Britta Velten
| Snapshot Date: 2025-12-11 13:45 -0500 (Thu, 11 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: RELEASE_3_22 |
| git_last_commit: 76fc31b |
| git_last_commit_date: 2025-10-29 10:49:21 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-15 12:07 -0500 (Mon, 15 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4882 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 922/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.26.0 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: graper |
| Version: 1.26.0 |
| Command: /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_1.26.0.tar.gz |
| StartedAt: 2025-12-13 06:38:31 -0500 (Sat, 13 Dec 2025) |
| EndedAt: 2025-12-13 06:40:16 -0500 (Sat, 13 Dec 2025) |
| EllapsedTime: 104.8 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_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
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 ‘1.26.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.22-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/4.5-arm64/Resources/library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.26.0’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.1.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/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++17 -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/4.5-arm64/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 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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=-851.82
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-592.325
ELB improved by 259.495
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-531.786
ELB improved by 60.5385
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-482.509
ELB improved by 49.2774
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.329
ELB improved by 28.1805
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.911
ELB improved by 11.4173
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.886
ELB improved by 5.02493
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.535
ELB improved by 3.35131
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.629
ELB improved by 2.90644
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.675
ELB improved by 2.95392
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.429
ELB improved by 3.24577
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.841
ELB improved by 3.58755
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.084
ELB improved by 3.75688
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.518
ELB improved by 3.56644
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.476
ELB improved by 3.04235
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.041
ELB improved by 2.43515
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.046
ELB improved by 1.99475
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.232
ELB improved by 1.8136
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.42
ELB improved by 1.81196
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.603
ELB improved by 1.81754
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.826
ELB improved by 1.77671
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.105
ELB improved by 1.72086
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.439
ELB improved by 1.66644
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.812
ELB improved by 1.62639
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.2
ELB improved by 1.61231
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.543
ELB improved by 1.6571
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.703
ELB improved by 1.83955
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.723
ELB improved by 1.98036
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.983
ELB improved by 1.74033
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.562
ELB improved by 1.42032
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.36
ELB improved by 1.20216
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.254
ELB improved by 1.10611
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.228
ELB improved by 1.02616
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.488
ELB improved by 0.739438
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.066
ELB improved by 0.422852
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.813
ELB improved by 0.252086
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.644
ELB improved by 0.169548
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.52
ELB improved by 0.123461
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.426
ELB improved by 0.0940991
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.352
ELB improved by 0.0739477
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.293
ELB improved by 0.0595489
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.244
ELB improved by 0.0489811
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.203
ELB improved by 0.0410494
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.168
ELB improved by 0.0349702
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.138
ELB improved by 0.0302169
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.111
ELB improved by 0.0264292
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.088
ELB improved by 0.0233575
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.067
ELB improved by 0.0208264
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.048
ELB improved by 0.0187107
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.031
ELB improved by 0.0169197
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.016
ELB improved by 0.0153869
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.002
ELB improved by 0.0140626
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.989
ELB improved by 0.0129089
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.977
ELB improved by 0.0118969
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.966
ELB improved by 0.0110039
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.956
ELB improved by 0.0102117
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.946
ELB improved by 0.00950598
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-869.757
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-578.9
ELB improved by 290.856
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-517.966
ELB improved by 60.9344
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-480.432
ELB improved by 37.5336
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.035
ELB improved by 16.3969
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.935
ELB improved by 7.10008
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.549
ELB improved by 4.38638
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.995
ELB improved by 3.5537
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.614
ELB improved by 3.3806
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.149
ELB improved by 3.46525
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.561
ELB improved by 3.58856
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.011
ELB improved by 3.54918
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.839
ELB improved by 3.1721
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.351
ELB improved by 2.48843
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.587
ELB improved by 1.76351
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.364
ELB improved by 1.22356
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.463
ELB improved by 0.900654
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.737
ELB improved by 0.726544
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.102
ELB improved by 0.634644
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.517
ELB improved by 0.585
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.959
ELB improved by 0.55804
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.412
ELB improved by 0.547358
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.857
ELB improved by 0.554877
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.274
ELB improved by 0.583029
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.654
ELB improved by 0.619255
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.022
ELB improved by 0.632522
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.412
ELB improved by 0.610317
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.84
ELB improved by 0.571139
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.309
ELB improved by 0.531698
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.811
ELB improved by 0.498137
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.338
