Britta Velten
| Snapshot Date: 2026-04-23 13:45 -0400 (Thu, 23 Apr 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 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-04-24 11:33 -0400 (Fri, 24 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4800 |
| 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 917/2351 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.27.0 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 24.04.4 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-3.24-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings graper_1.27.0.tar.gz |
| StartedAt: 2026-04-24 00:06:51 -0400 (Fri, 24 Apr 2026) |
| EndedAt: 2026-04-24 00:08:25 -0400 (Fri, 24 Apr 2026) |
| EllapsedTime: 94.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings graper_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/graper.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-24 04:06:52 UTC
* 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 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... INFO
installed size is 6.2Mb
sub-directories of 1Mb or more:
libs 6.0Mb
* 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-3.24-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.24-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 13.3.0-6ubuntu2~24.04.1) 13.3.0’ g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.24-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++20 -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.24-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++20 -shared -L/home/biocbuild/bbs-3.24-bioc/R/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -llapack -L/home/biocbuild/bbs-3.24-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.24-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.24-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 version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
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=-880.258
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-572.788
ELB improved by 307.47
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-512.68
ELB improved by 60.1077
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-477.566
ELB improved by 35.114
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.29
ELB improved by 15.276
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.362
ELB improved by 6.92836
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.094
ELB improved by 4.26796
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.685
ELB improved by 3.40892
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.584
ELB improved by 3.10069
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.614
ELB improved by 2.9709
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.734
ELB improved by 2.87916
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.968
ELB improved by 2.76683
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.366
ELB improved by 2.60127
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431
ELB improved by 2.36585
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.932
ELB improved by 2.06852
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.189
ELB improved by 1.74334
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.755
ELB improved by 1.43345
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.585
ELB improved by 1.17036
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.619
ELB improved by 0.965832
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.808
ELB improved by 0.810726
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.13
ELB improved by 0.678392
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.579
ELB improved by 0.551191
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.137
ELB improved by 0.441352
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.775
ELB improved by 0.362494
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.463
ELB improved by 0.311399
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.184
ELB improved by 0.279064
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.926
ELB improved by 0.258146
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.682
ELB improved by 0.243741
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.45
ELB improved by 0.232872
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.226
ELB improved by 0.223894
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.01
ELB improved by 0.215988
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.801
ELB improved by 0.208812
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.599
ELB improved by 0.202293
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.402
ELB improved by 0.196504
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.21
ELB improved by 0.191592
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.023
ELB improved by 0.187732
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.838
ELB improved by 0.185094
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.654
ELB improved by 0.18384
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.47
ELB improved by 0.184113
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.284
ELB improved by 0.186051
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.094
ELB improved by 0.189798
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.898
ELB improved by 0.195515
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.695
ELB improved by 0.203408
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.481
ELB improved by 0.213749
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.254
ELB improved by 0.226904
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.011
ELB improved by 0.243368
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.747
ELB improved by 0.263747
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.459
ELB improved by 0.288629
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.14
ELB improved by 0.318103
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.79
ELB improved by 0.350821
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.406
ELB improved by 0.383211
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.996
ELB improved by 0.41086
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.563
ELB improved by 0.43275
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.109
ELB improved by 0.453411
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.635
ELB improved by 0.474814
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.156
ELB improved by 0.478108
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.721
ELB improved by 0.434967
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.364
ELB improved by 0.357532
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.085
ELB improved by 0.278844
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.873
ELB improved by 0.212207
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.714
ELB improved by 0.159133
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.595
ELB improved by 0.119105
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.504
ELB improved by 0.0903118
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.434
ELB improved by 0.0700238
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.379
ELB improved by 0.0556431
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.333
ELB improved by 0.0452357
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.296
ELB improved by 0.0375132
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.264
ELB improved by 0.0316422
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.237
ELB improved by 0.0270768
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.214
ELB improved by 0.023451
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.193
ELB improved by 0.0205139
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.175
ELB improved by 0.0180914
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.159
ELB improved by 0.0160625
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.145
ELB improved by 0.0143422
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.132
ELB improved by 0.0128706
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.12
ELB improved by 0.0116043
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.11
ELB improved by 0.010511
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.1
ELB improved by 0.00956495
