Britta Velten
| Snapshot Date: 2026-05-01 13:40 -0400 (Fri, 01 May 2026) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: RELEASE_3_23 |
| git_last_commit: 7354ec6 |
| git_last_commit_date: 2026-04-28 08:49:19 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-02 11:35 -0400 (Sat, 02 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" | 4988 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There" | 4718 |
| 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 | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: /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_1.28.0.tar.gz |
| StartedAt: 2026-05-01 19:57:38 -0400 (Fri, 01 May 2026) |
| EndedAt: 2026-05-01 19:58:08 -0400 (Fri, 01 May 2026) |
| EllapsedTime: 29.4 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_1.28.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/graper.Rcheck’
* using R version 4.6.0 Patched (2026-04-24 r89963)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-01 23:57:39 UTC
* using option ‘--no-vignettes’
* 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: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.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/Resources/library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.28.0’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’ using SDK: ‘MacOSX26.2.sdk’ clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fit_graper.cpp -o fit_graper.o clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/aarch64-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/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 version 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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=-888.229
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-591.399
ELB improved by 296.83
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-526.622
ELB improved by 64.7773
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-481.047
ELB improved by 45.575
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.286
ELB improved by 20.7601
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.342
ELB improved by 7.9447
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.066
ELB improved by 4.2758
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.635
ELB improved by 3.43117
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.258
ELB improved by 3.37646
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.633
ELB improved by 3.62554
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.645
ELB improved by 3.98786
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.364
ELB improved by 4.28066
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.1
ELB improved by 4.26416
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.319
ELB improved by 3.78127
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.371
ELB improved by 2.94776
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.299
ELB improved by 2.07208
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.903
ELB improved by 1.3955
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.94
ELB improved by 0.963757
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.237
ELB improved by 0.70307
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.706
ELB improved by 0.531123
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.297
ELB improved by 0.408968
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.97
ELB improved by 0.326358
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.696
ELB improved by 0.273916
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.457
ELB improved by 0.239592
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.243
ELB improved by 0.2137
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.051
ELB improved by 0.192017
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.876
ELB improved by 0.175289
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.711
ELB improved by 0.165073
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.55
ELB improved by 0.160767
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.39
ELB improved by 0.160259
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.228
ELB improved by 0.161504
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.065
ELB improved by 0.163222
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.9
ELB improved by 0.164874
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.734
ELB improved by 0.166307
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.566
ELB improved by 0.167381
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.399
ELB improved by 0.167794
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.231
ELB improved by 0.167157
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.066
ELB improved by 0.165252
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.904
ELB improved by 0.162272
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.745
ELB improved by 0.158841
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.589
ELB improved by 0.155777
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.435
ELB improved by 0.153773
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.282
ELB improved by 0.153031
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.13
ELB improved by 0.152803
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.978
ELB improved by 0.151167
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.832
ELB improved by 0.14596
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.696
ELB improved by 0.136711
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.571
ELB improved by 0.125187
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.457
ELB improved by 0.113669
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.353
ELB improved by 0.103409
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.259
ELB improved by 0.0946315
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.172
ELB improved by 0.0871247
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.091
ELB improved by 0.0806188
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.016
ELB improved by 0.0748998
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.946
ELB improved by 0.0698154
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.881
ELB improved by 0.0652564
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.82
ELB improved by 0.0611415
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.763
ELB improved by 0.0574069
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.709
ELB improved by 0.0540011
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.658
ELB improved by 0.0508813
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.61
ELB improved by 0.0480114
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.564
ELB improved by 0.0453608
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.521
ELB improved by 0.0429034
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.481
ELB improved by 0.0406166
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.442
ELB improved by 0.0384814
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.406
ELB improved by 0.0364809
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.371
ELB improved by 0.0346011
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.338
ELB improved by 0.0328298
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.307
ELB improved by 0.0311564
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.278
ELB improved by 0.029572
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.25
ELB improved by 0.0280692
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.223
ELB improved by 0.0266413
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.198
ELB improved by 0.025283
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.174
ELB improved by 0.0239897
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.151
ELB improved by 0.0227575
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.129
ELB improved by 0.021583
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.109
ELB improved by 0.0204636
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.09
ELB improved by 0.0193969
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.071
ELB improved by 0.0183808
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.054
ELB improved by 0.0174135
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.037
ELB improved by 0.0164934
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.022
ELB improved by 0.015619
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.007
ELB improved by 0.0147889
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.993
ELB improved by 0.0140018
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.98
ELB improved by 0.0132564
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.967
ELB improved by 0.0125513
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.955
ELB improved by 0.0118852
