Britta Velten
| Snapshot Date: 2025-08-31 13:45 -0400 (Sun, 31 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: 82b0592 |
| git_last_commit_date: 2025-06-24 03:15:40 -0400 (Tue, 24 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-01 12:03 -0400 (Mon, 01 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
| 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 907/2320 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.25.2 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.25.2 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings graper_1.25.2.tar.gz |
| StartedAt: 2025-08-31 23:19:39 -0400 (Sun, 31 Aug 2025) |
| EndedAt: 2025-08-31 23:21:03 -0400 (Sun, 31 Aug 2025) |
| EllapsedTime: 84.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings graper_1.25.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.25.2’
* 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 ... INFO
installed size is 6.0Mb
sub-directories of 1Mb or more:
libs 5.8Mb
* 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 ... NOTE
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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.25.2’ ** 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-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-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-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-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-3.22-bioc/R/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -llapack -L/home/biocbuild/bbs-3.22-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-graper/00new/graper/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (graper)
graper.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root"
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=-886.303
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-572.41
ELB improved by 313.893
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-511.382
ELB improved by 61.0281
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-477.971
ELB improved by 33.4105
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.385
ELB improved by 14.5868
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.394
ELB improved by 6.99019
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.43
ELB improved by 4.96422
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.625
ELB improved by 4.80495
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.454
ELB improved by 5.17158
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.075
ELB improved by 5.37815
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.152
ELB improved by 4.92352
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.272
ELB improved by 3.87954
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.391
ELB improved by 2.88179
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.181
ELB improved by 2.20917
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.553
ELB improved by 1.62872
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.349
ELB improved by 1.20405
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.365
ELB improved by 0.983845
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.496
ELB improved by 0.869045
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.716
ELB improved by 0.780178
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.015
ELB improved by 0.700288
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.378
ELB improved by 0.63733
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.789
ELB improved by 0.58934
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.239
ELB improved by 0.550056
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.723
ELB improved by 0.51575
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.238
ELB improved by 0.485117
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.78
ELB improved by 0.45794
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.346
ELB improved by 0.434275
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.931
ELB improved by 0.414126
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.534
ELB improved by 0.397367
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.15
ELB improved by 0.383747
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.777
ELB improved by 0.372939
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.413
ELB improved by 0.364591
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.054
ELB improved by 0.358375
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.7
ELB improved by 0.35401
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.349
ELB improved by 0.351232
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.999
ELB improved by 0.349681
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.651
ELB improved by 0.348696
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.304
ELB improved by 0.347062
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.961
ELB improved by 0.342832
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.627
ELB improved by 0.333454
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.311
ELB improved by 0.316445
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.02
ELB improved by 0.290668
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.763
ELB improved by 0.257435
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.543
ELB improved by 0.220303
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.359
ELB improved by 0.183518
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.209
ELB improved by 0.150408
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.086
ELB improved by 0.122723
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.985
ELB improved by 0.100858
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.901
ELB improved by 0.0844337
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.828
ELB improved by 0.0728229
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.762
ELB improved by 0.0655003
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.7
ELB improved by 0.0622463
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.637
ELB improved by 0.0632198
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.568
ELB improved by 0.0687647
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.49
ELB improved by 0.078473
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.401
ELB improved by 0.0890257
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.308
ELB improved by 0.0928479
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.224
ELB improved by 0.0834664
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.16
ELB improved by 0.0642204
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.115
ELB improved by 0.0446443
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.085
ELB improved by 0.0302484
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.064
ELB improved by 0.0211878
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.048
ELB improved by 0.0157979
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.036
ELB improved by 0.0125817
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.025
ELB improved by 0.0105807
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.016
ELB improved by 0.00925103
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-938.509
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-561.008
ELB improved by 377.501
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-502.583
ELB improved by 58.4249
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-476.062
ELB improved by 26.5219
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.148
ELB improved by 9.91369
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.47
ELB improved by 4.67762
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.81
ELB improved by 2.66053
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.042
ELB improved by 1.7682
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.655
ELB improved by 1.3869
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.391
ELB improved by 1.26379
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.096
ELB improved by 1.29442
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.66
ELB improved by 1.43605
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.989
ELB improved by 1.67126
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.008
ELB improved by 1.98124
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.689
ELB improved by 2.31848
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.098
ELB improved by 2.591
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.404
ELB improved by 2.69439
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.805
ELB improved by 2.59876
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.415
ELB improved by 2.38999
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.269
ELB improved by 2.1467
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.408
ELB improved by 1.86092
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.795
ELB improved by 1.61298
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.265
ELB improved by 1.52995
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.739
ELB improved by 1.52607
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.415