ELB improved by 0.472655
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.883
ELB improved by 0.45478
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.446
ELB improved by 0.437693
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.036
ELB improved by 0.409694
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.668
ELB improved by 0.368069
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.345
ELB improved by 0.32234
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.065
ELB improved by 0.280725
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.819
ELB improved by 0.245361
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.604
ELB improved by 0.215649
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.413
ELB improved by 0.190528
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.244
ELB improved by 0.169074
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.094
ELB improved by 0.150573
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.959
ELB improved by 0.134474
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.839
ELB improved by 0.120357
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.731
ELB improved by 0.107894
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.634
ELB improved by 0.096829
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.547
ELB improved by 0.086964
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.469
ELB improved by 0.078144
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.399
ELB improved by 0.0702477
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.335
ELB improved by 0.063179
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.279
ELB improved by 0.0568601
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.227
ELB improved by 0.0512257
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.181
ELB improved by 0.0462195
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.139
ELB improved by 0.0417917
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.101
ELB improved by 0.0378973
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.067
ELB improved by 0.0344967
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.035
ELB improved by 0.0315567
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.006
ELB improved by 0.0290529
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.979
ELB improved by 0.0269741
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.954
ELB improved by 0.0253307
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.93
ELB improved by 0.0241693
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.906
ELB improved by 0.0236025
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.882
ELB improved by 0.023872
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.857
ELB improved by 0.025488
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.827
ELB improved by 0.029554
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.789
ELB improved by 0.0385277
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.731
ELB improved by 0.0578167
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.634
ELB improved by 0.0973878
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.47
ELB improved by 0.16332
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.249
ELB improved by 0.221308
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.037
ELB improved by 0.211691
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.878
ELB improved by 0.159622
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.76
ELB improved by 0.118119
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.663
ELB improved by 0.0966898
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.573
ELB improved by 0.0893985
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.481
ELB improved by 0.0920549
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.378
ELB improved by 0.103747
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.252
ELB improved by 0.126071
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.09
ELB improved by 0.16148
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.883
ELB improved by 0.20739
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.635
ELB improved by 0.247411
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.373
ELB improved by 0.262686
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.114
ELB improved by 0.25895
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.857
ELB improved by 0.256344
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.583
ELB improved by 0.273828
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.25
ELB improved by 0.333476
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.842
ELB improved by 0.40828
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.496
ELB improved by 0.345559
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.302
ELB improved by 0.194062
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.196
ELB improved by 0.106521
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.131
ELB improved by 0.0641706
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.091
ELB improved by 0.0406527
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.064
ELB improved by 0.0268678
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.045
ELB improved by 0.0186222
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.032
ELB improved by 0.0135434
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.021
ELB improved by 0.0102908
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.013
ELB improved by 0.0081217
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-901.495
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-577.284
ELB improved by 324.212
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-519.629
ELB improved by 57.6547
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-482.141
ELB improved by 37.4879
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.115
ELB improved by 17.0255
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.561
ELB improved by 7.5545
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.701
ELB improved by 4.86018
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.627
ELB improved by 4.0742
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.743
ELB improved by 3.88369
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.844
ELB improved by 3.89867
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.867
ELB improved by 3.97709
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.819
ELB improved by 4.04846
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.782
ELB improved by 4.03707
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.943
ELB improved by 3.8385
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.565
ELB improved by 3.37772
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.85
ELB improved by 2.71543
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.82
ELB improved by 2.03012
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.353
ELB improved by 1.46719
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.294
ELB improved by 1.05909
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.522
ELB improved by 0.771785
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.954
ELB improved by 0.568226
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.528
ELB improved by 0.425148
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.202
ELB improved by 0.326264
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.944
ELB improved by 0.257911
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.735
ELB improved by 0.209458
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.561
ELB improved by 0.173784
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.414
ELB improved by 0.146539
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.289
ELB improved by 0.125117
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.181
ELB improved by 0.107906
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.088
ELB improved by 0.0938514
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.005
ELB improved by 0.0822245
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.933
ELB improved by 0.0724995
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.869
ELB improved by 0.0642856
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.811
ELB improved by 0.0572873
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.76
ELB improved by 0.0512784
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.714
ELB improved by 0.0460833
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.672
ELB improved by 0.0415641
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.635
ELB improved by 0.0376117
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.601
