Britta Velten
| Snapshot Date: 2026-03-04 13:40 -0500 (Wed, 04 Mar 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 2026-03-05 11:34 -0500 (Thu, 05 Mar 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" | 4891 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4583 |
| 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 926/2357 | 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 | | ||||||||
| 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: 2026-03-05 00:27:31 -0500 (Thu, 05 Mar 2026) |
| EndedAt: 2026-03-05 00:29:02 -0500 (Thu, 05 Mar 2026) |
| EllapsedTime: 91.1 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=-883.31
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-590.468
ELB improved by 292.842
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-531.577
ELB improved by 58.8908
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-487.666
ELB improved by 43.9112
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.584
ELB improved by 22.0825
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.367
ELB improved by 9.21682
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.9
ELB improved by 5.46678
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.249
ELB improved by 4.651
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.626
ELB improved by 4.62336
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.8
ELB improved by 4.82549
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.903
ELB improved by 4.89733
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.326
ELB improved by 4.57658
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.497
ELB improved by 3.82935
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.632
ELB improved by 2.86496
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.622
ELB improved by 2.01006
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.167
ELB improved by 1.45494
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.996
ELB improved by 1.17145
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.94
ELB improved by 1.05616
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.91
ELB improved by 1.02964
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.862
ELB improved by 1.04757
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.774
ELB improved by 1.08781
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.636
ELB improved by 1.13812
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.449
ELB improved by 1.18711
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.224
ELB improved by 1.22527
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.965
ELB improved by 1.25873
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.661
ELB improved by 1.30385
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.301
ELB improved by 1.36073
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.896
ELB improved by 1.40447
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.499
ELB improved by 1.39672
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.189
ELB improved by 1.31093
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.032
ELB improved by 1.15632
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.057
ELB improved by 0.975715
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.237
ELB improved by 0.819074
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.518
ELB improved by 0.719938
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.82
ELB improved by 0.697437
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.041
ELB improved by 0.779388
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.134
ELB improved by 0.906316
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.348
ELB improved by 0.786186
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.825
ELB improved by 0.523284
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.47
ELB improved by 0.355184
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.207
ELB improved by 0.263215
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.996
ELB improved by 0.210512
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.812
ELB improved by 0.183676
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.64
ELB improved by 0.172065
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.48
ELB improved by 0.160459
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.344
ELB improved by 0.135672
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.244
ELB improved by 0.10037
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.175
ELB improved by 0.0685132
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.128
ELB improved by 0.0471137
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.094
ELB improved by 0.0343678
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.067
ELB improved by 0.0267192
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.045
ELB improved by 0.0218051
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.027
ELB improved by 0.0183902
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.011
ELB improved by 0.0158579
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.997
ELB improved by 0.0138897
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.985
ELB improved by 0.0123094
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.974
ELB improved by 0.0110116
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.964
ELB improved by 0.00992813
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-843.214
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-551.831
ELB improved by 291.383
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-493.117
ELB improved by 58.7142
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.647
ELB improved by 35.4701
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.975
ELB improved by 13.6712
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.571
ELB improved by 5.40452
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.116
ELB improved by 3.45432
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.25
ELB improved by 2.8665
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.535
ELB improved by 2.71499
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.766
ELB improved by 2.76921
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.828
ELB improved by 2.93737
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.685
ELB improved by 3.1431
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.42
ELB improved by 3.26513
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.275
ELB improved by 3.14544
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.573
ELB improved by 2.7018
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.525
ELB improved by 2.048
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.095
ELB improved by 1.42958
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.079
ELB improved by 1.01622
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.25
ELB improved by 0.828828
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.433
ELB improved by 0.817226
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.545
ELB improved by 0.887643
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.622
ELB improved by 0.923188
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.7
ELB improved by 0.922705
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.74
ELB improved by 0.959617
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.684
ELB improved by 1.05634
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.48
ELB improved by 1.20331
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.087
ELB improved by 1.39369
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.444
ELB improved by 1.64235
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.451
ELB improved by 1.99374
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.944
ELB improved by 2.50695
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.763
ELB improved by 3.18061
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.954
ELB improved by 3.80913
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.945
ELB improved by 4.00857
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.382
ELB improved by 3.56365
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.681
ELB improved by 2.70031
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.819
