Britta Velten
| Snapshot Date: 2026-02-26 13:40 -0500 (Thu, 26 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 2026-02-27 11:32 -0500 (Fri, 27 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" | 4877 |
| 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 | | ||||||||
| 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: 2026-02-27 00:22:32 -0500 (Fri, 27 Feb 2026) |
| EndedAt: 2026-02-27 00:24:04 -0500 (Fri, 27 Feb 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=-862.834
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-563.197
ELB improved by 299.637
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-499.566
ELB improved by 63.6309
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.695
ELB improved by 40.8713
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.532
ELB improved by 18.1629
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.706
ELB improved by 7.8265
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.917
ELB improved by 4.78923
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.11
ELB improved by 3.80667
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.537
ELB improved by 3.57325
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.829
ELB improved by 3.70735
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.796
ELB improved by 4.03337
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.409
ELB improved by 4.38643
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.896
ELB improved by 4.5133
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.748
ELB improved by 4.14806
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.471
ELB improved by 3.27672
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.221
ELB improved by 2.25012
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.779
ELB improved by 1.44256
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.837
ELB improved by 0.941765
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.18
ELB improved by 0.657197
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.687
ELB improved by 0.492979
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.294
ELB improved by 0.392645
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.966
ELB improved by 0.32759
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.683
ELB improved by 0.283301
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.431
ELB improved by 0.251959
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.202
ELB improved by 0.229027
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.991
ELB improved by 0.211696
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.792
ELB improved by 0.198143
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.605
ELB improved by 0.187156
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.427
ELB improved by 0.177919
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.257
ELB improved by 0.169874
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.095
ELB improved by 0.162629
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.939
ELB improved by 0.155919
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.789
ELB improved by 0.149575
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.646
ELB improved by 0.143511
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.508
ELB improved by 0.137717
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.376
ELB improved by 0.132234
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.249
ELB improved by 0.127152
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.126
ELB improved by 0.122591
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.007
ELB improved by 0.118707
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.892
ELB improved by 0.115693
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.778
ELB improved by 0.1138
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.665
ELB improved by 0.113355
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.55
ELB improved by 0.114765
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.431
ELB improved by 0.118419
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.307
ELB improved by 0.124367
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.175
ELB improved by 0.131611
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.038
ELB improved by 0.137476
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.899
ELB improved by 0.138477
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.766
ELB improved by 0.133132
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.643
ELB improved by 0.123359
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.531
ELB improved by 0.11223
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.429
ELB improved by 0.101613
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.337
ELB improved by 0.0920558
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.254
ELB improved by 0.0835327
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.178
ELB improved by 0.0758963
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.109
ELB improved by 0.069014
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.046
ELB improved by 0.0627841
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.989
ELB improved by 0.0571278
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.937
ELB improved by 0.0519814
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.889
ELB improved by 0.0472918
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.846
ELB improved by 0.043014
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.807
ELB improved by 0.0391088
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.772
ELB improved by 0.0355418
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.739
ELB improved by 0.032283
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.71
ELB improved by 0.0293055
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.684
ELB improved by 0.026586
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.659
ELB improved by 0.0241041
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.638
ELB improved by 0.0218423
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.618
ELB improved by 0.0197855
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.6
ELB improved by 0.0179202
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.584
ELB improved by 0.0162345
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.569
ELB improved by 0.0147167
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.556
ELB improved by 0.0133553
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.543
ELB improved by 0.0121387
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.532
ELB improved by 0.011055
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.522
ELB improved by 0.0100921
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.513
ELB improved by 0.00923806
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-893.378
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-557.423
ELB improved by 335.956
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-503.131
ELB improved by 54.2918
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-474.249
ELB improved by 28.8824
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.182
ELB improved by 13.0662
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.828
ELB improved by 6.3539
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.31
ELB improved by 4.51816
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.394
ELB improved by 3.9167
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.797
ELB improved by 3.59686
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.464
ELB improved by 3.33295
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.414
ELB improved by 3.04943
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.698
ELB improved by 2.71676
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.358
ELB improved by 2.33959
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.408
ELB improved by 1.95003
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.824
ELB improved by 1.58377
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.564
ELB improved by 1.25973
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.579
ELB improved by 0.985506
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.812
ELB improved by 0.766715
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.21
ELB improved by 0.602612
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.726
ELB improved by 0.483676
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.329
ELB improved by 0.396903
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.998
ELB improved by 0.331407
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.717
ELB improved by 0.280134
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.479
ELB improved by 0.238944
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.273
ELB improved by 0.205337
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.096
ELB improved by 0.177671
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.941
ELB improved by 0.154776
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.805
ELB improved by 0.135756
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.685
ELB improved by 0.119882
