Britta Velten
| Snapshot Date: 2025-12-16 13:40 -0500 (Tue, 16 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: 95474d7 |
| git_last_commit_date: 2025-10-29 10:49:21 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-17 11:34 -0500 (Wed, 17 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4875 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4589 |
| 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 915/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.27.0 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: graper |
| Version: 1.27.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings graper_1.27.0.tar.gz |
| StartedAt: 2025-12-16 23:52:55 -0500 (Tue, 16 Dec 2025) |
| EndedAt: 2025-12-16 23:54:26 -0500 (Tue, 16 Dec 2025) |
| EllapsedTime: 91.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings graper_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.27.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) predict.graper.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:23-24: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.27.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c fit_graper.cpp -o fit_graper.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -llapack -L/home/biocbuild/bbs-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-graper/00new/graper/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (graper)
graper.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(graper)
>
> test_check("graper")
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-862.745
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-560.926
ELB improved by 301.819
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-500.104
ELB improved by 60.822
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.039
ELB improved by 33.0647
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.506
ELB improved by 13.5332
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.431
ELB improved by 7.07502
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.769
ELB improved by 5.662
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.827
ELB improved by 5.94128
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.217
ELB improved by 6.61025
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.516
ELB improved by 6.70078
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.841
ELB improved by 5.67567
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.739
ELB improved by 4.10177
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.912
ELB improved by 2.82672
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.967
ELB improved by 1.94482
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.624
ELB improved by 1.34308
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.631
ELB improved by 0.993466
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.841
ELB improved by 0.790133
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.184
ELB improved by 0.656764
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.625
ELB improved by 0.558593
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.145
ELB improved by 0.480157
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.731
ELB improved by 0.414434
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.373
ELB improved by 0.358252
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.063
ELB improved by 0.310046
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.794
ELB improved by 0.268805
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.56
ELB improved by 0.233667
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.356
ELB improved by 0.203811
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.178
ELB improved by 0.178459
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.021
ELB improved by 0.156906
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.882
ELB improved by 0.138532
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.76
ELB improved by 0.12281
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.65
ELB improved by 0.109298
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.553
ELB improved by 0.0976332
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.465
ELB improved by 0.0875159
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.386
ELB improved by 0.0787008
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.315
ELB improved by 0.0709869
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.251
ELB improved by 0.0642087
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.193
ELB improved by 0.0582296
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.14
ELB improved by 0.0529363
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.092
ELB improved by 0.0482342
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.048
ELB improved by 0.0440441
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.007
ELB improved by 0.0402993
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.97
ELB improved by 0.0369433
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.937
ELB improved by 0.0339281
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.905
ELB improved by 0.0312125
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.877
ELB improved by 0.0287613
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.85
ELB improved by 0.0265441
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.826
ELB improved by 0.0245346
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.803
ELB improved by 0.02271
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.782
ELB improved by 0.0210503
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.762
ELB improved by 0.019538
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.744
ELB improved by 0.018158
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.727
ELB improved by 0.0168968
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.711
ELB improved by 0.0157424
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.697
ELB improved by 0.0146845
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.683
ELB improved by 0.0137137
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.67
ELB improved by 0.0128217
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.658
ELB improved by 0.0120012
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.647
ELB improved by 0.0112455
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.636
ELB improved by 0.0105488
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.626
ELB improved by 0.00990582
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-864.813
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-567.466
ELB improved by 297.348
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-506.574
ELB improved by 60.8919
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.634
ELB improved by 38.9403
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.25
ELB improved by 16.3833
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.561
ELB improved by 6.68909
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.414
ELB improved by 4.14755
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.912
ELB improved by 3.50172
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.506
ELB improved by 3.40614
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.964
ELB improved by 3.54207
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.193
ELB improved by 3.77106
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.24
ELB improved by 3.95316
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.351
ELB improved by 3.88893
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.918
ELB improved by 3.43316
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.224
ELB improved by 2.69333
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.268
ELB improved by 1.95592
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.866
ELB improved by 1.4021
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.829
ELB improved by 1.03697
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.029
ELB improved by 0.800092
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.391
ELB improved by 0.638508
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.873
ELB improved by 0.517737
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.454
ELB improved by 0.418942
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.117
ELB improved by 0.337349
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.843
ELB improved by 0.273837
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.616
ELB improved by 0.226828
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.424
ELB improved by 0.192422
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.257
ELB improved by 0.166899
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.109
ELB improved by 0.147611
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.976
ELB improved by 0.13283
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.855
ELB improved by 0.121432
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.742
ELB improved by 0.11267
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.636
ELB improved by 0.106028
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.535
ELB improved by 0.10114
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.437
ELB improved by 0.0977432
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.342
ELB improved by 0.095637
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.247
ELB improved by 0.0946668
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.152
