Britta Velten
| Snapshot Date: 2026-02-15 13:40 -0500 (Sun, 15 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 2026-02-16 11:32 -0500 (Mon, 16 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" | 4865 |
| 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 926/2352 | 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: 2026-02-16 00:19:31 -0500 (Mon, 16 Feb 2026) |
| EndedAt: 2026-02-16 00:21:02 -0500 (Mon, 16 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=-845.949
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-574.282
ELB improved by 271.667
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-510.984
ELB improved by 63.2979
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.418
ELB improved by 42.5661
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.64
ELB improved by 19.7788
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.787
ELB improved by 8.85226
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.041
ELB improved by 5.74632
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.962
ELB improved by 5.07896
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.801
ELB improved by 5.16093
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.385
ELB improved by 5.41585
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.86
ELB improved by 5.52556
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.491
ELB improved by 5.36869
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.582
ELB improved by 4.90908
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.525
ELB improved by 4.05704
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.502
ELB improved by 3.02315
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.401
ELB improved by 2.10095
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.01
ELB improved by 1.39096
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.041
ELB improved by 0.968348
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.286
ELB improved by 0.755727
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.643
ELB improved by 0.642468
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.071
ELB improved by 0.57193
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.552
ELB improved by 0.518967
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.08
ELB improved by 0.472812
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.65
ELB improved by 0.429421
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.262
ELB improved by 0.387841
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.914
ELB improved by 0.348362
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.602
ELB improved by 0.311565
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.324
ELB improved by 0.277896
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.077
ELB improved by 0.24754
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.856
ELB improved by 0.220453
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.66
ELB improved by 0.196438
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.485
ELB improved by 0.175219
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.328
ELB improved by 0.156496
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.188
ELB improved by 0.139979
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.063
ELB improved by 0.125397
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.95
ELB improved by 0.112509
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.849
ELB improved by 0.101103
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.758
ELB improved by 0.0909936
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.676
ELB improved by 0.0820213
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.602
ELB improved by 0.0740461
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.535
ELB improved by 0.0669471
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.475
ELB improved by 0.0606191
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.42
ELB improved by 0.0549706
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.37
ELB improved by 0.0499217
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.324
ELB improved by 0.0454029
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.283
ELB improved by 0.0413532
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.245
ELB improved by 0.0377193
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.211
ELB improved by 0.0344544
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.179
ELB improved by 0.0315176
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.151
ELB improved by 0.0288726
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.124
ELB improved by 0.0264878
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.1
ELB improved by 0.024335
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.077
ELB improved by 0.0223896
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.057
ELB improved by 0.0206296
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.038
ELB improved by 0.0190356
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.02
ELB improved by 0.0175905
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.004
ELB improved by 0.016279
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.989
ELB improved by 0.0150875
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.975
ELB improved by 0.014004
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.962
ELB improved by 0.0130176
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.95
ELB improved by 0.0121188
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.938
ELB improved by 0.011299
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.928
ELB improved by 0.0105504
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.918
ELB improved by 0.00986628
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-842.869
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-580.059
ELB improved by 262.81
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-524.111
ELB improved by 55.9478
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-482.64
ELB improved by 41.471
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.092
ELB improved by 19.5477
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.729
ELB improved by 7.36374
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.029
ELB improved by 3.70002
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.367
ELB improved by 2.66133
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.993
ELB improved by 2.3739
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.632
ELB improved by 2.36151
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.165
ELB improved by 2.46724
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.561
ELB improved by 2.60333
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.896
ELB improved by 2.66544
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.359
ELB improved by 2.5374
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.17
ELB improved by 2.18873
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.444
ELB improved by 1.72565
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.151
ELB improved by 1.29349
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.191
ELB improved by 0.959486
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.478
ELB improved by 0.713053
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.947
ELB improved by 0.531523
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.543
ELB improved by 0.403813
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.224
ELB improved by 0.318838
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.961
ELB improved by 0.263365
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.734
ELB improved by 0.226489
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.533
ELB improved by 0.20108
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.35
ELB improved by 0.182936
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.18
ELB improved by 0.16966
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.021
ELB improved by 0.159868
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.868
ELB improved by 0.152741
