Britta Velten
| Snapshot Date: 2026-02-06 13:40 -0500 (Fri, 06 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 2026-02-07 11:32 -0500 (Sat, 07 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" | 4858 |
| 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 922/2347 | 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: 2026-02-07 00:13:40 -0500 (Sat, 07 Feb 2026) |
| EndedAt: 2026-02-07 00:15:11 -0500 (Sat, 07 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=-853.377
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-572.725
ELB improved by 280.652
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-513.579
ELB improved by 59.1455
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-475.659
ELB improved by 37.92
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.933
ELB improved by 16.7263
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.515
ELB improved by 6.41723
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.916
ELB improved by 3.59966
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.849
ELB improved by 3.06715
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.789
ELB improved by 3.06005
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.591
ELB improved by 3.19737
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.276
ELB improved by 3.31495
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.999
ELB improved by 3.2776
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.012
ELB improved by 2.98669
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.549
ELB improved by 2.46302
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.695
ELB improved by 1.85432
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.372
ELB improved by 1.32222
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.433
ELB improved by 0.939137
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.743
ELB improved by 0.690442
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.207
ELB improved by 0.536051
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.763
ELB improved by 0.443968
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.371
ELB improved by 0.391847
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.006
ELB improved by 0.364781
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.652
ELB improved by 0.354011
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.297
ELB improved by 0.355143
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.931
ELB improved by 0.366423
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.543
ELB improved by 0.38707
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.129
ELB improved by 0.414855
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.685
ELB improved by 0.443386
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.221
ELB improved by 0.463737
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.749
ELB improved by 0.472574
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.274
ELB improved by 0.475341
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.794
ELB improved by 0.479696
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.302
ELB improved by 0.491947
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.782
ELB improved by 0.519822
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.205
ELB improved by 0.57685
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.519
ELB improved by 0.686408
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.646
ELB improved by 0.872457
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.545
ELB improved by 1.10184
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.262
ELB improved by 1.2826
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.841
ELB improved by 1.42089
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.299
ELB improved by 1.54252
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.717
ELB improved by 1.58189
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.26
ELB improved by 1.45667
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.067
ELB improved by 1.19255
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.171
ELB improved by 0.896545
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.529
ELB improved by 0.641478
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.085
ELB improved by 0.444318
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.785
ELB improved by 0.30018
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.584
ELB improved by 0.20109
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.447
ELB improved by 0.136937
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.35
ELB improved by 0.0967352
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.279
ELB improved by 0.0714683
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.224
ELB improved by 0.0550846
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.18
ELB improved by 0.0439557
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.144
ELB improved by 0.0360118
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.114
ELB improved by 0.0300824
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.088
ELB improved by 0.0254926
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.066
ELB improved by 0.0218398
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.047
ELB improved by 0.0188724
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.031
ELB improved by 0.0164256
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.017
ELB improved by 0.014386
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.004
ELB improved by 0.012672
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.993
ELB improved by 0.0112229
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.983
ELB improved by 0.00999168
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-832.89
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-567.708
ELB improved by 265.182
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-512.803
ELB improved by 54.9047
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-477.537
ELB improved by 35.266
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.819
ELB improved by 17.7175
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.862
ELB improved by 8.95692
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.185
ELB improved by 5.67777
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.481
ELB improved by 4.70329
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.996
ELB improved by 4.48519
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.67
ELB improved by 4.32613
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.713
ELB improved by 3.95679
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.365
ELB improved by 3.34833
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.724
ELB improved by 2.64073
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.73
ELB improved by 1.99406
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.253
ELB improved by 1.47754
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.167
ELB improved by 1.08604
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.368
ELB improved by 0.798387
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.775
ELB improved by 0.592822
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.328
ELB improved by 0.447389
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.983
ELB improved by 0.344805
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.71
ELB improved by 0.27294
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.488
ELB improved by 0.222743
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.3
ELB improved by 0.187326
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.138
ELB improved by 0.161772
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.996
ELB improved by 0.1428
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.867
ELB improved by 0.128305
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.75
ELB improved by 0.116951
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.642
ELB improved by 0.107877
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.542
ELB improved by 0.100518
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.447
ELB improved by 0.0944843
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.358
ELB improved by 0.0895018
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.273
ELB improved by 0.0853673
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.191
ELB improved by 0.0819275
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.112
ELB improved by 0.0790638
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.035
ELB improved by 0.0766834
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.96
ELB improved by 0.0747133
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.887
ELB improved by 0.0730959
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.815