ELB improved by 1.86275
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.555
ELB improved by 1.26382
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.71
ELB improved by 0.844975
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.175
ELB improved by 0.535141
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.844
ELB improved by 0.330749
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.63
ELB improved by 0.213399
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.482
ELB improved by 0.148241
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.372
ELB improved by 0.109905
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.287
ELB improved by 0.0852351
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.219
ELB improved by 0.0681249
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.163
ELB improved by 0.0556574
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.117
ELB improved by 0.046275
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.078
ELB improved by 0.0390426
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.045
ELB improved by 0.0333536
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.016
ELB improved by 0.0287985
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.991
ELB improved by 0.0250947
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.969
ELB improved by 0.0220435
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.949
ELB improved by 0.0195022
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.932
ELB improved by 0.0173664
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.916
ELB improved by 0.0155579
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.902
ELB improved by 0.0140166
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.89
ELB improved by 0.0126959
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.878
ELB improved by 0.0115585
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.867
ELB improved by 0.0105747
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.858
ELB improved by 0.00972021
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-889.012
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-585.945
ELB improved by 303.067
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-525.071
ELB improved by 60.8747
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-484.358
ELB improved by 40.7126
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.168
ELB improved by 18.1904
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.954
ELB improved by 7.21382
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.583
ELB improved by 4.37089
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.947
ELB improved by 3.63594
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.422
ELB improved by 3.52496
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.739
ELB improved by 3.68331
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.832
ELB improved by 3.90654
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.878
ELB improved by 3.95396
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.264
ELB improved by 3.61441
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.312
ELB improved by 2.9523
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.027
ELB improved by 2.28485
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.259
ELB improved by 1.76796
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.948
ELB improved by 1.3109
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.025
ELB improved by 0.922555
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.346
ELB improved by 0.679347
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.792
ELB improved by 0.553643
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.304
ELB improved by 0.488594
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.852
ELB improved by 0.451398
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.422
ELB improved by 0.4299
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.003
ELB improved by 0.419157
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.588
ELB improved by 0.414901
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.175
ELB improved by 0.413679
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.761
ELB improved by 0.413295
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.349
ELB improved by 0.412195
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.94
ELB improved by 0.408835
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.539
ELB improved by 0.40175
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.148
ELB improved by 0.390279
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.773
ELB improved by 0.374951
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.416
ELB improved by 0.356923
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.079
ELB improved by 0.337189
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.763
ELB improved by 0.31637
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.468
ELB improved by 0.294888
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.195
ELB improved by 0.273162
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.943
ELB improved by 0.251674
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.712
ELB improved by 0.230947
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.501
ELB improved by 0.211506
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.307
ELB improved by 0.193823
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.129
ELB improved by 0.178301
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.963
ELB improved by 0.165277
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.808
ELB improved by 0.155105
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.66
ELB improved by 0.148309
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.514
ELB improved by 0.145912
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.364
ELB improved by 0.150114
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.198
ELB improved by 0.165845
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.994
ELB improved by 0.204476
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.703
ELB improved by 0.290496
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.251
ELB improved by 0.452269
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.624
ELB improved by 0.626476
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.964
ELB improved by 0.660707
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.381
ELB improved by 0.582248
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.916
ELB improved by 0.464953
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.569
ELB improved by 0.347589
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.314
ELB improved by 0.255078
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.125
ELB improved by 0.18917
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.982
ELB improved by 0.142749
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.872
ELB improved by 0.109818
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.785
ELB improved by 0.0867865
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.714
ELB improved by 0.0715056
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.651
ELB improved by 0.0626099
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.592
ELB improved by 0.0593374
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.53
ELB improved by 0.0613747
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.462
ELB improved by 0.0681716
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.385
ELB improved by 0.0773477
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.301
ELB improved by 0.0834832
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.22
ELB improved by 0.0810491
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.15
ELB improved by 0.070275
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.093
ELB improved by 0.0567362
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.048
ELB improved by 0.0453394
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.01
ELB improved by 0.0378065
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.976
ELB improved by 0.0340517
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.942
ELB improved by 0.0338321
