Britta Velten
| Snapshot Date: 2026-01-21 13:40 -0500 (Wed, 21 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 2026-01-22 11:34 -0500 (Thu, 22 Jan 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" | 4808 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4542 |
| 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 921/2345 | 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: 2026-01-22 00:11:32 -0500 (Thu, 22 Jan 2026) |
| EndedAt: 2026-01-22 00:13:04 -0500 (Thu, 22 Jan 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=-832.557
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-578.804
ELB improved by 253.753
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-518.027
ELB improved by 60.777
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-476.162
ELB improved by 41.8648
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.612
ELB improved by 18.5505
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.144
ELB improved by 7.46805
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.059
ELB improved by 5.08471
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.952
ELB improved by 5.10714
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.144
ELB improved by 5.80759
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.412
ELB improved by 6.73185
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.216
ELB improved by 7.19677
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.937
ELB improved by 6.2789
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.748
ELB improved by 4.18845
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.393
ELB improved by 2.3549
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.077
ELB improved by 1.31661
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.274
ELB improved by 0.802644
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.738
ELB improved by 0.536117
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.351
ELB improved by 0.386653
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.054
ELB improved by 0.297402
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.813
ELB improved by 0.240688
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.611
ELB improved by 0.202064
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.437
ELB improved by 0.173803
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.286
ELB improved by 0.151669
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.152
ELB improved by 0.133341
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.035
ELB improved by 0.117651
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.931
ELB improved by 0.104119
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.838
ELB improved by 0.0925706
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.755
ELB improved by 0.08286
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.68
ELB improved by 0.0747655
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.612
ELB improved by 0.06801
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.55
ELB improved by 0.0623197
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.493
ELB improved by 0.0574625
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.439
ELB improved by 0.0532589
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.39
ELB improved by 0.0495747
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.343
ELB improved by 0.0463105
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.3
ELB improved by 0.0433917
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.259
ELB improved by 0.0407609
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.221
ELB improved by 0.0383734
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.185
ELB improved by 0.0361934
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.151
ELB improved by 0.0341922
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.118
ELB improved by 0.0323461
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.088
ELB improved by 0.030636
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.059
ELB improved by 0.029046
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.031
ELB improved by 0.0275627
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.005
ELB improved by 0.0261752
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.98
ELB improved by 0.0248744
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.956
ELB improved by 0.0236524
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.934
ELB improved by 0.0225026
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.912
ELB improved by 0.0214195
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.892
ELB improved by 0.0203982
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.872
ELB improved by 0.0194344
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.854
ELB improved by 0.0185246
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.836
ELB improved by 0.0176653
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.819
ELB improved by 0.0168536
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.803
ELB improved by 0.0160868
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.788
ELB improved by 0.0153624
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.773
ELB improved by 0.014678
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.759
ELB improved by 0.0140315
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.746
ELB improved by 0.0134208
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.733
ELB improved by 0.012844
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.721
ELB improved by 0.0122992
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.709
ELB improved by 0.0117846
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.698
ELB improved by 0.0112987
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.687
ELB improved by 0.0108397
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.676
ELB improved by 0.0104062
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.666
ELB improved by 0.00999667
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-861.353
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-575.96
ELB improved by 285.394
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-514.877
ELB improved by 61.0827
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-474.716
ELB improved by 40.161
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.138
ELB improved by 16.5775
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.97
ELB improved by 6.16854
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.543
ELB improved by 3.42697
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.812
ELB improved by 2.73111
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.265
ELB improved by 2.54679
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.736
ELB improved by 2.5293
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.155
ELB improved by 2.58024
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.493
ELB improved by 2.66245
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.748
ELB improved by 2.74484
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.969
ELB improved by 2.77883
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.25
ELB improved by 2.71965
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.675
ELB improved by 2.5751
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.319
ELB improved by 2.3558
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.264
ELB improved by 2.05474
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.527
ELB improved by 1.7365
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.177
ELB improved by 1.35045
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.227
ELB improved by 0.949845
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.567
ELB improved by 0.660618
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.076
ELB improved by 0.490445
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.671
ELB improved by 0.404802
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.3
ELB improved by 0.371088
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.932
ELB improved by 0.368311
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.546
ELB improved by 0.385524
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.129
ELB improved by 0.417846
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.665
ELB improved by 0.463505
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.143