ELB improved by 0.0947058
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.056
ELB improved by 0.0956435
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.959
ELB improved by 0.0973788
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.859
ELB improved by 0.099816
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.756
ELB improved by 0.102866
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.65
ELB improved by 0.106448
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.539
ELB improved by 0.110505
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.424
ELB improved by 0.11501
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.304
ELB improved by 0.119989
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.179
ELB improved by 0.125547
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.047
ELB improved by 0.131905
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.908
ELB improved by 0.139444
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.759
ELB improved by 0.148787
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.598
ELB improved by 0.160914
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.421
ELB improved by 0.177299
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.221
ELB improved by 0.199789
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.992
ELB improved by 0.229145
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.731
ELB improved by 0.260561
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.45
ELB improved by 0.280708
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.169
ELB improved by 0.281269
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.896
ELB improved by 0.273259
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.626
ELB improved by 0.270016
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.351
ELB improved by 0.274468
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.066
ELB improved by 0.285512
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.763
ELB improved by 0.30242
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.439
ELB improved by 0.324504
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.09
ELB improved by 0.34888
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.722
ELB improved by 0.368543
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.346
ELB improved by 0.37557
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.977
ELB improved by 0.368679
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.624
ELB improved by 0.353537
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.288
ELB improved by 0.336215
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.966
ELB improved by 0.321055
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.654
ELB improved by 0.312232
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.341
ELB improved by 0.312753
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.023
ELB improved by 0.318399
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.711
ELB improved by 0.312404
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.433
ELB improved by 0.277576
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.213
ELB improved by 0.22002
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.051
ELB improved by 0.161993
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.935
ELB improved by 0.116555
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.85
ELB improved by 0.0844102
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.788
ELB improved by 0.0621733
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.741
ELB improved by 0.0466762
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.706
ELB improved by 0.0357166
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.678
ELB improved by 0.027851
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.656
ELB improved by 0.0221288
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.638
ELB improved by 0.0179127
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.623
ELB improved by 0.014768
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.61
ELB improved by 0.0123936
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.6
ELB improved by 0.0105788
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.591
ELB improved by 0.00917434
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-816.222
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-578.63
ELB improved by 237.593
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-519.45
ELB improved by 59.1798
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-474.848
ELB improved by 44.6018
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.459
ELB improved by 22.3885
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.438
ELB improved by 9.02161
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.501
ELB improved by 4.93735
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.487
ELB improved by 4.01353
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.623
ELB improved by 3.86409
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.734
ELB improved by 3.88924
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.909
ELB improved by 3.82485
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.409
ELB improved by 3.50007
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.498
ELB improved by 2.91101
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.267
ELB improved by 2.23047
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.612
ELB improved by 1.65536
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.353
ELB improved by 1.25902
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.354
ELB improved by 0.999196
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.538
ELB improved by 0.81532
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.853
ELB improved by 0.685216
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.249
ELB improved by 0.60388
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.691
ELB improved by 0.558695
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.159
ELB improved by 0.531991
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.657
ELB improved by 0.501851
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.206
ELB improved by 0.450218
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.82
ELB improved by 0.386116
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.488
ELB improved by 0.332616
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.191
ELB improved by 0.296811
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.918
ELB improved by 0.273075
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.663
ELB improved by 0.255338
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.422
ELB improved by 0.240264
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.196
ELB improved by 0.226386
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.983
ELB improved by 0.213138
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.782
ELB improved by 0.20036
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.594
ELB improved by 0.188064
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.418
ELB improved by 0.176338
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.253
ELB improved by 0.165294
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.098
ELB improved by 0.155042
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.952
ELB improved by 0.145683
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.815
ELB improved by 0.137308
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.685
ELB improved by 0.130012
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.561
ELB improved by 0.123915
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.442
ELB improved by 0.119192
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.325
ELB improved by 0.116146
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.21
ELB improved by 0.115314
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.092
ELB improved by 0.117701
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.967
ELB improved by 0.125207
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.826
ELB improved by 0.141306
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.655
ELB improved by 0.17122
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.438
ELB improved by 0.216945
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.179
ELB improved by 0.258283
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.929
ELB improved by 0.250308
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.73
ELB improved by 0.198623
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.575
ELB improved by 0.155243
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.444
ELB improved by 0.131367
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.327
ELB improved by 0.117252
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.219
ELB improved by 0.10743
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.119
ELB improved by 0.0998835
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.026
ELB improved by 0.0937396
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.937
ELB improved by 0.088522
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.853
ELB improved by 0.0839331
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.773
ELB improved by 0.0797719
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.697
ELB improved by 0.0758962
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.625
ELB improved by 0.0722034
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.557