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.72
ELB improved by 0.14778
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.575
ELB improved by 0.144681
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.432
ELB improved by 0.143267
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.289
ELB improved by 0.143457
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.143
ELB improved by 0.145243
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.995
ELB improved by 0.148683
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.841
ELB improved by 0.153897
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.68
ELB improved by 0.16108
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.509
ELB improved by 0.170509
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.327
ELB improved by 0.18259
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.129
ELB improved by 0.197898
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.911
ELB improved by 0.217244
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.67
ELB improved by 0.241738
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.397
ELB improved by 0.272845
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.084
ELB improved by 0.312385
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.722
ELB improved by 0.362434
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.297
ELB improved by 0.425
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.796
ELB improved by 0.501353
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.205
ELB improved by 0.590967
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.515
ELB improved by 0.690236
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.723
ELB improved by 0.79139
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.841
ELB improved by 0.882157
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.894
ELB improved by 0.947323
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.92
ELB improved by 0.973306
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.967
ELB improved by 0.953214
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.08
ELB improved by 0.887506
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.296
ELB improved by 0.783414
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.638
ELB improved by 0.658168
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.101
ELB improved by 0.536848
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.661
ELB improved by 0.440367
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.283
ELB improved by 0.377658
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.935
ELB improved by 0.347749
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.596
ELB improved by 0.339116
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.276
ELB improved by 0.320633
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.011
ELB improved by 0.264184
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.824
ELB improved by 0.187816
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.7
ELB improved by 0.124023
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.618
ELB improved by 0.0819664
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.561
ELB improved by 0.056777
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.519
ELB improved by 0.0419389
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.486
ELB improved by 0.0328816
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.459
ELB improved by 0.026987
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.436
ELB improved by 0.022876
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.416
ELB improved by 0.0198334
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.399
ELB improved by 0.017476
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.383
ELB improved by 0.0155864
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.369
ELB improved by 0.0140325
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.357
ELB improved by 0.0127295
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.345
ELB improved by 0.0116196
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.334
ELB improved by 0.0106623
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.324
ELB improved by 0.00982826
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-834.411
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-577.79
ELB improved by 256.622
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-517.294
ELB improved by 60.4959
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.964
ELB improved by 44.3304
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.751
ELB improved by 22.2128
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.246
ELB improved by 10.5047
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.532
ELB improved by 6.71381
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.196
ELB improved by 6.33612
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.418
ELB improved by 6.77858
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.383
ELB improved by 7.03455
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.634
ELB improved by 6.74874
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.473
ELB improved by 6.16107
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.235
ELB improved by 5.23795
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.59
ELB improved by 3.64554
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.189
ELB improved by 2.40097
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.429
ELB improved by 1.75943
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.967
ELB improved by 1.46213
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.636
ELB improved by 1.3314
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.361
ELB improved by 1.27455
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.116
ELB improved by 1.24486
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.896
ELB improved by 1.22057
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.701
ELB improved by 1.19479
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.532
ELB improved by 1.16856
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.388
ELB improved by 1.14425
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.268
ELB improved by 1.12053
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.177
ELB improved by 1.09016
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.136
ELB improved by 1.04137
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.173
ELB improved by 0.963556
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.317
ELB improved by 0.855086
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.591
ELB improved by 0.726712
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.994
ELB improved by 0.596484
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.514
ELB improved by 0.480381
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.127
ELB improved by 0.386629
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.811
ELB improved by 0.316459
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.543
ELB improved by 0.267745
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.306
ELB improved by 0.237286
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.085
ELB improved by 0.220537
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.874
ELB improved by 0.210775
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.673
ELB improved by 0.201457
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.482
ELB improved by 0.190611
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.303
ELB improved by 0.179302
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-368.137
ELB improved by 0.166541
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.986
ELB improved by 0.150106
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.857
ELB improved by 0.129538
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.751
ELB improved by 0.106177
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.668
ELB improved by 0.082843
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.605
ELB improved by 0.0626926