ELB improved by 1.32402
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.355
ELB improved by 1.05973
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.47
ELB improved by 0.88488
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.697
ELB improved by 0.773349
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.003
ELB improved by 0.693617
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.372
ELB improved by 0.630549
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.795
ELB improved by 0.577324
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.265
ELB improved by 0.530601
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.776
ELB improved by 0.488449
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.327
ELB improved by 0.449568
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.913
ELB improved by 0.413059
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.535
ELB improved by 0.378368
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.19
ELB improved by 0.345241
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.876
ELB improved by 0.313661
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.592
ELB improved by 0.283752
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.337
ELB improved by 0.255704
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.107
ELB improved by 0.229698
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.901
ELB improved by 0.205871
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.717
ELB improved by 0.184288
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.552
ELB improved by 0.164933
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.404
ELB improved by 0.147723
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.272
ELB improved by 0.132519
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.153
ELB improved by 0.119145
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.045
ELB improved by 0.107413
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.948
ELB improved by 0.0971323
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.86
ELB improved by 0.0881266
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.78
ELB improved by 0.0802375
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.706
ELB improved by 0.073329
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.639
ELB improved by 0.0672883
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.577
ELB improved by 0.0620264
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.52
ELB improved by 0.0574777
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.466
ELB improved by 0.0536026
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.416
ELB improved by 0.0503927
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.368
ELB improved by 0.0478832
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.321
ELB improved by 0.0461791
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.276
ELB improved by 0.0455077
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.23
ELB improved by 0.0463255
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.18
ELB improved by 0.0495334
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.123
ELB improved by 0.0568724
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.052
ELB improved by 0.0714205
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.955
ELB improved by 0.0970169
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.822
ELB improved by 0.132398
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.663
ELB improved by 0.159746
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.506
ELB improved by 0.156373
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.376
ELB improved by 0.129999
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.274
ELB improved by 0.102726
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.191
ELB improved by 0.0822611
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.124
ELB improved by 0.0674054
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.068
ELB improved by 0.056167
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.02
ELB improved by 0.0473059
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.98
ELB improved by 0.0400999
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.946
ELB improved by 0.0341066
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.917
ELB improved by 0.0290564
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.892
ELB improved by 0.0247908
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.871
ELB improved by 0.0212113
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.853
ELB improved by 0.0182393
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.837
ELB improved by 0.0157963
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.823
ELB improved by 0.0138018
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.811
ELB improved by 0.0121774
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.8
ELB improved by 0.0108524
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.791
ELB improved by 0.00976696
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-899.309
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-554.771
ELB improved by 344.539
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-497.304
ELB improved by 57.4666
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.971
ELB improved by 29.3331
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.01
ELB improved by 11.9616
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.984
ELB improved by 6.02526
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.481
ELB improved by 4.50302
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.299
ELB improved by 4.1826
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.962
ELB improved by 4.33639
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.305
ELB improved by 4.6568
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.417
ELB improved by 4.88863
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.666
ELB improved by 4.75124
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.581
ELB improved by 4.0845
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.509
ELB improved by 3.07255
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.413
ELB improved by 2.09579
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.025
ELB improved by 1.38783
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.071
ELB improved by 0.953838
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.365
ELB improved by 0.70609
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.799
ELB improved by 0.566101
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.313
ELB improved by 0.485719
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.874
ELB improved by 0.438948
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.462
ELB improved by 0.412305
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.063
ELB improved by 0.398892
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.668
ELB improved by 0.395359
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.267
ELB improved by 0.400449
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.853
ELB improved by 0.414131
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.417
ELB improved by 0.436481
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.951
ELB improved by 0.465763
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.454
ELB improved by 0.49707
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.929
ELB improved by 0.524934
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.381
ELB improved by 0.548302
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.81
ELB improved by 0.570389
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.216
ELB improved by 0.594363
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.595
ELB improved by 0.621219
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.944
ELB improved by 0.650077
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.266
ELB improved by 0.678371
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.565
ELB improved by 0.700861
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.856
ELB improved by 0.709083
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.161
ELB improved by 0.695112
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.504
ELB improved by 0.657326
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.905
ELB improved by 0.599004
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.381
ELB improved by 0.523385
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.945
ELB improved by 0.436619
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.594
ELB improved by 0.35028
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.32
ELB improved by 0.274501
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.107
ELB improved by 0.213071
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.942
ELB improved by 0.165343
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.812
ELB improved by 0.129225
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.71
ELB improved by 0.102522
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.627
ELB improved by 0.0832332