ELB improved by 0.0717866
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.745
ELB improved by 0.0707514
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.675
ELB improved by 0.0699652
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.605
ELB improved by 0.0694109
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.536
ELB improved by 0.0690783
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.467
ELB improved by 0.0689629
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.398
ELB improved by 0.0690655
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.329
ELB improved by 0.0693906
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.259
ELB improved by 0.0699463
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.188
ELB improved by 0.0707423
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.116
ELB improved by 0.0717889
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.043
ELB improved by 0.0730951
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.968
ELB improved by 0.074667
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.892
ELB improved by 0.0765051
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.813
ELB improved by 0.0786028
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.732
ELB improved by 0.0809449
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.649
ELB improved by 0.0835079
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.563
ELB improved by 0.0862624
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.473
ELB improved by 0.0891788
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.381
ELB improved by 0.0922348
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.286
ELB improved by 0.0954232
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.187
ELB improved by 0.098758
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.085
ELB improved by 0.102274
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.979
ELB improved by 0.106022
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.869
ELB improved by 0.110056
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.754
ELB improved by 0.114421
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.635
ELB improved by 0.11914
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.511
ELB improved by 0.124205
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.381
ELB improved by 0.129574
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.246
ELB improved by 0.135165
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.105
ELB improved by 0.140861
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.959
ELB improved by 0.146509
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.807
ELB improved by 0.151926
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.65
ELB improved by 0.156906
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.489
ELB improved by 0.161233
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.324
ELB improved by 0.164688
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.157
ELB improved by 0.167075
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.989
ELB improved by 0.168243
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.821
ELB improved by 0.168116
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.654
ELB improved by 0.166724
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.49
ELB improved by 0.164231
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.329
ELB improved by 0.160958
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.171
ELB improved by 0.157445
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.017
ELB improved by 0.154592
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.863
ELB improved by 0.153885
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.705
ELB improved by 0.157592
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.537
ELB improved by 0.168694
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.346
ELB improved by 0.190052
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.124
ELB improved by 0.222313
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.864
ELB improved by 0.260351
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.576
ELB improved by 0.288288
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.295
ELB improved by 0.28019
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.068
ELB improved by 0.227028
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.91
ELB improved by 0.158667
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.802
ELB improved by 0.10743
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.722
ELB improved by 0.0797424
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.654
ELB improved by 0.0686286
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.588
ELB improved by 0.0661706
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.522
ELB improved by 0.0652971
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.462
ELB improved by 0.0601337
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.413
ELB improved by 0.0490614
iteration 99
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.378
ELB improved by 0.0356281
iteration 100
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.353
ELB improved by 0.0241692
iteration 101
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.337
ELB improved by 0.0162945
iteration 102
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.326
ELB improved by 0.0114622
iteration 103
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.317
ELB improved by 0.00860708
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-863.79
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-559.847
ELB improved by 303.943
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-501.2
ELB improved by 58.6476
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.702
ELB improved by 32.4975
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.131
ELB improved by 12.5705
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.06
ELB improved by 5.07128
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.018
ELB improved by 3.04218
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.487
ELB improved by 2.53057
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.026
ELB improved by 2.46144
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.426
ELB improved by 2.60027
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.552
ELB improved by 2.87358
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.374
ELB improved by 3.17809
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.075
ELB improved by 3.2991
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.074
ELB improved by 3.00112
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.748
ELB improved by 2.32616
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.142
ELB improved by 1.60527
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.058
ELB improved by 1.08475
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.274
ELB improved by 0.783674
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.651
ELB improved by 0.623489
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.115
ELB improved by 0.535406
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.634
ELB improved by 0.480938
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.192
ELB improved by 0.442024
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.781
ELB improved by 0.410948
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.397
ELB improved by 0.384645
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.035
ELB improved by 0.361949
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.692
ELB improved by 0.342411
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.366
ELB improved by 0.325868
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.054
ELB improved by 0.312327
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.752
ELB improved by 0.301958
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.457
ELB improved by 0.295139
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.164
ELB improved by 0.292586
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.869
ELB improved by 0.29568
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.561
ELB improved by 0.307221
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.228
ELB improved by 0.333114
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.843
ELB improved by 0.385724
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.355
ELB improved by 0.487306
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.695
ELB improved by 0.659873
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.81
ELB improved by 0.885638
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.728
ELB improved by 1.08138
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.541
ELB improved by 1.18776
