Britta Velten
| Snapshot Date: 2025-11-07 13:40 -0500 (Fri, 07 Nov 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 Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-08 11:32 -0500 (Sat, 08 Nov 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" | 4821 |
| 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 911/2323 | 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 | | ||||||||
|
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: 2025-11-08 00:10:53 -0500 (Sat, 08 Nov 2025) |
| EndedAt: 2025-11-08 00:12:23 -0500 (Sat, 08 Nov 2025) |
| EllapsedTime: 90.2 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=-840.449
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-581.464
ELB improved by 258.985
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-521.544
ELB improved by 59.9202
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-475.944
ELB improved by 45.5994
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.368
ELB improved by 23.5758
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.566
ELB improved by 9.80236
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.506
ELB improved by 5.06038
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.738
ELB improved by 3.7674
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.41
ELB improved by 3.32788
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.269
ELB improved by 3.14122
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.247
ELB improved by 3.02189
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.367
ELB improved by 2.88051
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.735
ELB improved by 2.63165
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.508
ELB improved by 2.22727
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.79
ELB improved by 1.71794
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.563
ELB improved by 1.22735
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.711
ELB improved by 0.85145
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.105
ELB improved by 0.606389
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.646
ELB improved by 0.458879
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.276
ELB improved by 0.369547
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.966
ELB improved by 0.310659
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.699
ELB improved by 0.266764
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.468
ELB improved by 0.230821
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.268
ELB improved by 0.200292
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.093
ELB improved by 0.174353
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.941
ELB improved by 0.15249
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.807
ELB improved by 0.134117
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.688
ELB improved by 0.118628
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.583
ELB improved by 0.105477
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.489
ELB improved by 0.0942196
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.404
ELB improved by 0.0845069
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.328
ELB improved by 0.0760674
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.259
ELB improved by 0.0686896
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.197
ELB improved by 0.0622073
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.141
ELB improved by 0.0564873
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.089
ELB improved by 0.0514215
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.042
ELB improved by 0.0469207
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.999
ELB improved by 0.0429104
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.96
ELB improved by 0.0393277
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.924
ELB improved by 0.0361188
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.891
ELB improved by 0.0332379
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.86
ELB improved by 0.0306451
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.832
ELB improved by 0.0283064
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.805
ELB improved by 0.0261922
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.781
ELB improved by 0.0242767
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.759
ELB improved by 0.0225377
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.738
ELB improved by 0.0209557
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.718
ELB improved by 0.0195138
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.7
ELB improved by 0.0181971
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.683
ELB improved by 0.0169928
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.667
ELB improved by 0.0158895
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.652
ELB improved by 0.014877
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.638
ELB improved by 0.0139466
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.625
ELB improved by 0.0130904
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.613
ELB improved by 0.0123014
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.601
ELB improved by 0.0115735
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.59
ELB improved by 0.0109012
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.58
ELB improved by 0.0102794
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.57
ELB improved by 0.00970384
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-857.631
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-562.251
ELB improved by 295.38
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-498.778
ELB improved by 63.4734
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.19
ELB improved by 37.5876
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.064
ELB improved by 17.1259
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.271
ELB improved by 6.79341
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.981
ELB improved by 3.29049
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.903
ELB improved by 2.07744
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.329
ELB improved by 1.57365
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.976
ELB improved by 1.3532
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.722
ELB improved by 1.25402
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.509
ELB improved by 1.2128
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.303
ELB improved by 1.20631
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.077
ELB improved by 1.22604
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.809
ELB improved by 1.26777
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.484
ELB improved by 1.32565
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.096
ELB improved by 1.38787
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.661
ELB improved by 1.4346
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.22
ELB improved by 1.44166
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.828
ELB improved by 1.39207
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.539
ELB improved by 1.289
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.381
ELB improved by 1.15719
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.352
ELB improved by 1.02905
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.425
ELB improved by 0.927057
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.568
ELB improved by 0.856848
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.756
ELB improved by 0.812479
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.971
ELB improved by 0.784809
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.205
ELB improved by 0.766506
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.451
ELB improved by 0.753294
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.708
ELB improved by 0.743389
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.971
ELB improved by 0.736544
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.238
ELB improved by 0.733219
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.504
ELB improved by 0.734303
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.761
ELB improved by 0.742464
