Britta Velten
| Snapshot Date: 2026-02-10 13:40 -0500 (Tue, 10 Feb 2026) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: 95474d7 |
| git_last_commit_date: 2025-10-29 10:49:21 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-11 11:32 -0500 (Wed, 11 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4862 |
| 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 926/2351 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.27.0 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for graper in R Universe. | ||||||||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: graper |
| Version: 1.27.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings graper_1.27.0.tar.gz |
| StartedAt: 2026-02-11 00:38:02 -0500 (Wed, 11 Feb 2026) |
| EndedAt: 2026-02-11 00:39:34 -0500 (Wed, 11 Feb 2026) |
| EllapsedTime: 91.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings graper_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.27.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) predict.graper.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:23-24: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.27.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c fit_graper.cpp -o fit_graper.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -llapack -L/home/biocbuild/bbs-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-graper/00new/graper/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (graper)
graper.Rcheck/tests/testthat.Rout
R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(graper)
>
> test_check("graper")
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-868.425
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-583.472
ELB improved by 284.953
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-522.569
ELB improved by 60.9029
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-477.825
ELB improved by 44.7436
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.196
ELB improved by 21.6291
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.288
ELB improved by 7.90791
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.323
ELB improved by 3.96531
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.418
ELB improved by 2.90532
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.905
ELB improved by 2.51241
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.547
ELB improved by 2.35876
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.257
ELB improved by 2.29008
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.013
ELB improved by 2.2432
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.829
ELB improved by 2.18433
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.742
ELB improved by 2.08727
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.807
ELB improved by 1.9351
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.078
ELB improved by 1.72872
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.591
ELB improved by 1.48706
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.356
ELB improved by 1.2346
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.368
ELB improved by 0.988097
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.602
ELB improved by 0.766088
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.01
ELB improved by 0.59223
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.536
ELB improved by 0.473969
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.134
ELB improved by 0.401589
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.773
ELB improved by 0.361775
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.428
ELB improved by 0.344393
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.085
ELB improved by 0.34336
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.729
ELB improved by 0.355959
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.347
ELB improved by 0.382057
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.924
ELB improved by 0.423109
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.444
ELB improved by 0.4801
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.893
ELB improved by 0.550982
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.259
ELB improved by 0.633689
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.521
ELB improved by 0.73768
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.636
ELB improved by 0.885397
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.538
ELB improved by 1.09734
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.146
ELB improved by 1.39252
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.424
ELB improved by 1.72188
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.456
ELB improved by 1.96802
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.24
ELB improved by 2.21586
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.69
ELB improved by 2.55064
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.816
ELB improved by 2.874
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.942
ELB improved by 2.87369
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.385
ELB improved by 2.55658
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.275
ELB improved by 2.11019
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.666
ELB improved by 1.60856
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.549
ELB improved by 1.11748
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.82
ELB improved by 0.728688
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.337
ELB improved by 0.483432
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.993
ELB improved by 0.34365
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.739
ELB improved by 0.254751
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.552
ELB improved by 0.186084
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.421
ELB improved by 0.131831
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.328
ELB improved by 0.0928907
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.261
ELB improved by 0.0669642
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.211
ELB improved by 0.049976
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.172
ELB improved by 0.0385432
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.142
ELB improved by 0.0305026
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.117
ELB improved by 0.0245988
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.097
ELB improved by 0.0201151
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.08
ELB improved by 0.0166293
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.066
ELB improved by 0.0138776
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.055
ELB improved by 0.0116844
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.045
ELB improved by 0.00992531
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-866.066
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-589.982
ELB improved by 276.083
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-529.906
ELB improved by 60.0763
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-487.312
ELB improved by 42.5935
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.158
ELB improved by 23.1543
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.468
ELB improved by 10.6904
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.83
ELB improved by 6.63746
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.651
ELB improved by 6.17904
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.072
ELB improved by 6.57879
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.227
ELB improved by 6.84508
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.801
ELB improved by 6.42648
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.507
ELB improved by 5.29352
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.521
ELB improved by 3.98668
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.596
ELB improved by 2.92469
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.564
ELB improved by 2.0315
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.207
ELB improved by 1.35765
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.262
ELB improved by 0.945008
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.555
ELB improved by 0.707205
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.986
ELB improved by 0.568281
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.502
ELB improved by 0.484746
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.068
ELB improved by 0.433631
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.665
ELB improved by 0.403007
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.278
ELB improved by 0.386632
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.897
ELB improved by 0.381304
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.511
ELB improved by 0.385726
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.111
ELB improved by 0.399885
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.687
ELB improved by 0.424043
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.231
ELB improved by 0.456341
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.741
ELB improved by 0.489965
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.226
ELB improved by 0.515319