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.233
ELB improved by 1.30735
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.743
ELB improved by 1.48985
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.224
ELB improved by 1.51928
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.914
ELB improved by 1.31051
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.882
ELB improved by 1.03145
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.129
ELB improved by 0.753371
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.607
ELB improved by 0.521962
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.249
ELB improved by 0.357789
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.998
ELB improved by 0.250692
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.816
ELB improved by 0.182616
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.677
ELB improved by 0.138877
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.567
ELB improved by 0.109871
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.477
ELB improved by 0.0898635
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.402
ELB improved by 0.0755694
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.336
ELB improved by 0.0651508
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.279
ELB improved by 0.0576275
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.226
ELB improved by 0.0525713
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.176
ELB improved by 0.0499853
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.126
ELB improved by 0.0502838
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.072
ELB improved by 0.054229
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.009
ELB improved by 0.0624504
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.935
ELB improved by 0.0740221
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.85
ELB improved by 0.0849757
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.759
ELB improved by 0.0908373
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.666
ELB improved by 0.0929666
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.569
ELB improved by 0.0970981
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.467
ELB improved by 0.102439
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.369
ELB improved by 0.0979249
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.292
ELB improved by 0.0771541
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.241
ELB improved by 0.0503752
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.212
ELB improved by 0.0298054
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.194
ELB improved by 0.0178545
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.182
ELB improved by 0.0117613
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.173
ELB improved by 0.00875247
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-850.389
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-594.787
ELB improved by 255.602
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-537.069
ELB improved by 57.7183
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-491.666
ELB improved by 45.403
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.292
ELB improved by 25.3733
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.527
ELB improved by 11.7657
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.236
ELB improved by 6.29053
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.184
ELB improved by 5.0524
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.096
ELB improved by 5.08746
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.428
ELB improved by 5.66824
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.775
ELB improved by 6.65258
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.028
ELB improved by 7.74785
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.918
ELB improved by 8.1095
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.059
ELB improved by 6.85879
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.407
ELB improved by 4.65229
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.535
ELB improved by 2.87252
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.766
ELB improved by 1.76853
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.666
ELB improved by 1.09958
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.946
ELB improved by 0.719966
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.432
ELB improved by 0.51461
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.03
ELB improved by 0.401921
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.693
ELB improved by 0.337421
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.393
ELB improved by 0.29918
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.117
ELB improved by 0.276454
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.853
ELB improved by 0.263758
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.595
ELB improved by 0.258108
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.337
ELB improved by 0.257783
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.075
ELB improved by 0.261775
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.806
ELB improved by 0.269558
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.525
ELB improved by 0.281007
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.228
ELB improved by 0.296426
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.912
ELB improved by 0.316624
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.569
ELB improved by 0.343078
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.191
ELB improved by 0.378177
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.765
ELB improved by 0.425672
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.273
ELB improved by 0.491519
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.688
ELB improved by 0.585643
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.962
ELB improved by 0.725357
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.025
ELB improved by 0.937619
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.793
ELB improved by 1.23181
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.289
ELB improved by 1.50369
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.701
ELB improved by 1.58817
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.217
ELB improved by 1.48406
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.95
ELB improved by 1.26712
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.943
ELB improved by 1.0072
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.181
ELB improved by 0.762121
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.62
ELB improved by 0.560646
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.215
ELB improved by 0.405174
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.925
ELB improved by 0.289676
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.717
ELB improved by 0.208547
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.561
ELB improved by 0.155439
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.438
ELB improved by 0.123014
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.334
ELB improved by 0.104564
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.239
ELB improved by 0.0945294
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.151
ELB improved by 0.0879564
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.071
ELB improved by 0.080467
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.001
ELB improved by 0.0696406
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.945
ELB improved by 0.0562766
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.902
ELB improved by 0.043163
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.869
ELB improved by 0.0324737
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.844
ELB improved by 0.0247108
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.825
ELB improved by 0.0193416
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.809
ELB improved by 0.0156257
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.796
ELB improved by 0.0129809
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.785
ELB improved by 0.0110277
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.776
ELB improved by 0.009534
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.403 0.215 2.608
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.058 | 0.018 | 0.076 | |
| getPIPs | 0.051 | 0.012 | 0.063 | |
| graper | 0.079 | 0.020 | 0.099 | |
| makeExampleData | 0.009 | 0.002 | 0.011 | |
| makeExampleDataWithUnequalGroups | 0.009 | 0.004 | 0.013 | |
| plotELBO | 0.353 | 0.023 | 0.375 | |
| plotGroupPenalties | 1.144 | 0.046 | 1.190 | |
| plotPosterior | 0.658 | 0.017 | 0.677 | |
| predict.graper | 2.049 | 0.075 | 2.124 | |
| print.graper | 0.049 | 0.014 | 0.063 | |