Britta Velten
| Snapshot Date: 2026-01-19 13:45 -0500 (Mon, 19 Jan 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 2026-01-22 11:58 -0500 (Thu, 22 Jan 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" | 4886 |
| 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 | | ||||||||
|
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: 2026-01-20 00:18:26 -0500 (Tue, 20 Jan 2026) |
| EndedAt: 2026-01-20 00:19:58 -0500 (Tue, 20 Jan 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=-828.31
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-550.998
ELB improved by 277.311
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-491.914
ELB improved by 59.0838
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.213
ELB improved by 38.7013
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.16
ELB improved by 16.0527
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.173
ELB improved by 5.98785
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.958
ELB improved by 3.21496
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.661
ELB improved by 2.29696
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.753
ELB improved by 1.90791
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.016
ELB improved by 1.73647
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.346
ELB improved by 1.67027
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.685
ELB improved by 1.66124
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.997
ELB improved by 1.68799
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.26
ELB improved by 1.73682
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.469
ELB improved by 1.79068
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.646
ELB improved by 1.82372
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.841
ELB improved by 1.80418
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.132
ELB improved by 1.70908
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.59
ELB improved by 1.54242
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.255
ELB improved by 1.33499
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.133
ELB improved by 1.1218
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.204
ELB improved by 0.92865
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.431
ELB improved by 0.773922
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.766
ELB improved by 0.664969
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.169
ELB improved by 0.597034
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.609
ELB improved by 0.559653
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.067
ELB improved by 0.541879
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.533
ELB improved by 0.534082
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.005
ELB improved by 0.528153
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.487
ELB improved by 0.517891
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.987
ELB improved by 0.500181
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.511
ELB improved by 0.475411
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.065
ELB improved by 0.44597
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.651
ELB improved by 0.414553
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.266
ELB improved by 0.384264
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.907
ELB improved by 0.35921
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.566
ELB improved by 0.341612
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.24
ELB improved by 0.325191
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.943
ELB improved by 0.297935
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.683
ELB improved by 0.259129
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.464
ELB improved by 0.219339
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.279
ELB improved by 0.185388
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.121
ELB improved by 0.158006
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.985
ELB improved by 0.135939
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.867
ELB improved by 0.117909
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.764
ELB improved by 0.102963
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.673
ELB improved by 0.0904209
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.594
ELB improved by 0.0797902
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.523
ELB improved by 0.0707075
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.46
ELB improved by 0.0628965
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.404
ELB improved by 0.0561423
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.354
ELB improved by 0.0502739
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.308
ELB improved by 0.045153
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.268
ELB improved by 0.0406665
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.231
ELB improved by 0.0367211
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.198
ELB improved by 0.0332392
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.168
ELB improved by 0.030156
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.14
ELB improved by 0.0274174
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.115
ELB improved by 0.024978
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.093
ELB improved by 0.0227992
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.072
ELB improved by 0.0208487
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.053
ELB improved by 0.0190988
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.035
ELB improved by 0.0175257
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.019
ELB improved by 0.0161092
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.004
ELB improved by 0.0148317
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.99
ELB improved by 0.0136779
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.978
ELB improved by 0.0126345
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.966
ELB improved by 0.0116898
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.955
ELB improved by 0.0108336
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.945
ELB improved by 0.0100567
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.936
ELB improved by 0.009351
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-860.129
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-586.789
ELB improved by 273.34
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-527.892
ELB improved by 58.8969
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-483.459
ELB improved by 44.4333
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.758
ELB improved by 21.7014
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.103
ELB improved by 8.65424
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.736
ELB improved by 4.36746
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.324
ELB improved by 3.41226
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.98
ELB improved by 3.34314
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.436
ELB improved by 3.5448
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.554
ELB improved by 3.88128
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.284
ELB improved by 4.2704
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.728
ELB improved by 4.55626
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.247
ELB improved by 4.48058
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.366
ELB improved by 3.88137
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.439
ELB improved by 2.92681
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.467
ELB improved by 1.9721
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.202
ELB improved by 1.2644
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.37
ELB improved by 0.832285
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.78
ELB improved by 0.590168
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.326
ELB improved by 0.454246
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.952
ELB improved by 0.373708
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.63
ELB improved by 0.322485
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.342
ELB improved by 0.287718
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.079
ELB improved by 0.26289
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.834