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.697
ELB improved by 0.528235
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.166
ELB improved by 0.531785
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.636
ELB improved by 0.529884
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.112
ELB improved by 0.524103
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.597
ELB improved by 0.514352
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.098
ELB improved by 0.499705
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.619
ELB improved by 0.47893
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.168
ELB improved by 0.451074
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.752
ELB improved by 0.41605
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.377
ELB improved by 0.375002
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.046
ELB improved by 0.330237
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.762
ELB improved by 0.284698
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.52
ELB improved by 0.241186
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.319
ELB improved by 0.20173
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.151
ELB improved by 0.167334
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.013
ELB improved by 0.138125
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.9
ELB improved by 0.113696
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.806
ELB improved by 0.093437
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.729
ELB improved by 0.07674
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.666
ELB improved by 0.0630662
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.614
ELB improved by 0.0519455
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.571
ELB improved by 0.0429592
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.536
ELB improved by 0.0357324
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.506
ELB improved by 0.0299354
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.48
ELB improved by 0.0252859
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.459
ELB improved by 0.0215495
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.44
ELB improved by 0.0185353
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.424
ELB improved by 0.016091
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.41
ELB improved by 0.0140965
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.398
ELB improved by 0.0124576
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.387
ELB improved by 0.0111007
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.377
ELB improved by 0.00996867
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-891.891
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-580.649
ELB improved by 311.242
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-519.563
ELB improved by 61.0867
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-484.238
ELB improved by 35.3249
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.347
ELB improved by 14.8903
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.472
ELB improved by 7.87546
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.725
ELB improved by 6.74712
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.28
ELB improved by 7.44429
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.186
ELB improved by 8.09462
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.7
ELB improved by 7.4863
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.986
ELB improved by 5.71389
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.057
ELB improved by 3.92872
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.33
ELB improved by 2.72737
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.356
ELB improved by 1.97356
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.897
ELB improved by 1.45915
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.806
ELB improved by 1.09073
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.998
ELB improved by 0.807856
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.399
ELB improved by 0.599516
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.934
ELB improved by 0.464582
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.553
ELB improved by 0.380676
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.227
ELB improved by 0.326271
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.938
ELB improved by 0.289052
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.675
ELB improved by 0.262672
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.432
ELB improved by 0.243656
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.202
ELB improved by 0.229902
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.982
ELB improved by 0.22003
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.769
ELB improved by 0.213083
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.56
ELB improved by 0.20838
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.355
ELB improved by 0.205431
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.151
ELB improved by 0.203895
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.948
ELB improved by 0.203542
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.743
ELB improved by 0.204235
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.537
ELB improved by 0.205903
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.329
ELB improved by 0.208519
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.117
ELB improved by 0.212078
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.9
ELB improved by 0.216574
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.678
ELB improved by 0.221974
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.45
ELB improved by 0.228205
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.215
ELB improved by 0.235134
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.972
ELB improved by 0.242558
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.722
ELB improved by 0.250203
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.464
ELB improved by 0.257723
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.2
ELB improved by 0.264712
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.929
ELB improved by 0.270723
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.654
ELB improved by 0.2753
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.376
ELB improved by 0.278015
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.097
ELB improved by 0.27852
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.821
ELB improved by 0.276587
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.548
ELB improved by 0.272129
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.283
ELB improved by 0.265168
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.028
ELB improved by 0.255741
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.784
ELB improved by 0.243769
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.555
ELB improved by 0.229066
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.343
ELB improved by 0.21169
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.151
ELB improved by 0.192487
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.977
ELB improved by 0.173121
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.822
ELB improved by 0.155272
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.682
ELB improved by 0.139713
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.556
ELB improved by 0.126055
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.443
ELB improved by 0.113193
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.343
ELB improved by 0.10015
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.256
ELB improved by 0.0868154
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.182
ELB improved by 0.0739185
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.12
ELB improved by 0.0623366
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.067
ELB improved by 0.0525234
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.023
ELB improved by 0.0444623
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.985
ELB improved by 0.0378934
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.953
ELB improved by 0.0325108
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.925
ELB improved by 0.0280533
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.9
ELB improved by 0.0243221
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.879
ELB improved by 0.0211714
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.861
ELB improved by 0.0184932
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.844
ELB improved by 0.0162054
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.83
ELB improved by 0.0142439
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.818
ELB improved by 0.012557
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.806
ELB improved by 0.0111027
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.797
ELB improved by 0.00984603
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-847.941
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-568.853
ELB improved by 279.088