ELB improved by 0.52203
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.55
ELB improved by 0.593055
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.875
ELB improved by 0.67539
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.108
ELB improved by 0.766345
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.246
ELB improved by 0.86173
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.289
ELB improved by 0.957049
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.24
ELB improved by 1.04972
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.099
ELB improved by 1.14029
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.87
ELB improved by 1.22975
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.557
ELB improved by 1.31231
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.189
ELB improved by 1.36856
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.82
ELB improved by 1.36839
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.532
ELB improved by 1.28847
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.401
ELB improved by 1.13054
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.478
ELB improved by 0.923737
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.766
ELB improved by 0.711554
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.234
ELB improved by 0.532576
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.826
ELB improved by 0.407234
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.486
ELB improved by 0.340428
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.154
ELB improved by 0.331695
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.791
ELB improved by 0.363196
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.435
ELB improved by 0.356169
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.175
ELB improved by 0.259558
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.017
ELB improved by 0.158119
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.917
ELB improved by 0.10011
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.846
ELB improved by 0.0711882
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.79
ELB improved by 0.0555676
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.744
ELB improved by 0.0458068
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.706
ELB improved by 0.0388797
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.672
ELB improved by 0.0335501
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.643
ELB improved by 0.0292626
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.617
ELB improved by 0.025727
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.594
ELB improved by 0.0227667
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.574
ELB improved by 0.0202621
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.556
ELB improved by 0.0181266
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.54
ELB improved by 0.0162943
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.525
ELB improved by 0.0147143
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.512
ELB improved by 0.013346
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.499
ELB improved by 0.0121564
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.488
ELB improved by 0.0111189
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.478
ELB improved by 0.0102112
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.469
ELB improved by 0.00941481
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-851.65
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-567.027
ELB improved by 284.623
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-508.941
ELB improved by 58.0853
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.852
ELB improved by 37.0897
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.681
ELB improved by 17.1705
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.631
ELB improved by 8.0507
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.453
ELB improved by 5.17768
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.013
ELB improved by 4.44025
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.656
ELB improved by 4.35644
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.207
ELB improved by 4.44931
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.828
ELB improved by 4.37879
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.951
ELB improved by 3.87676
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.971
ELB improved by 2.97999
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.928
ELB improved by 2.04329
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.571
ELB improved by 1.35723
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.63
ELB improved by 0.940599
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.93
ELB improved by 0.700026
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.368
ELB improved by 0.562368
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.887
ELB improved by 0.481106
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.46
ELB improved by 0.426477
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.076
ELB improved by 0.384199
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.725
ELB improved by 0.350882
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.399
ELB improved by 0.325951
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.092
ELB improved by 0.307604
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.798
ELB improved by 0.293355
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.517
ELB improved by 0.281159
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.247
ELB improved by 0.269708
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.989
ELB improved by 0.258288
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.742
ELB improved by 0.246578
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.508
ELB improved by 0.234515
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.286
ELB improved by 0.222181
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.076
ELB improved by 0.209737
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.879
ELB improved by 0.197367
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.693
ELB improved by 0.18524
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.52
ELB improved by 0.173497
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.358
ELB improved by 0.16224
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.206
ELB improved by 0.151537
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.065
ELB improved by 0.141428
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.933
ELB improved by 0.131929
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.81
ELB improved by 0.123039
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.695
ELB improved by 0.114748
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.588
ELB improved by 0.107034
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.488
ELB improved by 0.099872
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.395
ELB improved by 0.0932293
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.308
ELB improved by 0.0870721
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.226
ELB improved by 0.0813647
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.15
ELB improved by 0.0760708
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.079
ELB improved by 0.0711549
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.013
ELB improved by 0.0665827
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.95
ELB improved by 0.0623223
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.892
ELB improved by 0.0583442
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.837
ELB improved by 0.0546219
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.786
ELB improved by 0.0511318
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.738
ELB improved by 0.0478533
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.694
ELB improved by 0.0447684
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.652
ELB improved by 0.0418619
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.613
ELB improved by 0.0391208
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.576
ELB improved by 0.0365342
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.542
ELB improved by 0.0340928
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.51
