improved by 1.21175
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.466
ELB improved by 1.33766
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.979
ELB improved by 1.48706
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.353
ELB improved by 1.62629
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.649
ELB improved by 1.7035
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.978
ELB improved by 1.67075
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.465
ELB improved by 1.51384
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.203
ELB improved by 1.26118
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.232
ELB improved by 0.971539
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.527
ELB improved by 0.704407
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.034
ELB improved by 0.493315
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.692
ELB improved by 0.342454
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.452
ELB improved by 0.240102
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.28
ELB improved by 0.171705
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.154
ELB improved by 0.12567
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.06
ELB improved by 0.0941425
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.988
ELB improved by 0.0720995
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.932
ELB improved by 0.0563676
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.887
ELB improved by 0.0449195
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.85
ELB improved by 0.0364364
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.82
ELB improved by 0.0300426
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.795
ELB improved by 0.0251459
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.774
ELB improved by 0.0213385
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.755
ELB improved by 0.0183353
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.739
ELB improved by 0.015934
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.725
ELB improved by 0.0139891
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.713
ELB improved by 0.0123947
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.702
ELB improved by 0.0110729
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.692
ELB improved by 0.00996558
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-903.132
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-603.1
ELB improved by 300.032
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-541.596
ELB improved by 61.5034
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-500.209
ELB improved by 41.3874
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-481.091
ELB improved by 19.1183
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.905
ELB improved by 8.18592
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.254
ELB improved by 4.65126
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.702
ELB improved by 3.55155
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.538
ELB improved by 3.16422
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.497
ELB improved by 3.04123
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.412
ELB improved by 3.08494
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.174
ELB improved by 3.23767
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.84
ELB improved by 3.33405
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.701
ELB improved by 3.13852
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.101
ELB improved by 2.60039
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.183
ELB improved by 1.91805
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.849
ELB improved by 1.33436
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.914
ELB improved by 0.934562
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.243
ELB improved by 0.670764
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.753
ELB improved by 0.489774
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.383
ELB improved by 0.370029
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.087
ELB improved by 0.29651
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.833
ELB improved by 0.253649
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.605
ELB improved by 0.228802
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.391
ELB improved by 0.213202
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.19
ELB improved by 0.201554
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.998
ELB improved by 0.191562
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.815
ELB improved by 0.183008
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.639
ELB improved by 0.176385
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.467
ELB improved by 0.171947
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.297
ELB improved by 0.169522
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.129
ELB improved by 0.168726
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.959
ELB improved by 0.169155
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.789
ELB improved by 0.170469
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.617
ELB improved by 0.172413
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.442
ELB improved by 0.174819
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.264
ELB improved by 0.177602
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.083
ELB improved by 0.180772
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.899
ELB improved by 0.184429
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.71
ELB improved by 0.188776
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.516
ELB improved by 0.194118
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.315
ELB improved by 0.20087
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.106
ELB improved by 0.209569
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.885
ELB improved by 0.220897
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.649
ELB improved by 0.235729
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.394
ELB improved by 0.255215
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.113
ELB improved by 0.280899
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.798
ELB improved by 0.314891
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.438
ELB improved by 0.360003
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.018
ELB improved by 0.419666
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.521
ELB improved by 0.497343
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.926
ELB improved by 0.595453
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.211
ELB improved by 0.714325
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.361
ELB improved by 0.849891
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.37
ELB improved by 0.991714
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.234
ELB improved by 1.13564
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.968
ELB improved by 1.26623
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.744
ELB improved by 1.22396
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.823
ELB improved by 0.920284
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.204
ELB improved by 0.619785
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.779
ELB improved by 0.42515
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.481
ELB improved by 0.297254
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.271
ELB improved by 0.209829