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.579
ELB improved by 0.106562
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.483
ELB improved by 0.0953163
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.397
ELB improved by 0.0857712
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.32
ELB improved by 0.0776385
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.249
ELB improved by 0.0706985
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.184
ELB improved by 0.0647808
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.125
ELB improved by 0.0597498
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.069
ELB improved by 0.0554937
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.017
ELB improved by 0.0519177
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.968
ELB improved by 0.0489408
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.922
ELB improved by 0.0464934
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.877
ELB improved by 0.0445167
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.834
ELB improved by 0.0429623
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.792
ELB improved by 0.0417913
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.752
ELB improved by 0.0409738
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.711
ELB improved by 0.0404886
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.671
ELB improved by 0.0403223
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.63
ELB improved by 0.0404689
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.589
ELB improved by 0.0409295
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.548
ELB improved by 0.0417124
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.505
ELB improved by 0.0428326
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.46
ELB improved by 0.0443125
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.414
ELB improved by 0.0461825
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.366
ELB improved by 0.0484817
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.315
ELB improved by 0.051259
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.26
ELB improved by 0.054575
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.201
ELB improved by 0.058504
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.138
ELB improved by 0.0631367
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.07
ELB improved by 0.0685844
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.995
ELB improved by 0.0749835
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.912
ELB improved by 0.082503
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.821
ELB improved by 0.0913541
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.719
ELB improved by 0.101804
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.605
ELB improved by 0.114192
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.476
ELB improved by 0.128959
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.329
ELB improved by 0.146677
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.161
ELB improved by 0.168089
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.967
ELB improved by 0.19416
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.741
ELB improved by 0.226119
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.475
ELB improved by 0.265484
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.161
ELB improved by 0.314034
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.788
ELB improved by 0.373672
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.342
ELB improved by 0.446088
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.81
ELB improved by 0.532093
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.179
ELB improved by 0.630371
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.444
ELB improved by 0.735382
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.609
ELB improved by 0.834809
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.7
ELB improved by 0.909214
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.762
ELB improved by 0.937936
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.854
ELB improved by 0.907451
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.041
ELB improved by 0.812983
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.375
ELB improved by 0.666499
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.87
ELB improved by 0.504841
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.506
ELB improved by 0.364394
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.247
ELB improved by 0.259064
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.061
ELB improved by 0.185855
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.924
ELB improved by 0.136353
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.822
ELB improved by 0.102673
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.743
ELB improved by 0.0790547
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.681
ELB improved by 0.0617771
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.632
ELB improved by 0.0486542
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.594
ELB improved by 0.0384732
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.563
ELB improved by 0.0305356
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.539
ELB improved by 0.0243714
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.519
ELB improved by 0.0196117
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.503
ELB improved by 0.0159495
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.49
ELB improved by 0.0131334
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.479
ELB improved by 0.0109626
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.47
ELB improved by 0.00928136
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-901.854
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-577.258
ELB improved by 324.596
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-520.117
ELB improved by 57.1414
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-485.687
ELB improved by 34.4303
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.923
ELB improved by 15.7639
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.769
ELB improved by 8.15333
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.85
ELB improved by 5.91929
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.429
ELB improved by 5.42091
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.915
ELB improved by 5.51431
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.382
ELB improved by 5.5325
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.305
ELB improved by 5.07787
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.128
ELB improved by 4.17675
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.973
ELB improved by 3.1547
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.7
ELB improved by 2.27266
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.089
ELB improved by 1.61162
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.931
ELB improved by 1.15735
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.055
ELB improved by 0.875937
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.345
ELB improved by 0.710786
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.733
ELB improved by 0.611502
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.186
ELB improved by 0.54751
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.683
ELB improved by 0.502347
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.216
ELB improved by 0.467329
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.778
ELB improved by 0.437942
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.366
ELB improved by 0.411987
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.978
ELB improved by 0.388576
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.61
ELB improved by 0.367548
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.261
ELB improved by 0.349105
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.927
ELB improved by 0.333608
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.606
ELB improved by 0.32151
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.292
ELB improved by 0.313402
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.982
ELB improved by 0.310216
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.669
ELB improved by 0.313609
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.342
ELB improved by 0.326631
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.988
ELB improved by 0.354296
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.586
ELB improved by 0.401559
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.124
ELB improved by 0.461946
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.62
ELB improved by 0.504278
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.116
ELB improved by 0.503499
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.64
ELB improved by 0.476505
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.195
ELB improved by 0.444402
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.784
ELB improved by 0.411022
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.41
ELB improved by 0.374213
