Britta Velten
| Snapshot Date: 2026-02-25 13:45 -0500 (Wed, 25 Feb 2026) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: RELEASE_3_22 |
| git_last_commit: 76fc31b |
| git_last_commit_date: 2025-10-29 10:49:21 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-26 11:57 -0500 (Thu, 26 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4891 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 922/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.26.0 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for graper in R Universe. | ||||||||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: graper |
| Version: 1.26.0 |
| 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_1.26.0.tar.gz |
| StartedAt: 2026-02-26 00:41:33 -0500 (Thu, 26 Feb 2026) |
| EndedAt: 2026-02-26 00:43:04 -0500 (Thu, 26 Feb 2026) |
| EllapsedTime: 91.1 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_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘1.26.0’
* 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 ... INFO
installed size is 6.1Mb
sub-directories of 1Mb or more:
libs 6.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) predict.graper.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:23-24: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... 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 ‘1.26.0’ ** 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-3.22-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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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=-855.007
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-566.451
ELB improved by 288.557
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-508.15
ELB improved by 58.3011
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.144
ELB improved by 37.0054
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.348
ELB improved by 15.796
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.485
ELB improved by 6.86303
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.725
ELB improved by 3.76055
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.091
ELB improved by 2.63354
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.832
ELB improved by 2.25917
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.686
ELB improved by 2.14612
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.592
ELB improved by 2.09401
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.587
ELB improved by 2.00492
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.757
ELB improved by 1.8303
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.184
ELB improved by 1.57266
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.902
ELB improved by 1.28161
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.884
ELB improved by 1.01836
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.066
ELB improved by 0.817786
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.385
ELB improved by 0.681603
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.79
ELB improved by 0.594874
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.248
ELB improved by 0.541281
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.74
ELB improved by 0.508433
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.252
ELB improved by 0.487571
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.78
ELB improved by 0.472515
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.321
ELB improved by 0.459154
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.876
ELB improved by 0.445152
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.446
ELB improved by 0.42961
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.033
ELB improved by 0.412642
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.638
ELB improved by 0.394933
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.261
ELB improved by 0.377373
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.9
ELB improved by 0.360801
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.554
ELB improved by 0.345879
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.221
ELB improved by 0.333062
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.899
ELB improved by 0.322605
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.584
ELB improved by 0.31458
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.275
ELB improved by 0.308885
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.97
ELB improved by 0.305236
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.667
ELB improved by 0.303152
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.365
ELB improved by 0.301963
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.064
ELB improved by 0.300849
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.765
ELB improved by 0.298935
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.47
ELB improved by 0.2954
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.18
ELB improved by 0.289551
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.899
ELB improved by 0.280823
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.631
ELB improved by 0.268745
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.378
ELB improved by 0.252969
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.144
ELB improved by 0.233386
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.934
ELB improved by 0.210311
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.749
ELB improved by 0.18462
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.592
ELB improved by 0.157721
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.46
ELB improved by 0.131297
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.353
ELB improved by 0.106904
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.268
ELB improved by 0.0856137
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.2
ELB improved by 0.0678699
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.146
ELB improved by 0.0535877
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.104
ELB improved by 0.0423668
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.07
ELB improved by 0.0336895
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.043
ELB improved by 0.0270446
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.021
ELB improved by 0.0219832
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.003
ELB improved by 0.0181354
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.988
ELB improved by 0.0152064
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.975
ELB improved by 0.012967
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.964
ELB improved by 0.0112422
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.954
ELB improved by 0.00990005
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-832.545
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-595.708
ELB improved by 236.838
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-540.719
ELB improved by 54.9884
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-497.14
ELB improved by 43.5793
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.435
ELB improved by 24.7046
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.154
ELB improved by 11.2817
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.643
ELB improved by 5.51092
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.999
ELB improved by 3.64365
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.062
ELB improved by 2.93719
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.537
ELB improved by 2.52528
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.331
ELB improved by 2.20551
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.415
ELB improved by 1.91552
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.774
ELB improved by 1.64149
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.388
ELB improved by 1.38556
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.238
ELB improved by 1.15044
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.3
ELB improved by 0.938012
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.547
ELB improved by 0.752529
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.948
ELB improved by 0.599126
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.469
ELB improved by 0.47912
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.081
ELB improved by 0.388529
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.76
ELB improved by 0.320477
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.492
ELB improved by 0.268372
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.264
ELB improved by 0.227535
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.069
ELB improved by 0.195032
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.9
ELB improved by 0.168915
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.753
ELB improved by 0.147734
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.622
ELB improved by 0.130362
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.506
ELB improved by 0.11594
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.402
ELB improved by 0.103822
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.309
ELB improved by 0.0935305