ELB improved by 0.244503
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.604
ELB improved by 0.230565
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.384
ELB improved by 0.219879
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.172
ELB improved by 0.211717
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.967
ELB improved by 0.205655
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.765
ELB improved by 0.201505
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.566
ELB improved by 0.199298
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.366
ELB improved by 0.199322
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.164
ELB improved by 0.202227
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.955
ELB improved by 0.209268
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.732
ELB improved by 0.222765
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.485
ELB improved by 0.246836
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.198
ELB improved by 0.287626
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.848
ELB improved by 0.349407
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.426
ELB improved by 0.42256
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.942
ELB improved by 0.483681
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.412
ELB improved by 0.529851
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.828
ELB improved by 0.584334
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.158
ELB improved by 0.670188
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.359
ELB improved by 0.798278
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.424
ELB improved by 0.935589
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.409
ELB improved by 1.01441
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.365
ELB improved by 1.04476
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.262
ELB improved by 1.10223
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.018
ELB improved by 1.24447
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.604
ELB improved by 1.41359
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.089
ELB improved by 1.51573
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.475
ELB improved by 1.61334
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.983
ELB improved by 1.49234
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.005
ELB improved by 0.977798
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.495
ELB improved by 0.509845
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.232
ELB improved by 0.263199
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.086
ELB improved by 0.146371
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.997
ELB improved by 0.0892574
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.937
ELB improved by 0.0592989
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.895
ELB improved by 0.0422101
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.863
ELB improved by 0.0316626
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.839
ELB improved by 0.0247185
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.819
ELB improved by 0.0199133
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.802
ELB improved by 0.0164583
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.788
ELB improved by 0.0138973
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.776
ELB improved by 0.0119508
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.766
ELB improved by 0.0104392
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.757
ELB improved by 0.00924307
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-890.208
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-549.914
ELB improved by 340.294
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-496.597
ELB improved by 53.3163
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.184
ELB improved by 28.4132
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.296
ELB improved by 11.8878
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.554
ELB improved by 5.74232
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.687
ELB improved by 3.86702
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.369
ELB improved by 3.31746
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.108
ELB improved by 3.26133
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.724
ELB improved by 3.38439
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.203
ELB improved by 3.52091
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.694
ELB improved by 3.50856
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.481
ELB improved by 3.21365
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.838
ELB improved by 2.64228
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.879
ELB improved by 1.95926
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.523
ELB improved by 1.35596
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.598
ELB improved by 0.925204
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.943
ELB improved by 0.655135
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.449
ELB improved by 0.493571
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.054
ELB improved by 0.394977
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.723
ELB improved by 0.331323
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.435
ELB improved by 0.287556
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.18
ELB improved by 0.255867
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.947
ELB improved by 0.232113
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.733
ELB improved by 0.214007
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.533
ELB improved by 0.200257
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.343
ELB improved by 0.190169
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.16
ELB improved by 0.183465
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.979
ELB improved by 0.180214
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.798
ELB improved by 0.180798
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.613
ELB improved by 0.185846
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.417
ELB improved by 0.195998
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.205
ELB improved by 0.211393
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.974
ELB improved by 0.231088
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.721
ELB improved by 0.253297
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.444
ELB improved by 0.276818
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.142
ELB improved by 0.301708
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.814
ELB improved by 0.327986
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.46
ELB improved by 0.354585
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.08
ELB improved by 0.37958
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.679
ELB improved by 0.401128
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.26
ELB improved by 0.419246
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.824
ELB improved by 0.435853
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.372
ELB improved by 0.45225
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.904
ELB improved by 0.467732
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.424
ELB improved by 0.480114
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.937
ELB improved by 0.486645
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.452
ELB improved by 0.484844
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.979
ELB improved by 0.473361
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.526
ELB improved by 0.452876
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.099
ELB improved by 0.427228
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.694
ELB improved by 0.405017
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.293
ELB improved by 0.400861
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.866
ELB improved by 0.426632
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.411
ELB improved by 0.454983
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.976
ELB improved by 0.435837
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.569
ELB improved by 0.406488
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.121
ELB improved by 0.447967
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.517