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.994
ELB improved by 0.766889
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.163
ELB improved by 0.831488
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.204
ELB improved by 0.958915
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.153
ELB improved by 1.05114
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.196
ELB improved by 0.956717
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.41
ELB improved by 0.786445
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.774
ELB improved by 0.635915
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.269
ELB improved by 0.504944
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.878
ELB improved by 0.390829
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.581
ELB improved by 0.29729
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.356
ELB improved by 0.225227
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.184
ELB improved by 0.171349
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.053
ELB improved by 0.131074
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.952
ELB improved by 0.100687
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.875
ELB improved by 0.0777435
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.814
ELB improved by 0.0606059
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.766
ELB improved by 0.0479791
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.727
ELB improved by 0.0387515
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.695
ELB improved by 0.0319985
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.668
ELB improved by 0.0270023
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.645
ELB improved by 0.0232378
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.625
ELB improved by 0.0203357
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.607
ELB improved by 0.0180422
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.591
ELB improved by 0.0161849
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.576
ELB improved by 0.0146466
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.563
ELB improved by 0.0133473
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.55
ELB improved by 0.0122318
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.539
ELB improved by 0.011261
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.529
ELB improved by 0.0104073
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.519
ELB improved by 0.00965007
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-876.896
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-567.281
ELB improved by 309.614
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-508.797
ELB improved by 58.4844
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.5
ELB improved by 37.2969
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.317
ELB improved by 17.183
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.887
ELB improved by 7.43021
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.327
ELB improved by 4.55985
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.568
ELB improved by 3.7588
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.022
ELB improved by 3.54622
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.506
ELB improved by 3.51565
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.001
ELB improved by 3.50575
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.606
ELB improved by 3.3947
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.541
ELB improved by 3.0649
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.039
ELB improved by 2.50237
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.176
ELB improved by 1.86274
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.852
ELB improved by 1.32376
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.9
ELB improved by 0.951878
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.176
ELB improved by 0.724455
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.581
ELB improved by 0.594983
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.056
ELB improved by 0.524916
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.567
ELB improved by 0.489301
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.093
ELB improved by 0.473607
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.624
ELB improved by 0.469032
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.156
ELB improved by 0.468252
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.692
ELB improved by 0.463541
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.243
ELB improved by 0.449698
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.815
ELB improved by 0.427548
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.414
ELB improved by 0.401251
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.04
ELB improved by 0.373951
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.693
ELB improved by 0.347155
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.371
ELB improved by 0.321675
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.073
ELB improved by 0.29809
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.796
ELB improved by 0.276822
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.538
ELB improved by 0.258133
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.296
ELB improved by 0.242139
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.067
ELB improved by 0.228841
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.849
ELB improved by 0.218159
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.639
ELB improved by 0.209971
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.435
ELB improved by 0.204147
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.234
ELB improved by 0.200594
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.035
ELB improved by 0.199308
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.834
ELB improved by 0.200476
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.63
ELB improved by 0.204667
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.416
ELB improved by 0.213334
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.186
ELB improved by 0.230157
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.921
ELB improved by 0.26488
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.579
ELB improved by 0.342491
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.076
ELB improved by 0.502926
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.382
ELB improved by 0.693574
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.649
ELB improved by 0.733425
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.983
ELB improved by 0.666377
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.386
ELB improved by 0.596568
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.844
ELB improved by 0.541522
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.342
ELB improved by 0.502876
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.858
ELB improved by 0.483959
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.364
ELB improved by 0.493586
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.805
ELB improved by 0.559246
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.072
ELB improved by 0.733183
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.13
ELB improved by 0.941139
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.28
ELB improved by 0.850586
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.731
ELB improved by 0.549158
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.415
ELB improved by 0.315996
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.236
ELB improved by 0.178265
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.134
ELB improved by 0.102267
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.072
ELB improved by 0.0619534
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.032
ELB improved by 0.0406986
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.002
ELB improved by 0.0291562
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.98
ELB improved by 0.0225275
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.961
ELB improved by 0.0184336
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.946
ELB improved by 0.0156964