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.944
ELB improved by 0.0112566
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.933
ELB improved by 0.0106643
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.923
ELB improved by 0.0101068
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.914
ELB improved by 0.00958256
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-888.355
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-589.279
ELB improved by 299.076
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-526.472
ELB improved by 62.8064
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-482.03
ELB improved by 44.443
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.934
ELB improved by 21.0957
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.006
ELB improved by 7.92821
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.232
ELB improved by 4.77335
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.423
ELB improved by 3.80905
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.001
ELB improved by 3.42248
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.779
ELB improved by 3.22139
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.758
ELB improved by 3.02084
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.023
ELB improved by 2.73508
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.684
ELB improved by 2.33931
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.811
ELB improved by 1.87323
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.395
ELB improved by 1.41626
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.359
ELB improved by 1.03533
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.605
ELB improved by 0.754123
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.044
ELB improved by 0.561635
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.609
ELB improved by 0.434489
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.258
ELB improved by 0.351049
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.962
ELB improved by 0.295619
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.704
ELB improved by 0.258006
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.472
ELB improved by 0.231967
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.259
ELB improved by 0.213781
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.057
ELB improved by 0.20124
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.864
ELB improved by 0.193006
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.676
ELB improved by 0.18822
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.49
ELB improved by 0.186269
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.303
ELB improved by 0.18666
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.114
ELB improved by 0.188994
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.921
ELB improved by 0.19303
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.722
ELB improved by 0.198783
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.516
ELB improved by 0.206581
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.299
ELB improved by 0.217035
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.068
ELB improved by 0.230954
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.819
ELB improved by 0.249306
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.545
ELB improved by 0.273256
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.241
ELB improved by 0.304259
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.897
ELB improved by 0.344115
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.502
ELB improved by 0.394765
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.045
ELB improved by 0.457334
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.515
ELB improved by 0.529582
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.913
ELB improved by 0.602135
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.254
ELB improved by 0.658723
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.568
ELB improved by 0.685884
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.886
ELB improved by 0.681974
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.232
ELB improved by 0.654763
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.617
ELB improved by 0.614739
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.047
ELB improved by 0.569934
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.524
ELB improved by 0.523336
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.05
ELB improved by 0.474039
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.628
ELB improved by 0.421255
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.261
ELB improved by 0.366982
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.947
ELB improved by 0.314771
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.679
ELB improved by 0.267433
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.453
ELB improved by 0.226238
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.262
ELB improved by 0.191252
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.1
ELB improved by 0.161887
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.963
ELB improved by 0.137319
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.846
ELB improved by 0.116728
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.746
ELB improved by 0.0994135
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.662
ELB improved by 0.0848187
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.589
ELB improved by 0.0725088
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.527
ELB improved by 0.062135
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.474
ELB improved by 0.0534051
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.427
ELB improved by 0.0460665
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.388
ELB improved by 0.039899
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.353
ELB improved by 0.0347115
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.323
ELB improved by 0.0303409
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.296
ELB improved by 0.0266494
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.272
ELB improved by 0.0235222
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.251
ELB improved by 0.0208644
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.233
ELB improved by 0.0185978
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.216
ELB improved by 0.0166585
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.201
ELB improved by 0.0149935
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.188
ELB improved by 0.0135597
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.175
ELB improved by 0.0123211
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.164
ELB improved by 0.0112479
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.154
ELB improved by 0.0103156
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.144
ELB improved by 0.00950319
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-858.484
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-594.265
ELB improved by 264.219
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-535.711
ELB improved by 58.5536
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-489.333
ELB improved by 46.3775
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.621
ELB improved by 24.7128
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.163
ELB improved by 11.4581
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.794
ELB improved by 6.36833
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.062
ELB improved by 4.73235
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.624
ELB improved by 4.43832
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.04
ELB improved by 4.58355
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.184
ELB improved by 4.8565
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.174
ELB improved by 5.00984
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.427
ELB improved by 4.74675
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.493
ELB improved by 3.93415
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.616
ELB improved by 2.87636
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.576
ELB improved by 2.04092
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.079
ELB improved by 1.49626
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.933
ELB improved by 1.14588
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.975
ELB improved by 0.958485
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.099
ELB improved by 0.875847
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.252
ELB improved by 0.846576
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.41
ELB improved by 0.842849
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.558
ELB improved by 0.85153
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.691
ELB improved by 0.867046
