| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-13 11:32 -0400 (Wed, 13 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4994 |
| 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 944/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.28.0 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
| See other builds for graper in R Universe. | ||||||||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: graper |
| Version: 1.28.0 |
| 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_1.28.0.tar.gz |
| StartedAt: 2026-05-13 00:44:57 -0400 (Wed, 13 May 2026) |
| EndedAt: 2026-05-13 00:46:34 -0400 (Wed, 13 May 2026) |
| EllapsedTime: 97.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings graper_1.28.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-13 04:44:57 UTC
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.28.0’
* 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 13.3.0-6ubuntu2~24.04.1) 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
predict.graper 3.672 0.511 5.472
* 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 ‘1.28.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ g++ -std=gnu++20 -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++20 -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++20 -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 version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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=-873.398
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-586.075
ELB improved by 287.323
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-526.679
ELB improved by 59.3958
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-488.465
ELB improved by 38.2141
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.729
ELB improved by 15.736
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.014
ELB improved by 5.71515
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.834
ELB improved by 3.17919
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.36
ELB improved by 2.47458
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.117
ELB improved by 2.24313
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.916
ELB improved by 2.20031
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.671
ELB improved by 2.24556
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.348
ELB improved by 2.32297
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.98
ELB improved by 2.36818
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.666
ELB improved by 2.31335
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.547
ELB improved by 2.11964
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.744
ELB improved by 1.80247
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.319
ELB improved by 1.42554
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.254
ELB improved by 1.0643
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.483
ELB improved by 0.771719
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.918
ELB improved by 0.565023
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.485
ELB improved by 0.432223
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.135
ELB improved by 0.350509
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.835
ELB improved by 0.300118
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.567
ELB improved by 0.268063
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.32
ELB improved by 0.246777
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.088
ELB improved by 0.23201
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.867
ELB improved by 0.221333
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.653
ELB improved by 0.213285
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.446
ELB improved by 0.206925
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.245
ELB improved by 0.201604
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.048
ELB improved by 0.196851
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.856
ELB improved by 0.192327
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.668
ELB improved by 0.18779
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.485
ELB improved by 0.183087
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.307
ELB improved by 0.17814
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.134
ELB improved by 0.172937
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.966
ELB improved by 0.167512
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.804
ELB improved by 0.161936
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.648
ELB improved by 0.1563
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.497
ELB improved by 0.150697
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.352
ELB improved by 0.145215
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.212
ELB improved by 0.139931
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.077
ELB improved by 0.134902
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.947
ELB improved by 0.130171
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.821
ELB improved by 0.125759
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.7
ELB improved by 0.121674
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.582
ELB improved by 0.117911
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.467
ELB improved by 0.11445
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.356
ELB improved by 0.111267
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.248
ELB improved by 0.108329
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.142
ELB improved by 0.1056
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.039
ELB improved by 0.103042
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.938
ELB improved by 0.100614
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.84
ELB improved by 0.0982822
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.744
ELB improved by 0.0960122
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.65
ELB improved by 0.093777
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.559
ELB improved by 0.0915564
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.469
ELB improved by 0.089339
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.382
ELB improved by 0.0871236
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.297
ELB improved by 0.0849207
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.215
ELB improved by 0.0827535
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.134
ELB improved by 0.0806592
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.055
ELB improved by 0.0786903
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.978
ELB improved by 0.0769152
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.903
ELB improved by 0.0754188
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.829
ELB improved by 0.074301
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.755
ELB improved by 0.0736732
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.681
ELB improved by 0.0736501
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.607
ELB improved by 0.0743367
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.531
ELB improved by 0.0758125
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.453
ELB improved by 0.0781165
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.372
ELB improved by 0.0812461
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.287
ELB improved by 0.0851743
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.197
ELB improved by 0.0898839
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.101
ELB improved by 0.0953964
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432
ELB improved by 0.101773
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.89
ELB improved by 0.109079
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.773
ELB improved by 0.117321
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.647
ELB improved by 0.126374
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.511
ELB improved by 0.135912
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.366
ELB improved by 0.145324
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.212
ELB improved by 0.153516
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.054
ELB improved by 0.158529
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.896
ELB improved by 0.157415
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.749
ELB improved by 0.147588
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.619
ELB improved by 0.129501
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.512
ELB improved by 0.107274
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.426
ELB improved by 0.0857128
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.359
ELB improved by 0.0675
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.305
ELB improved by 0.0531172
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.263
ELB improved by 0.0420235
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.23