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.122
ELB improved by 0.149485
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.014
ELB improved by 0.10784
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.935
ELB improved by 0.0790409
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.876
ELB improved by 0.0589735
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.831
ELB improved by 0.0448306
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.797
ELB improved by 0.0347324
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.769
ELB improved by 0.0274267
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.747
ELB improved by 0.0220741
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.729
ELB improved by 0.0181057
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.714
ELB improved by 0.0151304
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.701
ELB improved by 0.0128751
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.69
ELB improved by 0.0111464
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.68
ELB improved by 0.00980592
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-829.035
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-558.726
ELB improved by 270.309
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-501.831
ELB improved by 56.8947
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.804
ELB improved by 35.0266
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.186
ELB improved by 13.6178
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.844
ELB improved by 5.34285
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.625
ELB improved by 3.21823
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.908
ELB improved by 2.71741
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.27
ELB improved by 2.63751
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.577
ELB improved by 2.69296
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.817
ELB improved by 2.76016
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.082
ELB improved by 2.73582
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.547
ELB improved by 2.53453
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.403
ELB improved by 2.14445
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.744
ELB improved by 1.65841
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.536
ELB improved by 1.20856
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.664
ELB improved by 0.871905
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.013
ELB improved by 0.650367
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.503
ELB improved by 0.510416
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.085
ELB improved by 0.418245
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.733
ELB improved by 0.351921
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.432
ELB improved by 0.30062
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.172
ELB improved by 0.259954
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.944
ELB improved by 0.227862
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.742
ELB improved by 0.202689
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.559
ELB improved by 0.182886
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.392
ELB improved by 0.167166
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.237
ELB improved by 0.154578
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.092
ELB improved by 0.144452
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.956
ELB improved by 0.136324
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.826
ELB improved by 0.129869
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.701
ELB improved by 0.124858
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.58
ELB improved by 0.12113
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.462
ELB improved by 0.118583
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.345
ELB improved by 0.117161
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.228
ELB improved by 0.116852
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.11
ELB improved by 0.117687
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.99
ELB improved by 0.119737
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.867
ELB improved by 0.12311
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.739
ELB improved by 0.12794
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.605
ELB improved by 0.134372
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.462
ELB improved by 0.142531
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.31
ELB improved by 0.152484
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.146
ELB improved by 0.164189
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.968
ELB improved by 0.177469
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.776
ELB improved by 0.192014
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.569
ELB improved by 0.207451
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.345
ELB improved by 0.223455
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.105
ELB improved by 0.239795
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.849
ELB improved by 0.256252
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.577
ELB improved by 0.272422
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.289
ELB improved by 0.287596
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.988
ELB improved by 0.300873
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.677
ELB improved by 0.311503
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.358
ELB improved by 0.319223
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.033
ELB improved by 0.324346
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.706
ELB improved by 0.327581
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.376
ELB improved by 0.329756
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.044
ELB improved by 0.331516
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.712
ELB improved by 0.332864
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.379
ELB improved by 0.332415
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.052
ELB improved by 0.326943
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.74
ELB improved by 0.312574
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.452
ELB improved by 0.287611
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.198
ELB improved by 0.254175
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.981
ELB improved by 0.216805
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.801
ELB improved by 0.17999
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.654
ELB improved by 0.146788
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.536
ELB improved by 0.118656
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.44
ELB improved by 0.0958385
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.362
ELB improved by 0.0778662
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.298
ELB improved by 0.0639718
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.245
ELB improved by 0.0533472
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.199
ELB improved by 0.0452706
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.16
ELB improved by 0.0391455
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.126
ELB improved by 0.0344982
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.095
ELB improved by 0.0309586
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.066
ELB improved by 0.0282411
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.04