ELB improved by 0.0317889
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.481
ELB improved by 0.0296156
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.453
ELB improved by 0.0275673
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.427
ELB improved by 0.0256388
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.404
ELB improved by 0.0238252
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.381
ELB improved by 0.0221224
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.361
ELB improved by 0.0205261
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.342
ELB improved by 0.0190322
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.324
ELB improved by 0.0176367
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.308
ELB improved by 0.0163356
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.293
ELB improved by 0.0151247
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.279
ELB improved by 0.014
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.266
ELB improved by 0.0129574
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.254
ELB improved by 0.0119926
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.243
ELB improved by 0.0111014
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.232
ELB improved by 0.0102796
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.223
ELB improved by 0.00952315
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-869.856
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-603.935
ELB improved by 265.921
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-539.76
ELB improved by 64.1756
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-490.288
ELB improved by 49.4717
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.052
ELB improved by 25.2358
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.873
ELB improved by 11.1797
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.385
ELB improved by 6.48757
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.818
ELB improved by 5.56696
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.14
ELB improved by 5.67823
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.109
ELB improved by 6.03129
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.04
ELB improved by 6.06828
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.541
ELB improved by 5.49885
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.973
ELB improved by 4.56868
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.256
ELB improved by 3.7172
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.347
ELB improved by 2.90809
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.251
ELB improved by 2.09608
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.774
ELB improved by 1.47756
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.683
ELB improved by 1.09111
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.81
ELB improved by 0.872979
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.054
ELB improved by 0.755764
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.374
ELB improved by 0.68018
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.771
ELB improved by 0.602745
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.246
ELB improved by 0.524584
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.78
ELB improved by 0.466502
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.348
ELB improved by 0.431615
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.935
ELB improved by 0.412929
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.531
ELB improved by 0.404347
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.129
ELB improved by 0.402006
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.726
ELB improved by 0.403173
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.32
ELB improved by 0.405491
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.914
ELB improved by 0.406846
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.508
ELB improved by 0.405598
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.107
ELB improved by 0.400765
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.715
ELB improved by 0.391962
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.336
ELB improved by 0.379224
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.973
ELB improved by 0.36289
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.63
ELB improved by 0.343586
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.307
ELB improved by 0.322216
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.007
ELB improved by 0.299882
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.73
ELB improved by 0.277736
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.473
ELB improved by 0.256793
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.235
ELB improved by 0.237745
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.014
ELB improved by 0.220816
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.809
ELB improved by 0.205706
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.617
ELB improved by 0.191681
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.439
ELB improved by 0.177846
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.276
ELB improved by 0.163513
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.127
ELB improved by 0.148495
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.994
ELB improved by 0.133112
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.876
ELB improved by 0.117967
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.772
ELB improved by 0.10368
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.682
ELB improved by 0.0907338
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.602
ELB improved by 0.0794327
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.532
ELB improved by 0.0699218
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.47
ELB improved by 0.0622164
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.414
ELB improved by 0.0562185
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.362
ELB improved by 0.0517075
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.314
ELB improved by 0.0483187
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.268
ELB improved by 0.0455472
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.225
ELB improved by 0.0428423
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.186
ELB improved by 0.0398011
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.149
ELB improved by 0.0363429
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.117
ELB improved by 0.0326977
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.087
ELB improved by 0.0292105
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.061
ELB improved by 0.0261409
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.038
ELB improved by 0.0235893
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.016
ELB improved by 0.0215289
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.996
ELB improved by 0.0198653
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.978
ELB improved by 0.018484
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.96
ELB improved by 0.0172776
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.944
ELB improved by 0.0161616
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.929
ELB improved by 0.0150817
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.915
ELB improved by 0.0140145
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.902
ELB improved by 0.0129623
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.89
ELB improved by 0.0119426
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.879
ELB improved by 0.0109778
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.869
ELB improved by 0.0100871
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.86
ELB improved by 0.00928275
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.333 0.198 2.519
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.053 | 0.020 | 0.075 | |
| getPIPs | 0.048 | 0.014 | 0.061 | |
| graper | 0.086 | 0.014 | 0.099 | |
| makeExampleData | 0.011 | 0.000 | 0.010 | |
| makeExampleDataWithUnequalGroups | 0.012 | 0.000 | 0.013 | |
| plotELBO | 0.330 | 0.029 | 0.359 | |
| plotGroupPenalties | 1.068 | 0.062 | 1.130 | |
| plotPosterior | 0.621 | 0.019 | 0.641 | |
| predict.graper | 2.056 | 0.067 | 2.124 | |
| print.graper | 0.048 | 0.015 | 0.063 | |