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.558
ELB improved by 0.0471633
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.522
ELB improved by 0.0358472
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.494
ELB improved by 0.0276904
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.473
ELB improved by 0.0217533
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.455
ELB improved by 0.0173676
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.441
ELB improved by 0.0140818
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.43
ELB improved by 0.0115893
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-367.42
ELB improved by 0.00967766
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-845.176
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-561.075
ELB improved by 284.101
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-497.625
ELB improved by 63.4502
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.294
ELB improved by 39.3305
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.692
ELB improved by 17.602
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.029
ELB improved by 7.6634
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.209
ELB improved by 4.82011
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.209
ELB improved by 4.00011
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.306
ELB improved by 3.9022
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.131
ELB improved by 4.17538
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.496
ELB improved by 4.63491
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.494
ELB improved by 5.00215
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.648
ELB improved by 4.84545
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.679
ELB improved by 3.96962
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.903
ELB improved by 2.77582
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.081
ELB improved by 1.82152
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.796
ELB improved by 1.28533
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.763
ELB improved by 1.03282
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.902
ELB improved by 0.860941
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.229
ELB improved by 0.672991
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.721
ELB improved by 0.508342
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.322
ELB improved by 0.398805
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.99
ELB improved by 0.332305
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.699
ELB improved by 0.290677
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.436
ELB improved by 0.262791
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.193
ELB improved by 0.242975
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.965
ELB improved by 0.228344
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.748
ELB improved by 0.217328
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.539
ELB improved by 0.208992
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.336
ELB improved by 0.20272
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.138
ELB improved by 0.198056
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.943
ELB improved by 0.194633
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.751
ELB improved by 0.192179
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.561
ELB improved by 0.190568
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.371
ELB improved by 0.18985
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.181
ELB improved by 0.190172
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.989
ELB improved by 0.191511
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.796
ELB improved by 0.193292
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.602
ELB improved by 0.194206
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.409
ELB improved by 0.192816
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.22
ELB improved by 0.18888
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.036
ELB improved by 0.183944
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.856
ELB improved by 0.180234
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.677
ELB improved by 0.179212
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.495
ELB improved by 0.18122
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.309
ELB improved by 0.18592
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.117
ELB improved by 0.19275
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.916
ELB improved by 0.201139
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.705
ELB improved by 0.210545
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.485
ELB improved by 0.220443
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.254
ELB improved by 0.230321
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.015
ELB improved by 0.239703
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.766
ELB improved by 0.248205
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.511
ELB improved by 0.25561
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.249
ELB improved by 0.26194
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.981
ELB improved by 0.267506
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.708
ELB improved by 0.27296
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.429
ELB improved by 0.279552
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.139
ELB improved by 0.289987
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.829
ELB improved by 0.310121
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.48
ELB improved by 0.348852
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.077
ELB improved by 0.40268
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.656
ELB improved by 0.420868
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.298
ELB improved by 0.358034
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.033
ELB improved by 0.26505
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.843
ELB improved by 0.189855
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.705
ELB improved by 0.138016
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.601
ELB improved by 0.104024
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.52
ELB improved by 0.0815374
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.454
ELB improved by 0.0659651
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.399
ELB improved by 0.0545994
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.353
ELB improved by 0.045935
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.314
ELB improved by 0.0391078
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.281
ELB improved by 0.0335841
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.252
ELB improved by 0.0290114
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.226
ELB improved by 0.0251477
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.205
ELB improved by 0.0218267
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.186
ELB improved by 0.0189371
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.169
ELB improved by 0.0164075
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.155
ELB improved by 0.0141934
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.143
ELB improved by 0.0122657
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.132
ELB improved by 0.0106018
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.123
ELB improved by 0.00918026
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.378 0.234 2.598
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.052 | 0.022 | 0.075 | |
| getPIPs | 0.046 | 0.017 | 0.063 | |
| graper | 0.084 | 0.017 | 0.100 | |
| makeExampleData | 0.008 | 0.003 | 0.010 | |
| makeExampleDataWithUnequalGroups | 0.009 | 0.005 | 0.013 | |
| plotELBO | 0.336 | 0.025 | 0.360 | |
| plotGroupPenalties | 1.077 | 0.067 | 1.145 | |
| plotPosterior | 0.627 | 0.026 | 0.653 | |
| predict.graper | 2.068 | 0.065 | 2.133 | |
| print.graper | 0.047 | 0.015 | 0.061 | |