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.804
ELB improved by 0.887302
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.893
ELB improved by 0.910898
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.958
ELB improved by 0.935
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.004
ELB improved by 0.954194
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.043
ELB improved by 0.961021
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.094
ELB improved by 0.948621
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.179
ELB improved by 0.914699
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.314
ELB improved by 0.865223
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.497
ELB improved by 0.817286
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.7
ELB improved by 0.797274
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.901
ELB improved by 0.798984
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.197
ELB improved by 0.703434
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.715
ELB improved by 0.482203
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.418
ELB improved by 0.296673
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.228
ELB improved by 0.190472
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.097
ELB improved by 0.130898
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.002
ELB improved by 0.0947618
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.931
ELB improved by 0.0713067
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.875
ELB improved by 0.0553602
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.831
ELB improved by 0.0441375
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.795
ELB improved by 0.0360048
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.765
ELB improved by 0.0299534
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.74
ELB improved by 0.0253403
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.718
ELB improved by 0.0217451
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.699
ELB improved by 0.0188868
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.683
ELB improved by 0.0165737
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.668
ELB improved by 0.0146724
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.655
ELB improved by 0.0130879
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.643
ELB improved by 0.0117514
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.633
ELB improved by 0.0106123
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.623
ELB improved by 0.00963241
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-853.529
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-558.999
ELB improved by 294.53
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-502.885
ELB improved by 56.1136
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.499
ELB improved by 31.3861
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.753
ELB improved by 12.7462
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.204
ELB improved by 6.54943
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.371
ELB improved by 4.83211
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.808
ELB improved by 4.56311
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.8
ELB improved by 5.00802
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.896
ELB improved by 5.90406
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.034
ELB improved by 6.86229
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.939
ELB improved by 7.09503
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.988
ELB improved by 5.95046
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.996
ELB improved by 3.99288
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.627
ELB improved by 2.36821
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.19
ELB improved by 1.4377
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.225
ELB improved by 0.964488
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.508
ELB improved by 0.717204
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.935
ELB improved by 0.572912
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.462
ELB improved by 0.473264
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.064
ELB improved by 0.397343
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.721
ELB improved by 0.343383
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.41
ELB improved by 0.310714
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.116
ELB improved by 0.2948
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.825
ELB improved by 0.290901
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.529
ELB improved by 0.296148
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.219
ELB improved by 0.309353
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.889
ELB improved by 0.330444
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.529
ELB improved by 0.360181
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.128
ELB improved by 0.400165
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.675
ELB improved by 0.453155
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.151
ELB improved by 0.523763
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.532
ELB improved by 0.619677
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.78
ELB improved by 0.752195
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.851
ELB improved by 0.928245
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.729
ELB improved by 1.1219
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.457
ELB improved by 1.27218
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.105
ELB improved by 1.35207
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.74
ELB improved by 1.36531
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.431
ELB improved by 1.30839
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.247
ELB improved by 1.18467
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.232
ELB improved by 1.01498
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.402
ELB improved by 0.829951
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.745
ELB improved by 0.656935
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.233
ELB improved by 0.511518
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.836
ELB improved by 0.39722
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.526
ELB improved by 0.310397
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.281
ELB improved by 0.245145
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.085
ELB improved by 0.195941
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.926
ELB improved by 0.158469
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.797
ELB improved by 0.129582
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.69
ELB improved by 0.107039
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.6
ELB improved by 0.0892442
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.525
ELB improved by 0.0750458
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.462
ELB improved by 0.0636046
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.407
ELB improved by 0.0543004
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.361
ELB improved by 0.0466694
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.32
ELB improved by 0.0403605
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.285
ELB improved by 0.0351052
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.255
ELB improved by 0.0306965
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.228
ELB improved by 0.0269731
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.204
ELB improved by 0.0238084
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.183
ELB improved by 0.0211025
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.164
ELB improved by 0.0187761
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.147
ELB improved by 0.0167654
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.132
ELB improved by 0.0150194
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.119
ELB improved by 0.0134968
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.106
ELB improved by 0.0121636
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.095
ELB improved by 0.0109922
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.086
ELB improved by 0.00995974
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
1.046 0.072 1.120
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.029 | 0.005 | 0.034 | |
| getPIPs | 0.027 | 0.005 | 0.032 | |
| graper | 0.044 | 0.006 | 0.050 | |
| makeExampleData | 0.004 | 0.000 | 0.004 | |
| makeExampleDataWithUnequalGroups | 0.004 | 0.000 | 0.005 | |
| plotELBO | 0.127 | 0.006 | 0.133 | |
| plotGroupPenalties | 0.416 | 0.008 | 0.424 | |
| plotPosterior | 0.219 | 0.009 | 0.227 | |
| predict.graper | 1.010 | 0.026 | 1.036 | |
| print.graper | 0.027 | 0.004 | 0.030 | |