Britta Velten
| Snapshot Date: 2025-12-08 13:40 -0500 (Mon, 08 Dec 2025) |
| 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 Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-09 11:35 -0500 (Tue, 09 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4576 |
| 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 914/2331 | 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 | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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: 2025-12-09 00:12:19 -0500 (Tue, 09 Dec 2025) |
| EndedAt: 2025-12-09 00:13:50 -0500 (Tue, 09 Dec 2025) |
| 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) (2025-10-20 r88955)
* 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) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 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=-877.539
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-578.468
ELB improved by 299.071
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-519.052
ELB improved by 59.4153
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-482.066
ELB improved by 36.9858
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.962
ELB improved by 17.1048
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.169
ELB improved by 7.79276
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.807
ELB improved by 4.36184
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.579
ELB improved by 3.22789
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.759
ELB improved by 2.82054
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.08
ELB improved by 2.67877
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.436
ELB improved by 2.64339
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.801
ELB improved by 2.63589
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.214
ELB improved by 2.5867
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.789
ELB improved by 2.42465
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.671
ELB improved by 2.11802
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.96
ELB improved by 1.7108
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.666
ELB improved by 1.29417
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.723
ELB improved by 0.94287
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.04
ELB improved by 0.683222
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.535
ELB improved by 0.505033
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.149
ELB improved by 0.385791
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.844
ELB improved by 0.305143
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.595
ELB improved by 0.248856
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.387
ELB improved by 0.208001
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.21
ELB improved by 0.177192
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.057
ELB improved by 0.153176
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.923
ELB improved by 0.133938
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.805
ELB improved by 0.118184
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.7
ELB improved by 0.105048
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.606
ELB improved by 0.0939317
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.521
ELB improved by 0.0844033
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.445
ELB improved by 0.0761474
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.376
ELB improved by 0.0689276
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.314
ELB improved by 0.0625648
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.257
ELB improved by 0.0569213
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.205
ELB improved by 0.0518904
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.158
ELB improved by 0.0473879
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.114
ELB improved by 0.0433461
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.075
ELB improved by 0.0397098
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.038
ELB improved by 0.0364328
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.005
ELB improved by 0.0334756
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.974
ELB improved by 0.0308038
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.945
ELB improved by 0.0283873
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.919
ELB improved by 0.0261994
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.895
ELB improved by 0.024216
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.873
ELB improved by 0.0224159
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.852
ELB improved by 0.02078
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.833
ELB improved by 0.0192913
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.815
ELB improved by 0.0179347
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.798
ELB improved by 0.0166967
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.782
ELB improved by 0.0155654
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.768
ELB improved by 0.01453
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.754
ELB improved by 0.0135811
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.742
ELB improved by 0.0127104
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.73
ELB improved by 0.0119103
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.718
ELB improved by 0.0111741
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.708
ELB improved by 0.010496
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.698
ELB improved by 0.00987067
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-873.11
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-578.124
ELB improved by 294.986
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-522.25
ELB improved by 55.8734
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-486.489
ELB improved by 35.7612
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.619
ELB improved by 16.8701
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.803
ELB improved by 7.81606
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.512
ELB improved by 5.29084
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.358
ELB improved by 5.15415
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.518
ELB improved by 5.84004
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.896
ELB improved by 6.6221
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.21
ELB improved by 6.68623
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.685
ELB improved by 5.52473
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.964
ELB improved by 3.72097
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.673
ELB improved by 2.29076
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.198
ELB improved by 1.47575
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.149
ELB improved by 1.04828
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.331
ELB improved by 0.818685
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.642
ELB improved by 0.689018
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.031
ELB improved by 0.610795
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.471
ELB improved by 0.559515
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.949
ELB improved by 0.522629
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.455
ELB improved by 0.493787
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.985
ELB improved by 0.469957
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.535
ELB improved by 0.449871
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.102
ELB improved by 0.433113
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.682
ELB improved by 0.419558
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.273
ELB improved by 0.409047
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.872
ELB improved by 0.401223
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.477
ELB improved by 0.395467
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.086
ELB improved by 0.390903
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.699
ELB improved by 0.386442
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.318
ELB improved by 0.380874
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.945