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.557
ELB improved by 0.0696524
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.496
ELB improved by 0.0604468
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.442
ELB improved by 0.0546816
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.39
ELB improved by 0.0517491
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.339
ELB improved by 0.0511911
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.286
ELB improved by 0.0523803
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.232
ELB improved by 0.0541179
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.178
ELB improved by 0.0545698
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.126
ELB improved by 0.0521549
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.079
ELB improved by 0.0469089
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.038
ELB improved by 0.0404933
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.004
ELB improved by 0.0346532
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.973
ELB improved by 0.0301486
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.946
ELB improved by 0.0269324
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.922
ELB improved by 0.0246947
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.899
ELB improved by 0.0231631
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.876
ELB improved by 0.0221714
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.855
ELB improved by 0.0216436
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.833
ELB improved by 0.0215694
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.811
ELB improved by 0.0219902
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.788
ELB improved by 0.0229957
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.764
ELB improved by 0.0247278
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.736
ELB improved by 0.0273866
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.705
ELB improved by 0.0312358
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.668
ELB improved by 0.0366073
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.624
ELB improved by 0.0439166
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.571
ELB improved by 0.0537218
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.504
ELB improved by 0.0668025
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.42
ELB improved by 0.0838849
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.316
ELB improved by 0.103845
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.196
ELB improved by 0.119829
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.077
ELB improved by 0.119613
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.978
ELB improved by 0.0990065
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.908
ELB improved by 0.0699162
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.862
ELB improved by 0.045469
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.833
ELB improved by 0.0292591
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.814
ELB improved by 0.0194268
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.8
ELB improved by 0.0135376
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.79
ELB improved by 0.00993965
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-843.096
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-586.443
ELB improved by 256.652
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-526.398
ELB improved by 60.0448
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-482.775
ELB improved by 43.6236
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.451
ELB improved by 22.3242
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.483
ELB improved by 9.96715
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.179
ELB improved by 5.30407
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.233
ELB improved by 3.94643
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.605
ELB improved by 3.62773
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.996
ELB improved by 3.60896
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.371
ELB improved by 3.62519
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.842
ELB improved by 3.52911
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.614
ELB improved by 3.22829
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.929
ELB improved by 2.68495
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.902
ELB improved by 2.0269
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.433
ELB improved by 1.46889
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.338
ELB improved by 1.09445
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.463
ELB improved by 0.875737
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.704
ELB improved by 0.758522
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.005
ELB improved by 0.698851
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.336
ELB improved by 0.66894
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.683
ELB improved by 0.653166
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.04
ELB improved by 0.643301
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.405
ELB improved by 0.635323
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.777
ELB improved by 0.62757
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.157
ELB improved by 0.619721
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.545
ELB improved by 0.612198
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.939
ELB improved by 0.605796
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.338
ELB improved by 0.601423
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.738
ELB improved by 0.599894
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.136
ELB improved by 0.601693
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.53
ELB improved by 0.606666
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.916
ELB improved by 0.613641
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.296
ELB improved by 0.620072
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.674
ELB improved by 0.621924
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.06
ELB improved by 0.614181
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.468
ELB improved by 0.592224
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.914
ELB improved by 0.55384
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.413
ELB improved by 0.500812
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.974
ELB improved by 0.438749
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.599
ELB improved by 0.374786
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.285
ELB improved by 0.3145
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.025
ELB improved by 0.260318
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.812
ELB improved by 0.212526
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.641
ELB improved by 0.171292
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.503
ELB improved by 0.137241
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.393
ELB improved by 0.110595
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.302
ELB improved by 0.0906388
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.226
ELB improved by 0.0760106
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.161
ELB improved by 0.065202
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.104
ELB improved by 0.0568939
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.054
ELB improved by 0.0501092
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.01
ELB improved by 0.0442439
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.971
ELB improved by 0.0390061
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.936
ELB improved by 0.0342997
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.906
ELB improved by 0.0301072
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.88
ELB improved by 0.0264156
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.857
ELB improved by 0.0231903
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.836
ELB improved by 0.0203812
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.818
ELB improved by 0.0179364
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.803
ELB improved by 0.0158113
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.789
ELB improved by 0.0139704
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.776
ELB improved by 0.0123839
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.765
ELB improved by 0.0110242
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.755
ELB improved by 0.00986329
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.316 0.302 2.564
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.061 | 0.003 | 0.057 | |
| getPIPs | 0.051 | 0.007 | 0.053 | |
| graper | 0.084 | 0.009 | 0.087 | |
| makeExampleData | 0.017 | 0.000 | 0.011 | |
| makeExampleDataWithUnequalGroups | 0.038 | 0.014 | 0.042 | |
| plotELBO | 0.210 | 0.006 | 0.205 | |
| plotGroupPenalties | 0.709 | 0.006 | 0.701 | |
| plotPosterior | 0.516 | 0.000 | 0.501 | |
| predict.graper | 2.074 | 0.009 | 2.054 | |
| print.graper | 0.055 | 0.002 | 0.050 | |