ELB improved by 0.0261283
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.016
ELB improved by 0.0244577
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.993
ELB improved by 0.0231117
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.971
ELB improved by 0.0220088
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.95
ELB improved by 0.0210946
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.929
ELB improved by 0.020334
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.91
ELB improved by 0.0197025
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.89
ELB improved by 0.0191801
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.872
ELB improved by 0.0187454
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.853
ELB improved by 0.0183717
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.835
ELB improved by 0.0180245
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.818
ELB improved by 0.0176614
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.8
ELB improved by 0.0172338
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.784
ELB improved by 0.016692
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.768
ELB improved by 0.0159931
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.753
ELB improved by 0.0151107
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.739
ELB improved by 0.0140432
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.726
ELB improved by 0.0128176
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.714
ELB improved by 0.011487
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.704
ELB improved by 0.0101203
iteration 99
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.695
ELB improved by 0.00878807
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-853.03
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-589.536
ELB improved by 263.494
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-530.708
ELB improved by 58.8279
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-485.546
ELB improved by 45.1616
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.747
ELB improved by 24.7991
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.084
ELB improved by 10.6634
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.408
ELB improved by 5.67578
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.821
ELB improved by 4.58741
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.315
ELB improved by 4.50625
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.467
ELB improved by 4.84748
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.185
ELB improved by 5.28254
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.792
ELB improved by 5.39275
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.983
ELB improved by 4.80852
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.325
ELB improved by 3.65824
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.824
ELB improved by 2.50139
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.154
ELB improved by 1.66963
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.007
ELB improved by 1.14681
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.17
ELB improved by 0.837388
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.508
ELB improved by 0.662214
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.943
ELB improved by 0.564946
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.432
ELB improved by 0.510429
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.954
ELB improved by 0.478383
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.495
ELB improved by 0.458668
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.047
ELB improved by 0.448657
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.597
ELB improved by 0.449746
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.133
ELB improved by 0.463829
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.641
ELB improved by 0.492337
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.104
ELB improved by 0.536759
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.506
ELB improved by 0.59804
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.832
ELB improved by 0.674009
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.074
ELB improved by 0.757924
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.231
ELB improved by 0.843168
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.301
ELB improved by 0.929376
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.281
ELB improved by 1.02071
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.161
ELB improved by 1.11928
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.941
ELB improved by 1.22025
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.631
ELB improved by 1.31056
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.259
ELB improved by 1.37127
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.872
ELB improved by 1.38719
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.511
ELB improved by 1.36133
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.175
ELB improved by 1.3357
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.774
ELB improved by 1.40064
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.149
ELB improved by 1.62504
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.2
ELB improved by 1.94948
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.057
ELB improved by 2.14249
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.378
ELB improved by 1.67936
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.198
ELB improved by 1.18028
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.989
ELB improved by 1.20868
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.508
ELB improved by 1.48077
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.148
ELB improved by 1.36015
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.137
ELB improved by 1.01083
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.36
ELB improved by 0.777333
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.802
ELB improved by 0.557671
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.484
ELB improved by 0.318116
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.325
ELB improved by 0.159547
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.242
ELB improved by 0.0828214
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.194
ELB improved by 0.0483116
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.161
ELB improved by 0.032073
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.138
ELB improved by 0.0236043
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.119
ELB improved by 0.0186004
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.104
ELB improved by 0.0152803
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.091
ELB improved by 0.012874
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.08
ELB improved by 0.0110244
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.071
ELB improved by 0.00955045
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.475 0.248 2.708
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.052 | 0.015 | 0.069 | |
| getPIPs | 0.058 | 0.019 | 0.077 | |
| graper | 0.099 | 0.014 | 0.114 | |
| makeExampleData | 0.009 | 0.002 | 0.010 | |
| makeExampleDataWithUnequalGroups | 0.013 | 0.000 | 0.013 | |
| plotELBO | 0.360 | 0.031 | 0.391 | |
| plotGroupPenalties | 1.192 | 0.051 | 1.244 | |
| plotPosterior | 0.665 | 0.019 | 0.685 | |
| predict.graper | 2.053 | 0.073 | 2.127 | |
| print.graper | 0.047 | 0.015 | 0.063 | |