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.224
ELB improved by 0.0847065
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.147
ELB improved by 0.0770785
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.077
ELB improved by 0.070437
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.012
ELB improved by 0.0646184
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.953
ELB improved by 0.0594925
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.898
ELB improved by 0.054955
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.847
ELB improved by 0.0509208
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.799
ELB improved by 0.0473199
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.755
ELB improved by 0.0440944
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.714
ELB improved by 0.0411956
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.676
ELB improved by 0.0385826
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.639
ELB improved by 0.0362204
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.605
ELB improved by 0.0340794
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.573
ELB improved by 0.0321338
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.543
ELB improved by 0.0303615
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.514
ELB improved by 0.0287433
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.487
ELB improved by 0.0272624
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.461
ELB improved by 0.0259041
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.436
ELB improved by 0.0246555
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.413
ELB improved by 0.0235052
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.39
ELB improved by 0.022443
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.369
ELB improved by 0.0214602
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.348
ELB improved by 0.0205488
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.329
ELB improved by 0.0197017
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.31
ELB improved by 0.0189127
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.291
ELB improved by 0.0181761
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.274
ELB improved by 0.0174869
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.257
ELB improved by 0.0168408
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.241
ELB improved by 0.0162336
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.225
ELB improved by 0.0156617
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.21
ELB improved by 0.0151221
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.195
ELB improved by 0.0146118
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.181
ELB improved by 0.0141282
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.168
ELB improved by 0.0136692
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.154
ELB improved by 0.0132325
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.142
ELB improved by 0.0128165
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.129
ELB improved by 0.0124196
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.117
ELB improved by 0.0120401
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.105
ELB improved by 0.011677
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.094
ELB improved by 0.0113291
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.083
ELB improved by 0.0109953
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.072
ELB improved by 0.0106748
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.062
ELB improved by 0.0103668
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.052
ELB improved by 0.0100706
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.042
ELB improved by 0.00978565
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-890.837
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-588.069
ELB improved by 302.768
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-524.332
ELB improved by 63.7375
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-481.355
ELB improved by 42.9764
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.473
ELB improved by 18.8828
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.724
ELB improved by 6.74861
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.211
ELB improved by 3.51297
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.59
ELB improved by 2.62065
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.287
ELB improved by 2.30306
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.09
ELB improved by 2.19698
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.913
ELB improved by 2.17709
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.712
ELB improved by 2.20114
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.452
ELB improved by 2.26001
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.099
ELB improved by 2.35285
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.628
ELB improved by 2.47084
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.047
ELB improved by 2.58093
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.427
ELB improved by 2.6205
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.904
ELB improved by 2.52254
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.637
ELB improved by 2.26694
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.728
ELB improved by 1.90977
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.172
ELB improved by 1.55524
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.882
ELB improved by 1.2902
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.743
ELB improved by 1.13922
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.666
ELB improved by 1.07658
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.607
ELB improved by 1.05953
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.558
ELB improved by 1.04848
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.539
ELB improved by 1.01947
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.57
ELB improved by 0.969309
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.662
ELB improved by 0.907743
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.813
ELB improved by 0.849332
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.001
ELB improved by 0.811772
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.193
ELB improved by 0.808138
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.377
ELB improved by 0.815685
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.597
ELB improved by 0.780322
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.893
ELB improved by 0.703942
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.267
ELB improved by 0.625703
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.704
ELB improved by 0.562943
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.187
ELB improved by 0.517504
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.699
ELB improved by 0.487333
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.228
ELB improved by 0.4716
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.751
ELB improved by 0.476543
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.23
ELB improved by 0.520828
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.614
ELB improved by 0.616043
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.938
ELB improved by 0.675874
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.357
ELB improved by 0.580834
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.931
ELB improved by 0.42653
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.624
ELB improved by 0.307106
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.399
ELB improved by 0.225158
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.23
ELB improved by 0.168608
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.101
ELB improved by 0.128889
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.001
ELB improved by 0.100439
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.921
ELB improved by 0.0796098
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.857
ELB improved by 0.0640343
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.805
ELB improved by 0.0521851
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.762
ELB improved by 0.0430585
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.726
ELB improved by 0.035963
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.696
ELB improved by 0.0303987
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.67
ELB improved by 0.0259932
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.647
ELB improved by 0.0224679
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.627
ELB improved by 0.0196151
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.61
ELB improved by 0.0172813
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.595
ELB improved by 0.0153532
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.581
ELB improved by 0.0137465
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.569
ELB improved by 0.0123979
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.557
ELB improved by 0.0112589
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.547