ELB improved by 0.0334893
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.203
ELB improved by 0.0268957
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.181
ELB improved by 0.0217747
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.163
ELB improved by 0.0177799
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.149
ELB improved by 0.0146523
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.137
ELB improved by 0.0121961
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.126
ELB improved by 0.0102611
iteration 99
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.118
ELB improved by 0.00873168
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-874.758
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-602.75
ELB improved by 272.009
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-540.41
ELB improved by 62.3394
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-493.989
ELB improved by 46.4211
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.718
ELB improved by 23.2711
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.197
ELB improved by 9.52051
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.391
ELB improved by 4.80591
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.833
ELB improved by 3.5585
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.614
ELB improved by 3.21877
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.559
ELB improved by 3.05523
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.694
ELB improved by 2.86475
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.121
ELB improved by 2.5737
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.937
ELB improved by 2.18381
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.186
ELB improved by 1.75063
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.84
ELB improved by 1.34559
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.825
ELB improved by 1.01589
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.054
ELB improved by 0.770815
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.458
ELB improved by 0.59589
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.987
ELB improved by 0.47134
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.605
ELB improved by 0.381093
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.291
ELB improved by 0.314113
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.028
ELB improved by 0.263172
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.805
ELB improved by 0.223544
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.613
ELB improved by 0.192085
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.446
ELB improved by 0.166668
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.3
ELB improved by 0.14582
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.172
ELB improved by 0.128493
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.058
ELB improved by 0.113933
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.956
ELB improved by 0.101577
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.865
ELB improved by 0.0910026
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.783
ELB improved by 0.0818863
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.709
ELB improved by 0.073975
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.642
ELB improved by 0.0670692
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.581
ELB improved by 0.0610093
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.525
ELB improved by 0.0556664
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.475
ELB improved by 0.0509353
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.428
ELB improved by 0.0467295
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.385
ELB improved by 0.0429771
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.345
ELB improved by 0.0396183
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.309
ELB improved by 0.0366026
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.275
ELB improved by 0.0338873
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.243
ELB improved by 0.031436
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.214
ELB improved by 0.0292178
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.187
ELB improved by 0.0272058
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.161
ELB improved by 0.0253771
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.138
ELB improved by 0.0237117
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.116
ELB improved by 0.0221921
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.095
ELB improved by 0.0208031
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.075
ELB improved by 0.0195314
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.057
ELB improved by 0.0183653
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.04
ELB improved by 0.0172943
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.023
ELB improved by 0.0163092
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.008
ELB improved by 0.0154021
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.993
ELB improved by 0.0145655
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.979
ELB improved by 0.013793
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.966
ELB improved by 0.0130788
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.954
ELB improved by 0.0124178
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.942
ELB improved by 0.0118052
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.931
ELB improved by 0.0112369
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.92
ELB improved by 0.0107091
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.91
ELB improved by 0.0102183
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.9
ELB improved by 0.00976154
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-916.067
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-567.473
ELB improved by 348.594
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-504.712
ELB improved by 62.7606
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.838
ELB improved by 35.8744
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.752
ELB improved by 15.0852
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.56
ELB improved by 8.19202
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.906
ELB improved by 6.65394
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.298
ELB improved by 6.60838
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.061
ELB improved by 7.23673
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.14
ELB improved by 7.92144
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.327
ELB improved by 7.81262
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.912
ELB improved by 6.41511
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.49
ELB improved by 4.42175
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.678
ELB improved by 2.81238
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.894
ELB improved by 1.78452
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.719
ELB improved by 1.17503
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.88
ELB improved by 0.838898
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.218
ELB improved by 0.661296
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.654
ELB improved by 0.564366
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.156
ELB improved by 0.498349
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.717
ELB improved by 0.438969
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.328
ELB improved by 0.389011
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.969
ELB improved by 0.358577
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.625
ELB improved by 0.343961
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.304
ELB improved by 0.320666
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.039
ELB improved by 0.265054
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.846
ELB improved by 0.193108
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.709
ELB improved by 0.13732
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.604
ELB improved by 0.10458
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.518
ELB improved by 0.0859101
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.445
ELB improved by 0.0738082
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.38
ELB improved by 0.0647987
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.322
ELB improved by 0.0575111
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.271
ELB improved by 0.0513792
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.225
ELB improved by 0.0461231
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.183
ELB improved by 0.0415723
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.146
ELB improved by 0.0376063
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.112
ELB improved by 0.034132
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.08
