Britta Velten
| Snapshot Date: 2025-11-16 13:40 -0500 (Sun, 16 Nov 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 2025-11-17 11:39 -0500 (Mon, 17 Nov 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" | 4826 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4491 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4562 |
| 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 911/2325 | 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 | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.27.0.tar.gz |
| StartedAt: 2025-11-17 03:14:09 -0500 (Mon, 17 Nov 2025) |
| EndedAt: 2025-11-17 03:15:32 -0500 (Mon, 17 Nov 2025) |
| EllapsedTime: 82.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.27.0’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’ using SDK: ‘MacOSX11.3.1.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fit_graper.cpp -o fit_graper.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o graper.so RcppExports.o fit_graper.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/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) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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=-827.243
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-561.399
ELB improved by 265.845
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-501.108
ELB improved by 60.2901
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.401
ELB improved by 38.7075
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.979
ELB improved by 16.4224
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.819
ELB improved by 6.15973
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.697
ELB improved by 3.12153
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.462
ELB improved by 2.23524
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.533
ELB improved by 1.92919
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.722
ELB improved by 1.81074
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.963
ELB improved by 1.75929
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.238
ELB improved by 1.7251
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.556
ELB improved by 1.68172
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.944
ELB improved by 1.61216
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.437
ELB improved by 1.50642
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.075
ELB improved by 1.36285
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.885
ELB improved by 1.18941
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.883
ELB improved by 1.00201
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.063
ELB improved by 0.820085
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.403
ELB improved by 0.660224
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.872
ELB improved by 0.531217
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.438
ELB improved by 0.433086
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.079
ELB improved by 0.359844
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.775
ELB improved by 0.303861
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.515
ELB improved by 0.259348
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.292
ELB improved by 0.223191
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.099
ELB improved by 0.193674
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.929
ELB improved by 0.169289
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.781
ELB improved by 0.148633
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.65
ELB improved by 0.130728
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.535
ELB improved by 0.115103
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.433
ELB improved by 0.101593
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.343
ELB improved by 0.0901031
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.263
ELB improved by 0.0804825
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.19
ELB improved by 0.0725
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.124
ELB improved by 0.0658816
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.064
ELB improved by 0.0603571
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.008
ELB improved by 0.0556907
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.957
ELB improved by 0.0516925
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.908
ELB improved by 0.0482169
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.863
ELB improved by 0.0451549
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.821
ELB improved by 0.0424254
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.781
ELB improved by 0.0399682
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.743
ELB improved by 0.0377381
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.707
ELB improved by 0.0357003
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.673
ELB improved by 0.0338277
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.641
ELB improved by 0.0320989
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.611
ELB improved by 0.0304962
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.582
ELB improved by 0.0290053
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.554
ELB improved by 0.027614
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.528
ELB improved by 0.026312
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.503
ELB improved by 0.0250902
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.479
ELB improved by 0.023941
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.456
ELB improved by 0.0228575
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.434
ELB improved by 0.0218336
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.413
ELB improved by 0.0208642
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.393
ELB improved by 0.0199447
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.374
ELB improved by 0.019071
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.356
ELB improved by 0.0182398
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.339
ELB improved by 0.017448
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.322
ELB improved by 0.0166934
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.306
ELB improved by 0.0159741
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.291
ELB improved by 0.0152886
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.276
ELB improved by 0.0146358
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.262
ELB improved by 0.0140149
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.249
ELB improved by 0.0134257
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.236
ELB improved by 0.0128677
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.223
ELB improved by 0.0123409
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.212
ELB improved by 0.0118451
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.2
ELB improved by 0.0113803
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.189
ELB improved by 0.0109463
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.179
ELB improved by 0.0105426
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.169
ELB improved by 0.010169
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.159
ELB improved by 0.00982479
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-877.775
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-590.353
ELB improved by 287.422
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-527.743
ELB improved by 62.6095
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-483.379
ELB improved by 44.3641
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.723
ELB improved by 21.6562
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.294
ELB improved by 8.42948
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.315
ELB improved by 3.97862
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.628
ELB improved by 2.68726
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.412
ELB improved by 2.21551
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.398
ELB improved by 2.0139
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.481
ELB improved by 1.9169
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.62
ELB improved by 1.86111
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.806
ELB improved by 1.81416
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.055
ELB improved by 1.75063
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.406