ELB improved by 0.603977
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.826
ELB improved by 0.690934
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.37
ELB improved by 0.456248
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.117
ELB improved by 0.252952
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.956
ELB improved by 0.161022
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.843
ELB improved by 0.113425
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.757
ELB improved by 0.0860784
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.688
ELB improved by 0.0688293
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.631
ELB improved by 0.0569988
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.582
ELB improved by 0.0483119
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.541
ELB improved by 0.041592
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.505
ELB improved by 0.0362132
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.473
ELB improved by 0.0318428
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.444
ELB improved by 0.0283018
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.419
ELB improved by 0.025486
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.396
ELB improved by 0.0233258
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.374
ELB improved by 0.0217726
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.353
ELB improved by 0.0207999
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.333
ELB improved by 0.02041
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.312
ELB improved by 0.0206434
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.29
ELB improved by 0.0215847
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.267
ELB improved by 0.0233626
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.241
ELB improved by 0.0261293
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.211
ELB improved by 0.0299964
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.176
ELB improved by 0.0348925
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.136
ELB improved by 0.0403317
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.09
ELB improved by 0.0451981
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.043
ELB improved by 0.047846
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.996
ELB improved by 0.0468208
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.954
ELB improved by 0.0419085
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.919
ELB improved by 0.0344841
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.893
ELB improved by 0.0266232
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.873
ELB improved by 0.0198731
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.858
ELB improved by 0.0147905
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.847
ELB improved by 0.0112377
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.838
ELB improved by 0.00882966
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-915.163
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-591.788
ELB improved by 323.375
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-529.204
ELB improved by 62.5831
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-488.791
ELB improved by 40.4134
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.705
ELB improved by 17.0856
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.753
ELB improved by 6.95262
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.216
ELB improved by 4.53704
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.377
ELB improved by 3.8392
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.845
ELB improved by 3.53211
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.528
ELB improved by 3.31635
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.414
ELB improved by 3.11432
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.505
ELB improved by 2.90861
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.81
ELB improved by 2.69535
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.34
ELB improved by 2.46979
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.117
ELB improved by 2.22272
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.171
ELB improved by 1.94614
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.526
ELB improved by 1.64486
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.186
ELB improved by 1.34004
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.128
ELB improved by 1.05802
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.31
ELB improved by 0.818782
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.678
ELB improved by 0.631159
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.186
ELB improved by 0.492478
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.793
ELB improved by 0.392754
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.473
ELB improved by 0.32061
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.206
ELB improved by 0.266895
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.98
ELB improved by 0.225473
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.788
ELB improved by 0.192573
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.622
ELB improved by 0.165891
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.478
ELB improved by 0.14394
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.352
ELB improved by 0.125684
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.242
ELB improved by 0.110363
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.144
ELB improved by 0.0974011
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.058
ELB improved by 0.0863543
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.981
ELB improved by 0.0768781
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.912
ELB improved by 0.0687016
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.851
ELB improved by 0.0616095
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.795
ELB improved by 0.0554286
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.745
ELB improved by 0.0500187
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.7
ELB improved by 0.0452648
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.659
ELB improved by 0.0410721
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.622
ELB improved by 0.0373621
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.588
ELB improved by 0.0340688
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.556
ELB improved by 0.031137
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.528
ELB improved by 0.0285199
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.502
ELB improved by 0.026178
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.478
ELB improved by 0.0240772
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.455
ELB improved by 0.0221887
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.435
ELB improved by 0.0204875
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.416
ELB improved by 0.0189519
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.398
ELB improved by 0.0175634
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.382
ELB improved by 0.0163055
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.367
ELB improved by 0.0151641
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.353
ELB improved by 0.0141268
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.34
ELB improved by 0.0131826
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.327
ELB improved by 0.012322
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.316
ELB improved by 0.0115364
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.305
ELB improved by 0.0108182
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.295
ELB improved by 0.0101609
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.285
ELB improved by 0.00955855
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.303 0.189 2.479
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.052 | 0.002 | 0.054 | |
| getPIPs | 0.048 | 0.011 | 0.059 | |
| graper | 0.078 | 0.008 | 0.086 | |
| makeExampleData | 0.010 | 0.001 | 0.011 | |
| makeExampleDataWithUnequalGroups | 0.012 | 0.001 | 0.013 | |
| plotELBO | 0.317 | 0.039 | 0.356 | |
| plotGroupPenalties | 1.082 | 0.048 | 1.131 | |
| plotPosterior | 0.636 | 0.007 | 0.643 | |
| predict.graper | 2.055 | 0.013 | 2.068 | |
| print.graper | 0.048 | 0.003 | 0.052 | |