ELB improved by 0.372984
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.584
ELB improved by 0.361716
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.237
ELB improved by 0.346346
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.911
ELB improved by 0.326626
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.608
ELB improved by 0.302865
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.332
ELB improved by 0.275894
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.085
ELB improved by 0.246937
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.868
ELB improved by 0.217395
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.679
ELB improved by 0.188616
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.517
ELB improved by 0.161707
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.38
ELB improved by 0.137412
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.264
ELB improved by 0.116103
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.166
ELB improved by 0.0978304
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.084
ELB improved by 0.0824223
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.014
ELB improved by 0.0695796
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.955
ELB improved by 0.058953
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.905
ELB improved by 0.0501945
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.862
ELB improved by 0.0429852
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.825
ELB improved by 0.0370473
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.793
ELB improved by 0.0321469
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.765
ELB improved by 0.0280905
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.74
ELB improved by 0.0247205
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.718
ELB improved by 0.0219094
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.698
ELB improved by 0.0195545
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.681
ELB improved by 0.0175736
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.665
ELB improved by 0.0159008
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.65
ELB improved by 0.0144833
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.637
ELB improved by 0.0132793
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.625
ELB improved by 0.0122552
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.613
ELB improved by 0.0113847
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.603
ELB improved by 0.0106473
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.593
ELB improved by 0.0100278
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.583
ELB improved by 0.00951518
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-879.746
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-590.093
ELB improved by 289.653
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-531.005
ELB improved by 59.0876
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-488.192
ELB improved by 42.8135
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.039
ELB improved by 23.1529
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.93
ELB improved by 12.1093
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.586
ELB improved by 9.3432
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.007
ELB improved by 10.5796
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.07
ELB improved by 11.9367
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.552
ELB improved by 10.5179
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.852
ELB improved by 6.70033
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.18
ELB improved by 3.67221
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.902
ELB improved by 2.2774
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.223
ELB improved by 1.67892
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.931
ELB improved by 1.29265
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.031
ELB improved by 0.899863
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.428
ELB improved by 0.602762
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.991
ELB improved by 0.437316
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.648
ELB improved by 0.343141
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.365
ELB improved by 0.282956
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.124
ELB improved by 0.241034
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.913
ELB improved by 0.210173
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.727
ELB improved by 0.186562
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.559
ELB improved by 0.167941
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.406
ELB improved by 0.152866
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.266
ELB improved by 0.140369
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.136
ELB improved by 0.129782
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.015
ELB improved by 0.120637
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.903
ELB improved by 0.112601
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.797
ELB improved by 0.105435
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.698
ELB improved by 0.0989687
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.605
ELB improved by 0.093077
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.518
ELB improved by 0.0876707
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.435
ELB improved by 0.0826844
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.357
ELB improved by 0.0780702
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.283
ELB improved by 0.073792
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.213
ELB improved by 0.0698224
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.147
ELB improved by 0.0661394
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.084
ELB improved by 0.0627248
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.025
ELB improved by 0.0595632
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.968
ELB improved by 0.0566406
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.914
ELB improved by 0.0539443
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.863
ELB improved by 0.0514625
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.814
ELB improved by 0.0491845
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.766
ELB improved by 0.0471002
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.721
ELB improved by 0.0452007
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.678
ELB improved by 0.0434786
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.636
ELB improved by 0.0419277
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.595
ELB improved by 0.040544
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.556
ELB improved by 0.0393261
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.518
ELB improved by 0.038276
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.48
ELB improved by 0.0374003
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.444
ELB improved by 0.0367121
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.407
ELB improved by 0.0362338
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.371
ELB improved by 0.0360027
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.335
ELB improved by 0.0360785
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.299
ELB improved by 0.0365592
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.261
ELB improved by 0.0376084
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.222
ELB improved by 0.0395096
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.179
ELB improved by 0.0427727
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.13
ELB improved by 0.0483489
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.072
ELB improved by 0.0580415
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.997
ELB improved by 0.0751109
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.893
ELB improved by 0.104152
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.747
ELB improved by 0.145982
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.563
ELB improved by 0.184154
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.371
ELB improved by 0.1917