ELB improved by 0.031075
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.052
ELB improved by 0.0283745
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.026
ELB improved by 0.0259801
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.002
ELB improved by 0.0238498
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.98
ELB improved by 0.0219485
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.96
ELB improved by 0.0202463
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.941
ELB improved by 0.0187182
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.924
ELB improved by 0.0173427
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.908
ELB improved by 0.0161014
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.893
ELB improved by 0.0149786
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.879
ELB improved by 0.0139607
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.866
ELB improved by 0.013036
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.854
ELB improved by 0.0121942
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.842
ELB improved by 0.0114264
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.832
ELB improved by 0.0107247
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.821
ELB improved by 0.0100825
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.812
ELB improved by 0.0094935
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-881.56
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-594.961
ELB improved by 286.599
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-532.555
ELB improved by 62.4058
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-486.559
ELB improved by 45.9963
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.655
ELB improved by 22.9041
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.082
ELB improved by 9.57225
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.113
ELB improved by 4.96924
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.54
ELB improved by 3.57353
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.444
ELB improved by 3.0953
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.542
ELB improved by 2.90248
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.749
ELB improved by 2.79235
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.052
ELB improved by 2.69706
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.474
ELB improved by 2.57874
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.06
ELB improved by 2.41327
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.862
ELB improved by 2.19836
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.932
ELB improved by 1.92983
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.347
ELB improved by 1.58527
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.147
ELB improved by 1.19998
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.286
ELB improved by 0.860925
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.671
ELB improved by 0.614904
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.213
ELB improved by 0.457751
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.849
ELB improved by 0.36444
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.538
ELB improved by 0.310585
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.259
ELB improved by 0.279369
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.998
ELB improved by 0.260776
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.749
ELB improved by 0.249159
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.508
ELB improved by 0.241363
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.272
ELB improved by 0.235604
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.041
ELB improved by 0.230868
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.815
ELB improved by 0.226594
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.592
ELB improved by 0.222507
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.374
ELB improved by 0.21852
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.159
ELB improved by 0.214669
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.948
ELB improved by 0.211069
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.74
ELB improved by 0.207873
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.535
ELB improved by 0.205246
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.331
ELB improved by 0.203354
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.129
ELB improved by 0.202348
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.927
ELB improved by 0.202373
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.723
ELB improved by 0.203573
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.517
ELB improved by 0.206109
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.307
ELB improved by 0.21019
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.091
ELB improved by 0.216115
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.866
ELB improved by 0.224341
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.631
ELB improved by 0.235593
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.38
ELB improved by 0.251014
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.107
ELB improved by 0.272359
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.805
ELB improved by 0.302064
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.463
ELB improved by 0.342718
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.068
ELB improved by 0.395034
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.612
ELB improved by 0.455042
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.096
ELB improved by 0.516838
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.51
ELB improved by 0.585152
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.828
ELB improved by 0.682285
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.008
ELB improved by 0.819766
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.087
ELB improved by 0.921149
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.211
ELB improved by 0.875939
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.502
ELB improved by 0.709829
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.969
ELB improved by 0.532303
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.568
ELB improved by 0.401399
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.254
ELB improved by 0.313621
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.997
ELB improved by 0.257595
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.76
ELB improved by 0.237025
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.495
ELB improved by 0.264246
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.154
ELB improved by 0.341758
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.722
ELB improved by 0.431946
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.261
ELB improved by 0.460313
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.862
ELB improved by 0.39909
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.554
ELB improved by 0.308517
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.309
ELB improved by 0.244873
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.106
ELB improved by 0.202431
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.946
ELB improved by 0.160378
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.831
ELB improved by 0.11531
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.754
ELB improved by 0.0765711
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.704
ELB improved by 0.0501881
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.669
ELB improved by 0.03463
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.643
ELB improved by 0.0258584
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.623
ELB improved by 0.020742
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.605
ELB improved by 0.0175057
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.59
ELB improved by 0.0152591
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.576
ELB improved by 0.01357
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.564
ELB improved by 0.0122243
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.553
ELB improved by 0.0111109
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.543
ELB improved by 0.0101671
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.534
ELB improved by 0.00935488
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.401 0.209 2.600
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.051 | 0.020 | 0.072 | |
| getPIPs | 0.076 | 0.023 | 0.099 | |
| graper | 0.084 | 0.016 | 0.100 | |
| makeExampleData | 0.009 | 0.000 | 0.009 | |
| makeExampleDataWithUnequalGroups | 0.011 | 0.000 | 0.012 | |
| plotELBO | 0.305 | 0.020 | 0.327 | |
| plotGroupPenalties | 0.955 | 0.014 | 0.969 | |
| plotPosterior | 0.663 | 0.011 | 0.673 | |
| predict.graper | 3.672 | 0.511 | 5.472 | |
| print.graper | 0.311 | 0.086 | 0.396 | |