ELB improved by 0.0102921
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.538
ELB improved by 0.00946759
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-877.741
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-591.028
ELB improved by 286.713
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-531.593
ELB improved by 59.4343
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-488.956
ELB improved by 42.6377
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.063
ELB improved by 19.8927
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.959
ELB improved by 8.10357
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.309
ELB improved by 4.65028
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.57
ELB improved by 3.73906
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.962
ELB improved by 3.60791
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.294
ELB improved by 3.6682
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.682
ELB improved by 3.61218
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.391
ELB improved by 3.29078
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.635
ELB improved by 2.75639
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.471
ELB improved by 2.16402
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.836
ELB improved by 1.63451
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.613
ELB improved by 1.2233
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.685
ELB improved by 0.927786
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.96
ELB improved by 0.725416
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.366
ELB improved by 0.593197
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.857
ELB improved by 0.508848
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.403
ELB improved by 0.454458
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.985
ELB improved by 0.418276
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.591
ELB improved by 0.393379
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.216
ELB improved by 0.375787
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.852
ELB improved by 0.36317
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.498
ELB improved by 0.354078
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.151
ELB improved by 0.34749
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.808
ELB improved by 0.342518
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.47
ELB improved by 0.338245
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.136
ELB improved by 0.333707
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.808
ELB improved by 0.328043
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.488
ELB improved by 0.32069
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.176
ELB improved by 0.311466
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.876
ELB improved by 0.300487
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.588
ELB improved by 0.288027
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.313
ELB improved by 0.274404
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.053
ELB improved by 0.259933
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.808
ELB improved by 0.24491
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.579
ELB improved by 0.229615
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.364
ELB improved by 0.214322
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.165
ELB improved by 0.199314
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.98
ELB improved by 0.184898
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.809
ELB improved by 0.171426
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.649
ELB improved by 0.159345
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.5
ELB improved by 0.149274
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.358
ELB improved by 0.142179
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.218
ELB improved by 0.139696
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.074
ELB improved by 0.144624
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.913
ELB improved by 0.161101
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.72
ELB improved by 0.192375
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.486
ELB improved by 0.234403
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.208
ELB improved by 0.277777
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.88
ELB improved by 0.32773
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.49
ELB improved by 0.390103
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.059
ELB improved by 0.43077
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.626
ELB improved by 0.433947
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.182
ELB improved by 0.443338
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.705
ELB improved by 0.477118
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.195
ELB improved by 0.509751
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.684
ELB improved by 0.511493
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.189
ELB improved by 0.494498
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.692
ELB improved by 0.497444
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.16
ELB improved by 0.531598
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.578
ELB improved by 0.582279
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.932
ELB improved by 0.646028
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.238
ELB improved by 0.693745
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.613
ELB improved by 0.625612
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.149
ELB improved by 0.46347
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.833
ELB improved by 0.316347
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.619
ELB improved by 0.213535
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.472
ELB improved by 0.147689
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.363
ELB improved by 0.10853
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.276
ELB improved by 0.0873991
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.198
ELB improved by 0.0777352
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.123
ELB improved by 0.0746377
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.049
ELB improved by 0.074328
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.975
ELB improved by 0.0743198
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.901
ELB improved by 0.0739509
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.827
ELB improved by 0.0740766
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.751
ELB improved by 0.0760236
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.669
ELB improved by 0.0811969
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.578
ELB improved by 0.0917331
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.466
ELB improved by 0.111195
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.323
ELB improved by 0.143351
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.137
ELB improved by 0.186553
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.91
ELB improved by 0.226588
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.67
ELB improved by 0.240168
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.455
ELB improved by 0.214751
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.288
ELB improved by 0.167199
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.164
ELB improved by 0.123763
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.07
ELB improved by 0.0938276
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.995
ELB improved by 0.0748061
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.933
ELB improved by 0.062031
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.881
ELB improved by 0.0520276
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.838
ELB improved by 0.0430213
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.804
ELB improved by 0.0346567
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.776
ELB improved by 0.0272993
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.755
ELB improved by 0.0213279
iteration 99
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.738
ELB improved by 0.0168067
iteration 100
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.725
ELB improved by 0.0135299
iteration 101
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.714
ELB improved by 0.0111919
iteration 102
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.704
ELB improved by 0.00950994
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.448 0.170 2.608
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.053 | 0.009 | 0.062 | |
| getPIPs | 0.048 | 0.003 | 0.051 | |
| graper | 0.082 | 0.003 | 0.085 | |
| makeExampleData | 0.009 | 0.002 | 0.011 | |
| makeExampleDataWithUnequalGroups | 0.010 | 0.003 | 0.013 | |
| plotELBO | 0.360 | 0.019 | 0.380 | |
| plotGroupPenalties | 1.184 | 0.044 | 1.228 | |
| plotPosterior | 0.774 | 0.009 | 0.783 | |
| predict.graper | 2.046 | 0.022 | 2.070 | |
| print.graper | 0.053 | 0.002 | 0.055 | |