ELB improved by 0.0686207
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.492
ELB improved by 0.0651006
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.43
ELB improved by 0.0616186
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.372
ELB improved by 0.0581703
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.317
ELB improved by 0.0547681
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.266
ELB improved by 0.0514365
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.217
ELB improved by 0.0482082
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.172
ELB improved by 0.0451198
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.13
ELB improved by 0.0422095
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.09
ELB improved by 0.0395158
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.053
ELB improved by 0.0370778
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.018
ELB improved by 0.0349375
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.985
ELB improved by 0.0331427
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.954
ELB improved by 0.031751
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.923
ELB improved by 0.0308324
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.892
ELB improved by 0.0304685
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.862
ELB improved by 0.0307389
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.83
ELB improved by 0.0316814
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.797
ELB improved by 0.0332088
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.762
ELB improved by 0.0349774
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.725
ELB improved by 0.03628
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.689
ELB improved by 0.0361513
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.655
ELB improved by 0.0338454
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.626
ELB improved by 0.0294332
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.602
ELB improved by 0.0238736
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.584
ELB improved by 0.0183912
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.57
ELB improved by 0.0138083
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.56
ELB improved by 0.0103706
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.552
ELB improved by 0.00794956
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-873.973
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-615.381
ELB improved by 258.593
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-553.631
ELB improved by 61.7502
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-498.929
ELB improved by 54.702
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.282
ELB improved by 32.6467
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.835
ELB improved by 13.4473
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.116
ELB improved by 5.71882
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.46
ELB improved by 3.6557
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.515
ELB improved by 2.94543
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.827
ELB improved by 2.6876
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.234
ELB improved by 2.59336
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.706
ELB improved by 2.52748
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.283
ELB improved by 2.42313
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.041
ELB improved by 2.24196
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.066
ELB improved by 1.97456
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.416
ELB improved by 1.65038
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.089
ELB improved by 1.32729
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.033
ELB improved by 1.05556
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.183
ELB improved by 0.850086
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.484
ELB improved by 0.698856
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.895
ELB improved by 0.58888
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.381
ELB improved by 0.514139
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.913
ELB improved by 0.468757
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.468
ELB improved by 0.444995
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.032
ELB improved by 0.435549
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.597
ELB improved by 0.434851
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.158
ELB improved by 0.439061
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.712
ELB improved by 0.44569
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.259
ELB improved by 0.453271
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.798
ELB improved by 0.461101
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.329
ELB improved by 0.469056
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.852
ELB improved by 0.477421
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.365
ELB improved by 0.486773
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.867
ELB improved by 0.497916
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.355
ELB improved by 0.511883
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.825
ELB improved by 0.529935
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.272
ELB improved by 0.5534
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.688
ELB improved by 0.583147
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.07
ELB improved by 0.618733
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.412
ELB improved by 0.657949
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.714
ELB improved by 0.697361
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.982
ELB improved by 0.732526
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.226
ELB improved by 0.755942
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.467
ELB improved by 0.758602
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.727
ELB improved by 0.740324
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.025
ELB improved by 0.701781
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.394
ELB improved by 0.630956
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.86
ELB improved by 0.534713
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.412
ELB improved by 0.447465
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.022
ELB improved by 0.390154
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.664
ELB improved by 0.358318
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.325
ELB improved by 0.338662
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.001
ELB improved by 0.323691
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.688
ELB improved by 0.313703
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.378
ELB improved by 0.309632
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.063
ELB improved by 0.315334
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.724
ELB improved by 0.339013
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.365
ELB improved by 0.358585
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.044
ELB improved by 0.320604
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.803
ELB improved by 0.241307
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.628
ELB improved by 0.174774
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.495
ELB improved by 0.132911
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.388
ELB improved by 0.107715
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.296
ELB improved by 0.0919161
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.215
ELB improved by 0.0811613
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.142
ELB improved by 0.0729733
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.076
ELB improved by 0.0660177
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.016
ELB improved by 0.0596687
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.962
ELB improved by 0.0536592
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.915
ELB improved by 0.0478276
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.872
ELB improved by 0.0420402
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.836
ELB improved by 0.0362598
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.806
ELB improved by 0.030613
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.78
ELB improved by 0.0253508
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.76
ELB improved by 0.0207255
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.743
ELB improved by 0.0168858
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.729
ELB improved by 0.0138483
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.717
ELB improved by 0.0115302
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.707
ELB improved by 0.0098015
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.45 0.20 2.64
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.059 | 0.016 | 0.075 | |
| getPIPs | 0.050 | 0.012 | 0.063 | |
| graper | 0.079 | 0.020 | 0.099 | |
| makeExampleData | 0.008 | 0.002 | 0.011 | |
| makeExampleDataWithUnequalGroups | 0.012 | 0.001 | 0.012 | |
| plotELBO | 0.326 | 0.023 | 0.349 | |
| plotGroupPenalties | 1.071 | 0.054 | 1.126 | |
| plotPosterior | 0.628 | 0.014 | 0.642 | |
| predict.graper | 2.056 | 0.069 | 2.125 | |
| print.graper | 0.049 | 0.012 | 0.061 | |