ELB improved by 1.64944
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.904
ELB improved by 1.5023
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.584
ELB improved by 1.31992
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.456
ELB improved by 1.12809
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.499
ELB improved by 0.957088
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.671
ELB improved by 0.827939
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.927
ELB improved by 0.744046
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.23
ELB improved by 0.696833
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.554
ELB improved by 0.675615
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.882
ELB improved by 0.672684
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.197
ELB improved by 0.684099
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.489
ELB improved by 0.708703
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.742
ELB improved by 0.746665
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.944
ELB improved by 0.798
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.083
ELB improved by 0.861207
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.151
ELB improved by 0.932292
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.146
ELB improved by 1.005
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.072
ELB improved by 1.07394
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.929
ELB improved by 1.14219
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.699
ELB improved by 1.23024
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.34
ELB improved by 1.35941
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.833
ELB improved by 1.50666
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.064
ELB improved by 1.76937
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.942
ELB improved by 2.12127
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.933
ELB improved by 2.00911
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.251
ELB improved by 1.68283
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.983
ELB improved by 1.26717
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.144
ELB improved by 0.839138
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.569
ELB improved by 0.574992
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.13
ELB improved by 0.43952
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.797
ELB improved by 0.332678
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.549
ELB improved by 0.247554
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.325
ELB improved by 0.224115
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.033
ELB improved by 0.292249
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.551
ELB improved by 0.481697
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.884
ELB improved by 0.667097
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.286
ELB improved by 0.598467
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.869
ELB improved by 0.417262
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.568
ELB improved by 0.30082
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.323
ELB improved by 0.245099
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.117
ELB improved by 0.20585
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.951
ELB improved by 0.166143
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.815
ELB improved by 0.135278
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.691
ELB improved by 0.123941
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.554
ELB improved by 0.137242
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.374
ELB improved by 0.179974
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.128
ELB improved by 0.246398
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.831
ELB improved by 0.296815
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.527
ELB improved by 0.304229
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.221
ELB improved by 0.306293
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.897
ELB improved by 0.323924
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.546
ELB improved by 0.350985
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.17
ELB improved by 0.37522
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.841
ELB improved by 0.329745
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.624
ELB improved by 0.216558
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.492
ELB improved by 0.132559
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.401
ELB improved by 0.0908255
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.333
ELB improved by 0.0680743
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.279
ELB improved by 0.0536059
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.235
ELB improved by 0.0435279
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.199
ELB improved by 0.0361545
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.169
ELB improved by 0.0306636
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.142
ELB improved by 0.0266134
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.118
ELB improved by 0.0237446
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.096
ELB improved by 0.0219028
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.075
ELB improved by 0.0210146
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.054
ELB improved by 0.0210874
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.032
ELB improved by 0.022214
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.008
ELB improved by 0.0245509
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.979
ELB improved by 0.0282046
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.946
ELB improved by 0.0329073
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.909
ELB improved by 0.0374556
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.87
ELB improved by 0.0394513
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.833
ELB improved by 0.0365833
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.804
ELB improved by 0.029153
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.783
ELB improved by 0.0203337
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.77
ELB improved by 0.013183
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.762
ELB improved by 0.00863006
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-838.524
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-597.538
ELB improved by 240.987
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-538.491
ELB improved by 59.0463
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-483.608
ELB improved by 54.8832
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.979
ELB improved by 33.6297
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.488
ELB improved by 13.4902
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.973
ELB improved by 5.51519
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.845
ELB improved by 3.12784
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.791
ELB improved by 2.05446
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.301
ELB improved by 1.48962
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.118
ELB improved by 1.18282
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.108
ELB improved by 1.01075
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.197
ELB improved by 0.910877
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.346
ELB improved by 0.850925
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.532
ELB improved by 0.813707
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.742
ELB improved by 0.789756
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.969
ELB improved by 0.773823
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.206
ELB improved by 0.763087
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.449
ELB improved by 0.75604
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.698
ELB improved by 0.75155
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.95
ELB improved by 0.74791
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.208
ELB improved by 0.741981
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.479
ELB improved by 0.728782
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.777
ELB improved by 0.702107
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.121