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.078
ELB improved by 0.332581
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.791
ELB improved by 0.286876
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.551
ELB improved by 0.239798
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.356
ELB improved by 0.194904
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.201
ELB improved by 0.155192
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.079
ELB improved by 0.122263
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.982
ELB improved by 0.0963447
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.905
ELB improved by 0.0768088
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.843
ELB improved by 0.062726
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.789
ELB improved by 0.0532705
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.741
ELB improved by 0.0480103
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.694
ELB improved by 0.0472518
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.641
ELB improved by 0.0527679
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.572
ELB improved by 0.069678
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.461
ELB improved by 0.111173
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.254
ELB improved by 0.206394
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.87
ELB improved by 0.384352
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.313
ELB improved by 0.556793
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.773
ELB improved by 0.539928
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.379
ELB improved by 0.393993
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.103
ELB improved by 0.275881
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.88
ELB improved by 0.223411
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.669
ELB improved by 0.211144
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.464
ELB improved by 0.205085
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.285
ELB improved by 0.178981
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.156
ELB improved by 0.128103
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.081
ELB improved by 0.0752275
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.041
ELB improved by 0.0404511
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.018
ELB improved by 0.022674
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.004
ELB improved by 0.014161
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.994
ELB improved by 0.00987956
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-897.531
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-562.824
ELB improved by 334.708
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-503.993
ELB improved by 58.8305
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.968
ELB improved by 30.0246
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.627
ELB improved by 10.3416
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.128
ELB improved by 4.49851
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.357
ELB improved by 2.77141
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.163
ELB improved by 2.19428
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.132
ELB improved by 2.03035
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.105
ELB improved by 2.02708
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.01
ELB improved by 2.09573
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.819
ELB improved by 2.19068
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.554
ELB improved by 2.26453
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.299
ELB improved by 2.25534
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.19
ELB improved by 2.109
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.364
ELB improved by 1.82592
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.89
ELB improved by 1.47395
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.75
ELB improved by 1.14006
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.872
ELB improved by 0.878233
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.171
ELB improved by 0.701057
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.574
ELB improved by 0.59699
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.026
ELB improved by 0.547523
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.489
ELB improved by 0.536948
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.934
ELB improved by 0.555164
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.337
ELB improved by 0.596634
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.679
ELB improved by 0.65835
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.941
ELB improved by 0.737971
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.109
ELB improved by 0.832539
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.17
ELB improved by 0.938271
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.119
ELB improved by 1.05158
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.949
ELB improved by 1.16994
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.659
ELB improved by 1.2902
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.255
ELB improved by 1.40411
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.761
ELB improved by 1.4935
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.232
ELB improved by 1.52882
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.756
ELB improved by 1.47662
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.434
ELB improved by 1.32157
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.345
ELB improved by 1.08945
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.506
ELB improved by 0.838091
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.887
ELB improved by 0.619405
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.432
ELB improved by 0.45549
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.088
ELB improved by 0.343792
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.815
ELB improved by 0.272354
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.585
ELB improved by 0.230004
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.375
ELB improved by 0.210298
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.162
ELB improved by 0.213299
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.913
ELB improved by 0.248985
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.57
ELB improved by 0.343007
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.047
ELB improved by 0.522971
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.318
ELB improved by 0.728791
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.514
ELB improved by 0.803837
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.825
ELB improved by 0.689006
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.35
ELB improved by 0.475654
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.043
ELB improved by 0.306243
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.834
ELB improved by 0.209664
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.673
ELB improved by 0.16091
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.531
ELB improved by 0.141556
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.39
ELB improved by 0.141488
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.241
ELB improved by 0.148761
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.097
ELB improved by 0.144114
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.979
ELB improved by 0.117788
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.895
ELB improved by 0.0838132
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.838
ELB improved by 0.0574229
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.797
ELB improved by 0.0408343
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.766
ELB improved by 0.0308295
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.742
ELB improved by 0.0245635
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.721
ELB improved by 0.0203926
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.704
ELB improved by 0.0174474
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.688
ELB improved by 0.0152606
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.675
ELB improved by 0.0135683
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.663
ELB improved by 0.012213
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.652
ELB improved by 0.011097
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.641
ELB improved by 0.0101577
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.632
ELB improved by 0.00935416
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.455 0.216 2.660
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.048 | 0.017 | 0.068 | |
| getPIPs | 0.046 | 0.018 | 0.062 | |
| graper | 0.082 | 0.019 | 0.103 | |
| makeExampleData | 0.010 | 0.000 | 0.011 | |
| makeExampleDataWithUnequalGroups | 0.011 | 0.002 | 0.013 | |
| plotELBO | 0.319 | 0.022 | 0.343 | |
| plotGroupPenalties | 1.087 | 0.051 | 1.137 | |
| plotPosterior | 0.628 | 0.019 | 0.648 | |
| predict.graper | 2.080 | 0.078 | 2.159 | |
| print.graper | 0.049 | 0.019 | 0.067 | |