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-894.473
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-565.333
ELB improved by 329.14
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-511.67
ELB improved by 53.663
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-483.122
ELB improved by 28.5474
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.85
ELB improved by 11.2722
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.882
ELB improved by 4.96822
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.397
ELB improved by 3.48475
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.269
ELB improved by 3.12807
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.222
ELB improved by 3.04726
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.181
ELB improved by 3.04079
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.163
ELB improved by 3.01751
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.259
ELB improved by 2.90458
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.604
ELB improved by 2.65445
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.326
ELB improved by 2.27878
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.477
ELB improved by 1.84843
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.028
ELB improved by 1.44965
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.883
ELB improved by 1.14441
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.925
ELB improved by 0.958056
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.073
ELB improved by 0.851888
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.321
ELB improved by 0.752427
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.672
ELB improved by 0.649223
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.107
ELB improved by 0.565012
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.603
ELB improved by 0.503251
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.141
ELB improved by 0.461886
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.703
ELB improved by 0.438311
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.275
ELB improved by 0.428119
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.848
ELB improved by 0.426939
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.416
ELB improved by 0.431743
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.975
ELB improved by 0.440904
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.522
ELB improved by 0.453823
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.051
ELB improved by 0.470466
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.56
ELB improved by 0.490805
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.046
ELB improved by 0.514359
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.506
ELB improved by 0.540328
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.937
ELB improved by 0.568501
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.337
ELB improved by 0.600134
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.699
ELB improved by 0.637908
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.014
ELB improved by 0.685142
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.269
ELB improved by 0.744518
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.453
ELB improved by 0.816409
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.554
ELB improved by 0.899408
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.555
ELB improved by 0.998255
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.421
ELB improved by 1.13453
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.087
ELB improved by 1.3343
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.509
ELB improved by 1.57804
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.723
ELB improved by 1.78511
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.85
ELB improved by 1.87356
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.063
ELB improved by 1.7865
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.519
ELB improved by 1.54449
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.252
ELB improved by 1.26707
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.164
ELB improved by 1.08783
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.11
ELB improved by 1.05416
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.193
ELB improved by 0.916621
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.615
ELB improved by 0.578395
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.298
ELB improved by 0.316486
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.121
ELB improved by 0.177078
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.013
ELB improved by 0.108039
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.94
ELB improved by 0.0730374
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.886
ELB improved by 0.0538282
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.844
ELB improved by 0.0421369
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.81
ELB improved by 0.0342974
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.781
ELB improved by 0.0286323
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.757
ELB improved by 0.0243208
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.736
ELB improved by 0.0209257
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.718
ELB improved by 0.0181926
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.702
ELB improved by 0.0159604
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.688
ELB improved by 0.0141193
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.675
ELB improved by 0.0125904
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.664
ELB improved by 0.0113139
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.654
ELB improved by 0.0102436
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.644
ELB improved by 0.00934268
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-868.823
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-586.066
ELB improved by 282.757
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-526.132
ELB improved by 59.9335
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-485.132
ELB improved by 41.0007
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.216
ELB improved by 18.9154
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.033
ELB improved by 8.18344
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.058
ELB improved by 4.97479
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.785
ELB improved by 4.27333
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.513
ELB improved by 4.27167
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.063
ELB improved by 4.44965
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.447
ELB improved by 4.61644
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.873
ELB improved by 4.5739
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.739
ELB improved by 4.13414
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.414
ELB improved by 3.32521
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.989
ELB improved by 2.42495
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.299
ELB improved by 1.68962
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.113
ELB improved by 1.18637
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.243
ELB improved by 0.870264
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.564
ELB improved by 0.678465
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.002
ELB improved by 0.562191
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.512
ELB improved by 0.49016
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.067
ELB improved by 0.44429
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.653
ELB improved by 0.414603
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.257
ELB improved by 0.395626
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.873
ELB improved by 0.384338
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.494
ELB improved by 0.379086
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.115
ELB improved by 0.378986
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.731
ELB improved by 0.38353
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.339
ELB improved by 0.392365
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.934
ELB improved by 0.405345
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.511