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.198
ELB improved by 0.173274
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.046
ELB improved by 0.152297
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.91
ELB improved by 0.135928
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.787
ELB improved by 0.122473
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.677
ELB improved by 0.110438
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.578
ELB improved by 0.0993005
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.489
ELB improved by 0.0889452
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.409
ELB improved by 0.0793838
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.339
ELB improved by 0.0706516
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.276
ELB improved by 0.0627702
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.22
ELB improved by 0.055735
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.171
ELB improved by 0.0495143
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.127
ELB improved by 0.0440548
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.087
ELB improved by 0.0392887
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.052
ELB improved by 0.0351418
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.021
ELB improved by 0.0315388
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.992
ELB improved by 0.0284083
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.966
ELB improved by 0.0256853
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.943
ELB improved by 0.0233121
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.922
ELB improved by 0.0212392
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.903
ELB improved by 0.0194244
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.885
ELB improved by 0.0178324
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.868
ELB improved by 0.0164337
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.853
ELB improved by 0.015204
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.839
ELB improved by 0.0141232
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.826
ELB improved by 0.0131743
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.813
ELB improved by 0.0123434
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.802
ELB improved by 0.0116182
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.791
ELB improved by 0.0109883
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.78
ELB improved by 0.0104438
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.77
ELB improved by 0.00997557
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-862.572
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-585.939
ELB improved by 276.633
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-526.041
ELB improved by 59.8982
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-482.625
ELB improved by 43.4157
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.396
ELB improved by 20.2292
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.771
ELB improved by 7.62495
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.791
ELB improved by 4.98038
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.971
ELB improved by 4.81962
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.513
ELB improved by 5.45764
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.933
ELB improved by 6.58048
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.227
ELB improved by 7.70592
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.387
ELB improved by 7.84015
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.936
ELB improved by 6.45091
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.337
ELB improved by 4.59932
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.205
ELB improved by 3.13184
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.122
ELB improved by 2.08301
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.655
ELB improved by 1.46642
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.553
ELB improved by 1.10207
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.679
ELB improved by 0.873749
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.917
ELB improved by 0.761974
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.196
ELB improved by 0.721724
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.482
ELB improved by 0.713963
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.761
ELB improved by 0.720639
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.028
ELB improved by 0.733345
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.28
ELB improved by 0.747735
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.519
ELB improved by 0.761423
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.746
ELB improved by 0.772992
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.964
ELB improved by 0.781614
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.177
ELB improved by 0.787062
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.387
ELB improved by 0.789631
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.598
ELB improved by 0.789725
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.81
ELB improved by 0.787485
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.027
ELB improved by 0.782739
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.253
ELB improved by 0.77479
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.491
ELB improved by 0.761733
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.751
ELB improved by 0.739877
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.047
ELB improved by 0.704224
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.396
ELB improved by 0.650437
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.819
ELB improved by 0.577703
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.328
ELB improved by 0.490627
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.93
ELB improved by 0.39835
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.619
ELB improved by 0.311104
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.382
ELB improved by 0.236487
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.204
ELB improved by 0.177665
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.07
ELB improved by 0.133927
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.968
ELB improved by 0.10248
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.888
ELB improved by 0.0800994
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.824
ELB improved by 0.0640334
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.772
ELB improved by 0.0522592
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.728
ELB improved by 0.0434038
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.692
ELB improved by 0.0365703
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.66
ELB improved by 0.0311777
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.634
ELB improved by 0.026844
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.61
ELB improved by 0.0233112
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.59
ELB improved by 0.0203985
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.572
ELB improved by 0.017975
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.556
ELB improved by 0.0159431
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.542
ELB improved by 0.014228
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.529
ELB improved by 0.0127715
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.517
ELB improved by 0.0115277
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.507
ELB improved by 0.01046
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.497
ELB improved by 0.00953904
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.383 0.193 2.563
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.051 | 0.015 | 0.067 | |
| getPIPs | 0.046 | 0.016 | 0.062 | |
| graper | 0.081 | 0.019 | 0.100 | |
| makeExampleData | 0.009 | 0.001 | 0.011 | |
| makeExampleDataWithUnequalGroups | 0.013 | 0.000 | 0.013 | |
| plotELBO | 0.313 | 0.029 | 0.342 | |
| plotGroupPenalties | 1.077 | 0.046 | 1.123 | |
| plotPosterior | 0.688 | 0.020 | 0.710 | |
| predict.graper | 2.052 | 0.065 | 2.119 | |
| print.graper | 0.050 | 0.012 | 0.061 | |