ELB improved by 0.65657
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.53
ELB improved by 0.590581
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.022
ELB improved by 0.508392
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.602
ELB improved by 0.419187
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.269
ELB improved by 0.333391
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.01
ELB improved by 0.25877
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.812
ELB improved by 0.198719
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.659
ELB improved by 0.152903
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.54
ELB improved by 0.118933
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.446
ELB improved by 0.0938602
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.371
ELB improved by 0.0750688
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.31
ELB improved by 0.0606271
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.261
ELB improved by 0.0492799
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.221
ELB improved by 0.0402682
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.187
ELB improved by 0.0331171
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.16
ELB improved by 0.0274834
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.137
ELB improved by 0.0230802
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.117
ELB improved by 0.0196555
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.1
ELB improved by 0.0169925
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.085
ELB improved by 0.0149122
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.072
ELB improved by 0.0132723
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.06
ELB improved by 0.0119631
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.049
ELB improved by 0.0109018
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.039
ELB improved by 0.0100269
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.03
ELB improved by 0.00929277
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-840.249
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-565.737
ELB improved by 274.512
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-505.937
ELB improved by 59.7993
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.095
ELB improved by 38.8428
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.598
ELB improved by 17.4966
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.039
ELB improved by 6.55914
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.522
ELB improved by 3.51723
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.8
ELB improved by 2.72194
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.393
ELB improved by 2.40634
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.136
ELB improved by 2.25691
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.963
ELB improved by 2.17316
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.845
ELB improved by 2.11879
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.768
ELB improved by 2.0763
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.742
ELB improved by 2.02604
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.804
ELB improved by 1.93771
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.026
ELB improved by 1.77812
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.488
ELB improved by 1.53881
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.23
ELB improved by 1.25803
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.231
ELB improved by 0.998872
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.428
ELB improved by 0.803012
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.755
ELB improved by 0.673135
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.164
ELB improved by 0.59039
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.627
ELB improved by 0.537296
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.121
ELB improved by 0.505584
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.629
ELB improved by 0.492054
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.135
ELB improved by 0.494643
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.623
ELB improved by 0.51193
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.079
ELB improved by 0.543625
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.488
ELB improved by 0.590898
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.831
ELB improved by 0.656689
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.086
ELB improved by 0.745782
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.222
ELB improved by 0.863742
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.208
ELB improved by 1.01382
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.016
ELB improved by 1.19184
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.635
ELB improved by 1.38076
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.085
ELB improved by 1.5502
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.42
ELB improved by 1.66512
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.727
ELB improved by 1.69349
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.119
ELB improved by 1.60726
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.727
ELB improved by 1.39236
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.647
ELB improved by 1.08029
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.887
ELB improved by 0.759329
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.382
ELB improved by 0.50494
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.051
ELB improved by 0.331885
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.829
ELB improved by 0.221824
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.676
ELB improved by 0.152865
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.567
ELB improved by 0.109101
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.486
ELB improved by 0.0806483
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.424
ELB improved by 0.0616394
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.376
ELB improved by 0.0485893
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.337
ELB improved by 0.0393958
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.304
ELB improved by 0.0327642
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.276
ELB improved by 0.0278798
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.252
ELB improved by 0.0242183
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.23
ELB improved by 0.021436
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.211
ELB improved by 0.0193033
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.193
ELB improved by 0.0176644
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.177
ELB improved by 0.016412
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.161
ELB improved by 0.0154695
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.147
ELB improved by 0.0147797
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.132
ELB improved by 0.0142943
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.118
ELB improved by 0.0139659
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.105
ELB improved by 0.0137414
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.091
ELB improved by 0.0135582
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.078
ELB improved by 0.0133448
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.065
ELB improved by 0.0130299
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.052
ELB improved by 0.0125579
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.04
ELB improved by 0.0119051
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.029
ELB improved by 0.0110884
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.019
ELB improved by 0.0101595
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.01
ELB improved by 0.0091865
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.735 0.300 3.056
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.049 | 0.013 | 0.062 | |
| getPIPs | 0.045 | 0.015 | 0.060 | |
| graper | 0.095 | 0.021 | 0.117 | |
| makeExampleData | 0.009 | 0.001 | 0.010 | |
| makeExampleDataWithUnequalGroups | 0.011 | 0.000 | 0.012 | |
| plotELBO | 0.344 | 0.024 | 0.373 | |
| plotGroupPenalties | 1.271 | 0.036 | 1.309 | |
| plotPosterior | 0.682 | 0.030 | 0.712 | |
| predict.graper | 1.897 | 0.072 | 1.975 | |
| print.graper | 0.045 | 0.010 | 0.054 | |