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.932
ELB improved by 0.0137237
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.92
ELB improved by 0.0122107
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.909
ELB improved by 0.0109951
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.899
ELB improved by 0.00998662
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-896.674
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-600.062
ELB improved by 296.612
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-540.147
ELB improved by 59.9156
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-498.772
ELB improved by 41.375
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-478.104
ELB improved by 20.668
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.942
ELB improved by 11.1613
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.089
ELB improved by 8.85303
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.653
ELB improved by 8.43657
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.508
ELB improved by 7.1448
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.59
ELB improved by 4.91834
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.58
ELB improved by 3.00956
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.689
ELB improved by 1.89087
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.453
ELB improved by 1.23561
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.653
ELB improved by 0.800627
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.107
ELB improved by 0.545955
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.696
ELB improved by 0.410592
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.36
ELB improved by 0.33626
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.068
ELB improved by 0.291679
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.806
ELB improved by 0.262182
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.565
ELB improved by 0.240842
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.341
ELB improved by 0.224226
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.131
ELB improved by 0.210546
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.932
ELB improved by 0.198841
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.743
ELB improved by 0.188603
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.564
ELB improved by 0.179579
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.392
ELB improved by 0.171674
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.227
ELB improved by 0.164875
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.068
ELB improved by 0.159204
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.913
ELB improved by 0.154648
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.762
ELB improved by 0.151059
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.614
ELB improved by 0.148033
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.469
ELB improved by 0.144848
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.329
ELB improved by 0.140646
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.194
ELB improved by 0.13491
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.066
ELB improved by 0.127885
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.945
ELB improved by 0.12042
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.832
ELB improved by 0.113382
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.725
ELB improved by 0.10724
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.623
ELB improved by 0.102073
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.525
ELB improved by 0.097775
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.431
ELB improved by 0.0942042
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.339
ELB improved by 0.0912567
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.251
ELB improved by 0.0888808
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.163
ELB improved by 0.0870785
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.078
ELB improved by 0.0859105
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.992
ELB improved by 0.0855102
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.906
ELB improved by 0.0861076
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.818
ELB improved by 0.0880523
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.726
ELB improved by 0.0917872
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.628
ELB improved by 0.0976507
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.523
ELB improved by 0.105318
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.41
ELB improved by 0.112989
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.293
ELB improved by 0.117512
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.176
ELB improved by 0.116781
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.064
ELB improved by 0.112038
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.957
ELB improved by 0.106317
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.856
ELB improved by 0.101524
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.758
ELB improved by 0.0979615
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.663
ELB improved by 0.0952616
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.57
ELB improved by 0.0930074
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.479
ELB improved by 0.0908998
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.39
ELB improved by 0.0887481
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.304
ELB improved by 0.0864368
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.22
ELB improved by 0.0838992
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.139
ELB improved by 0.0811025
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.061
ELB improved by 0.0780381
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.986
ELB improved by 0.0747157
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.915
ELB improved by 0.0711603
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.847
ELB improved by 0.0674101
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.784
ELB improved by 0.063515
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.724
ELB improved by 0.0595361
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.669
ELB improved by 0.0555437
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.617
ELB improved by 0.0516154
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.569
ELB improved by 0.0478329
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.525
ELB improved by 0.0442773
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.484
ELB improved by 0.0410237
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.446
ELB improved by 0.0381327
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.41
ELB improved by 0.0356386
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.377
ELB improved by 0.0335324
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.345
ELB improved by 0.0317396
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.315
ELB improved by 0.0301011
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.286
ELB improved by 0.0283761
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.26
ELB improved by 0.0262967
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.236
ELB improved by 0.0236804
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.216
ELB improved by 0.0205502
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.199
ELB improved by 0.017159
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.185
ELB improved by 0.0138716
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.174
ELB improved by 0.0109914
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.165
ELB improved by 0.00866
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.337 0.201 2.525
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.054 | 0.011 | 0.067 | |
| getPIPs | 0.047 | 0.014 | 0.061 | |
| graper | 0.078 | 0.022 | 0.100 | |
| makeExampleData | 0.008 | 0.002 | 0.010 | |
| makeExampleDataWithUnequalGroups | 0.012 | 0.000 | 0.013 | |
| plotELBO | 0.313 | 0.031 | 0.344 | |
| plotGroupPenalties | 1.087 | 0.046 | 1.133 | |
| plotPosterior | 0.613 | 0.021 | 0.635 | |
| predict.graper | 2.077 | 0.067 | 2.144 | |
| print.graper | 0.050 | 0.011 | 0.061 | |