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.905
ELB improved by 0.0376769
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.857
ELB improved by 0.0475175
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.79
ELB improved by 0.0669929
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.691
ELB improved by 0.0989315
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.557
ELB improved by 0.134657
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.409
ELB improved by 0.147807
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.282
ELB improved by 0.126798
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.189
ELB improved by 0.0930801
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.123
ELB improved by 0.0657555
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.075
ELB improved by 0.048141
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.037
ELB improved by 0.0377073
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.005
ELB improved by 0.0318265
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.977
ELB improved by 0.0287671
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.949
ELB improved by 0.0274717
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.922
ELB improved by 0.0272357
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.894
ELB improved by 0.0274826
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.867
ELB improved by 0.0276605
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.84
ELB improved by 0.0272708
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.814
ELB improved by 0.0260003
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.79
ELB improved by 0.0238401
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.769
ELB improved by 0.021061
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.751
ELB improved by 0.0180489
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.735
ELB improved by 0.0151388
iteration 99
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.723
ELB improved by 0.0125436
iteration 100
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.713
ELB improved by 0.0103628
iteration 101
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.704
ELB improved by 0.00861474
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-841.441
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-575.957
ELB improved by 265.484
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-515.647
ELB improved by 60.3095
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.038
ELB improved by 44.6094
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.761
ELB improved by 21.2771
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.696
ELB improved by 8.06506
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.494
ELB improved by 4.20214
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.197
ELB improved by 3.29724
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.963
ELB improved by 3.23326
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.317
ELB improved by 3.64651
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.916
ELB improved by 4.40116
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.677
ELB improved by 5.23851
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.047
ELB improved by 5.62979
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.97
ELB improved by 5.0777
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.223
ELB improved by 3.7463
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.851
ELB improved by 2.37194
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.419
ELB improved by 1.43288
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.512
ELB improved by 0.906533
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.889
ELB improved by 0.622507
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.427
ELB improved by 0.462764
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.059
ELB improved by 0.36785
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.75
ELB improved by 0.309126
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.478
ELB improved by 0.272148
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.228
ELB improved by 0.249256
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.992
ELB improved by 0.236331
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.761
ELB improved by 0.231234
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.528
ELB improved by 0.232898
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.287
ELB improved by 0.240598
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.034
ELB improved by 0.253353
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.764
ELB improved by 0.269858
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.475
ELB improved by 0.289554
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.16
ELB improved by 0.314538
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.809
ELB improved by 0.351373
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.396
ELB improved by 0.412616
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.88
ELB improved by 0.516356
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.207
ELB improved by 0.672734
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.363
ELB improved by 0.84411
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.424
ELB improved by 0.939256
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.476
ELB improved by 0.947113
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.534
ELB improved by 0.942296
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.595
ELB improved by 0.939333
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.68
ELB improved by 0.915238
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.826
ELB improved by 0.853231
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.073
ELB improved by 0.752838
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.445
ELB improved by 0.628409
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.945
ELB improved by 0.500074
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.561
ELB improved by 0.384195
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.272
ELB improved by 0.289038
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.056
ELB improved by 0.215718
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.895
ELB improved by 0.161339
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.773
ELB improved by 0.121757
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.68
ELB improved by 0.0931003
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.608
ELB improved by 0.0722921
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.551
ELB improved by 0.0570646
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.505
ELB improved by 0.045805
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.467
ELB improved by 0.037382
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.436
ELB improved by 0.0310031
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.41
ELB improved by 0.026111
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.388
ELB improved by 0.022311
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.369
ELB improved by 0.0193213
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.352
ELB improved by 0.0169388
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.337
ELB improved by 0.0150159
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.323
ELB improved by 0.0134446
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.311
ELB improved by 0.0121449
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.3
ELB improved by 0.0110574
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.29
ELB improved by 0.0101373
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.28
ELB improved by 0.00935077
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.442 0.226 2.662
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.049 | 0.020 | 0.070 | |
| getPIPs | 0.051 | 0.012 | 0.063 | |
| graper | 0.087 | 0.014 | 0.101 | |
| makeExampleData | 0.008 | 0.002 | 0.011 | |
| makeExampleDataWithUnequalGroups | 0.010 | 0.002 | 0.013 | |
| plotELBO | 0.316 | 0.030 | 0.346 | |
| plotGroupPenalties | 1.088 | 0.069 | 1.157 | |
| plotPosterior | 0.656 | 0.020 | 0.676 | |
| predict.graper | 2.07 | 0.05 | 2.12 | |
| print.graper | 0.049 | 0.011 | 0.060 | |