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-508.597
ELB improved by 60.256
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.355
ELB improved by 38.2427
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.16
ELB improved by 16.1946
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.034
ELB improved by 7.12562
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.047
ELB improved by 4.98726
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.478
ELB improved by 4.56902
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.677
ELB improved by 4.80128
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.357
ELB improved by 5.31943
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.572
ELB improved by 5.78523
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.837
ELB improved by 5.73561
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.963
ELB improved by 4.87316
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.404
ELB improved by 3.55937
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.974
ELB improved by 2.43023
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.315
ELB improved by 1.65889
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.187
ELB improved by 1.12818
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.395
ELB improved by 0.791717
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.794
ELB improved by 0.600719
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.3
ELB improved by 0.494674
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.862
ELB improved by 0.437442
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.45
ELB improved by 0.412195
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.042
ELB improved by 0.407766
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.641
ELB improved by 0.40151
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.28
ELB improved by 0.360322
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.994
ELB improved by 0.286767
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.775
ELB improved by 0.219006
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.599
ELB improved by 0.175234
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.449
ELB improved by 0.150621
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.311
ELB improved by 0.137658
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.178
ELB improved by 0.132778
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.042
ELB improved by 0.135894
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.893
ELB improved by 0.149087
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.72
ELB improved by 0.17359
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.518
ELB improved by 0.201394
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.309
ELB improved by 0.209688
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.124
ELB improved by 0.184744
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.979
ELB improved by 0.144957
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.867
ELB improved by 0.112355
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.775
ELB improved by 0.0914007
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.697
ELB improved by 0.0784004
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.627
ELB improved by 0.069867
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.563
ELB improved by 0.0638546
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.504
ELB improved by 0.0593853
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.448
ELB improved by 0.0559523
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.394
ELB improved by 0.0532712
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.343
ELB improved by 0.0511671
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.294
ELB improved by 0.0495217
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.246
ELB improved by 0.0482467
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.198
ELB improved by 0.0472701
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.152
ELB improved by 0.0465281
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.106
ELB improved by 0.0459619
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.06
ELB improved by 0.0455164
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.015
ELB improved by 0.0451405
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.97
ELB improved by 0.0447887
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.926
ELB improved by 0.044423
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.882
ELB improved by 0.0440139
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.838
ELB improved by 0.0435416
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.795
ELB improved by 0.0429952
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.753
ELB improved by 0.0423719
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.711
ELB improved by 0.0416754
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.67
ELB improved by 0.0409137
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.63
ELB improved by 0.0400972
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.591
ELB improved by 0.0392376
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.553
ELB improved by 0.0383459
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.515
ELB improved by 0.0374322
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.479
ELB improved by 0.0365043
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.443
ELB improved by 0.0355683
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.409
ELB improved by 0.0346284
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.375
ELB improved by 0.0336874
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.342
ELB improved by 0.0327474
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.31
ELB improved by 0.0318103
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.279
ELB improved by 0.0308784
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.249
ELB improved by 0.0299545
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.22
ELB improved by 0.029042
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.192
ELB improved by 0.0281447
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.165
ELB improved by 0.0272661
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.139
ELB improved by 0.0264092
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.113
ELB improved by 0.0255762
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.088
ELB improved by 0.0247684
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.064
ELB improved by 0.0239858
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.041
ELB improved by 0.0232279
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.019
ELB improved by 0.0224931
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.997
ELB improved by 0.0217795
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.976
ELB improved by 0.0210852
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.955
ELB improved by 0.0204079
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.936
ELB improved by 0.0197458
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.916
ELB improved by 0.019097
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.898
ELB improved by 0.0184601
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.88
ELB improved by 0.0178341
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.863
ELB improved by 0.0172182
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.846
ELB improved by 0.0166118
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.83
ELB improved by 0.0160149
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.815
ELB improved by 0.0154273
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.8
ELB improved by 0.0148494
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.786
ELB improved by 0.0142815
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.772
ELB improved by 0.013724
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.759
ELB improved by 0.0131776
iteration 99
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.746
ELB improved by 0.0126427
iteration 100
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.734
ELB improved by 0.0121199
iteration 101
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.722
ELB improved by 0.0116099
iteration 102
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.711
ELB improved by 0.0111132
iteration 103
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.701
ELB improved by 0.0106302
iteration 104
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.691
ELB improved by 0.0101614
iteration 105
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.681
ELB improved by 0.00970712
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.341 0.207 2.534
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.047 | 0.028 | 0.076 | |
| getPIPs | 0.047 | 0.015 | 0.062 | |
| graper | 0.081 | 0.020 | 0.101 | |
| makeExampleData | 0.009 | 0.002 | 0.011 | |
| makeExampleDataWithUnequalGroups | 0.011 | 0.002 | 0.014 | |
| plotELBO | 0.324 | 0.024 | 0.348 | |
| plotGroupPenalties | 1.077 | 0.061 | 1.139 | |
| plotPosterior | 0.637 | 0.016 | 0.653 | |
| predict.graper | 2.047 | 0.075 | 2.122 | |
| print.graper | 0.049 | 0.013 | 0.063 | |