ELB improved by 0.422931
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.064
ELB improved by 0.44672
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.584
ELB improved by 0.479702
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.058
ELB improved by 0.526152
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.467
ELB improved by 0.591156
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.788
ELB improved by 0.67895
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.999
ELB improved by 0.788636
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.089
ELB improved by 0.910059
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.058
ELB improved by 1.0308
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.906
ELB improved by 1.15233
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.62
ELB improved by 1.28603
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.222
ELB improved by 1.39776
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.855
ELB improved by 1.36726
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.672
ELB improved by 1.18278
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.716
ELB improved by 0.956049
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.991
ELB improved by 0.725291
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.486
ELB improved by 0.504608
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.158
ELB improved by 0.328695
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.947
ELB improved by 0.210748
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.809
ELB improved by 0.138097
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.715
ELB improved by 0.0941519
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.647
ELB improved by 0.0671823
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.597
ELB improved by 0.0501505
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.558
ELB improved by 0.0390104
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.527
ELB improved by 0.0314407
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.501
ELB improved by 0.0260935
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.479
ELB improved by 0.022172
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.459
ELB improved by 0.019195
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.443
ELB improved by 0.0168649
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.428
ELB improved by 0.0149928
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.414
ELB improved by 0.013456
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.402
ELB improved by 0.0121718
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.391
ELB improved by 0.0110837
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.381
ELB improved by 0.0101511
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.371
ELB improved by 0.00934458
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-865.693
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-568.5
ELB improved by 297.193
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-508.196
ELB improved by 60.3049
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.222
ELB improved by 35.973
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.99
ELB improved by 14.232
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.329
ELB improved by 5.66126
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.865
ELB improved by 3.4645
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.997
ELB improved by 2.86736
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.238
ELB improved by 2.75961
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.348
ELB improved by 2.88984
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.198
ELB improved by 3.15007
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.776
ELB improved by 3.42192
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.251
ELB improved by 3.5253
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.957
ELB improved by 3.29356
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.235
ELB improved by 2.72169
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.215
ELB improved by 2.02072
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.776
ELB improved by 1.43838
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.713
ELB improved by 1.06377
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.857
ELB improved by 0.855215
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.107
ELB improved by 0.750529
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.397
ELB improved by 0.709888
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.694
ELB improved by 0.702637
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.994
ELB improved by 0.70044
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.296
ELB improved by 0.698232
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.582
ELB improved by 0.713951
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.82
ELB improved by 0.761781
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.979
ELB improved by 0.840734
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.048
ELB improved by 0.931499
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.037
ELB improved by 1.01069
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.96
ELB improved by 1.07733
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.816
ELB improved by 1.14375
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.601
ELB improved by 1.21461
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.318
ELB improved by 1.28348
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.981
ELB improved by 1.33666
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.622
ELB improved by 1.3593
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.279
ELB improved by 1.34268
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.992
ELB improved by 1.28677
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.803
ELB improved by 1.18976
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.765
ELB improved by 1.03736
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.931
ELB improved by 0.834227
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.303
ELB improved by 0.627887
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.848
ELB improved by 0.454711
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.529
ELB improved by 0.319275
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.311
ELB improved by 0.218051
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.164
ELB improved by 0.14734
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.063
ELB improved by 0.10102
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.991
ELB improved by 0.0716884
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.938
ELB improved by 0.0531074
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.897
ELB improved by 0.0410322
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.864
ELB improved by 0.0328774
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.837
ELB improved by 0.0271355
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.814
ELB improved by 0.0229291
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.794
ELB improved by 0.019737
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.777
ELB improved by 0.0172394
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.762
ELB improved by 0.0152343
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.748
ELB improved by 0.0135894
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.736
ELB improved by 0.0122159
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.725
ELB improved by 0.0110524
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.715
ELB improved by 0.0100554
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.706
ELB improved by 0.00919286
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.274 0.217 2.479
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.048 | 0.010 | 0.058 | |
| getPIPs | 0.065 | 0.022 | 0.088 | |
| graper | 0.077 | 0.007 | 0.084 | |
| makeExampleData | 0.010 | 0.000 | 0.009 | |
| makeExampleDataWithUnequalGroups | 0.012 | 0.000 | 0.011 | |
| plotELBO | 0.290 | 0.021 | 0.310 | |
| plotGroupPenalties | 0.912 | 0.003 | 0.914 | |
| plotPosterior | 0.629 | 0.003 | 0.632 | |
| predict.graper | 2.059 | 0.013 | 2.073 | |
| print.graper | 0.046 | 0.006 | 0.053 | |