ELB improved by 0.0341382
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.57
ELB improved by 0.0310723
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.541
ELB improved by 0.0283557
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.515
ELB improved by 0.0259399
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.491
ELB improved by 0.0237849
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.47
ELB improved by 0.0218566
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.449
ELB improved by 0.0201266
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.431
ELB improved by 0.0185704
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.414
ELB improved by 0.0171673
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.398
ELB improved by 0.0158994
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.383
ELB improved by 0.0147513
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.369
ELB improved by 0.0137096
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.357
ELB improved by 0.0127627
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.345
ELB improved by 0.0119005
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.334
ELB improved by 0.0111141
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.323
ELB improved by 0.0103957
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.313
ELB improved by 0.00973835
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-840.177
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-557.839
ELB improved by 282.338
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-499.622
ELB improved by 58.2173
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.211
ELB improved by 35.4104
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.882
ELB improved by 15.3297
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.077
ELB improved by 6.8047
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.866
ELB improved by 4.21093
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.533
ELB improved by 3.33355
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.408
ELB improved by 3.12503
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.266
ELB improved by 3.14144
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.127
ELB improved by 3.13871
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.135
ELB improved by 2.99227
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.453
ELB improved by 2.68171
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.21
ELB improved by 2.24365
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.489
ELB improved by 1.72073
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.268
ELB improved by 1.22101
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.42
ELB improved by 0.847609
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.794
ELB improved by 0.626401
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.284
ELB improved by 0.510245
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.838
ELB improved by 0.445861
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.426
ELB improved by 0.411514
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.028
ELB improved by 0.39869
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.637
ELB improved by 0.390825
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.27
ELB improved by 0.367031
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.944
ELB improved by 0.326211
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.657
ELB improved by 0.286786
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.4
ELB improved by 0.256751
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.168
ELB improved by 0.232474
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.957
ELB improved by 0.210399
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.768
ELB improved by 0.189424
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.598
ELB improved by 0.169681
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.447
ELB improved by 0.151589
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.311
ELB improved by 0.135445
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.19
ELB improved by 0.121335
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.081
ELB improved by 0.109178
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.982
ELB improved by 0.0987944
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.892
ELB improved by 0.089964
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.809
ELB improved by 0.0824605
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.733
ELB improved by 0.0760725
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.663
ELB improved by 0.0706138
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.597
ELB improved by 0.0659266
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.535
ELB improved by 0.0618807
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.476
ELB improved by 0.0583705
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.421
ELB improved by 0.0553109
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.369
ELB improved by 0.0526343
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.318
ELB improved by 0.0502862
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.27
ELB improved by 0.0482231
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.224
ELB improved by 0.0464096
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.179
ELB improved by 0.0448167
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.135
ELB improved by 0.0434201
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.093
ELB improved by 0.0421995
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.052
ELB improved by 0.0411373
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.012
ELB improved by 0.0402178
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.972
ELB improved by 0.0394273
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.934
ELB improved by 0.0387528
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.895
ELB improved by 0.0381824
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.858
ELB improved by 0.0377044
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.82
ELB improved by 0.0373075
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.783
ELB improved by 0.0369804
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.747
ELB improved by 0.0367118
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.71
ELB improved by 0.03649
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.674
ELB improved by 0.0363032
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.638
ELB improved by 0.0361391
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.602
ELB improved by 0.0359854
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.566
ELB improved by 0.0358293
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.53
ELB improved by 0.0356581
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.495
ELB improved by 0.0354591
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.46
ELB improved by 0.0352199
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.425
ELB improved by 0.0349286
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.39
ELB improved by 0.0345743
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.356
ELB improved by 0.0341471
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.322
ELB improved by 0.0336386
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.289
ELB improved by 0.0330424
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.257
ELB improved by 0.032354
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.225
ELB improved by 0.0315711
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.195
ELB improved by 0.030694
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.165
ELB improved by 0.0297257
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.136
ELB improved by 0.0286713
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.109
ELB improved by 0.0275387
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.082
ELB improved by 0.0263379
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.057
ELB improved by 0.0250806
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.034
ELB improved by 0.0237804
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.011
ELB improved by 0.0224515
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.99
ELB improved by 0.0211091
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.97
ELB improved by 0.0197684
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.952
ELB improved by 0.0184443
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.935
ELB improved by 0.0171512
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.919
ELB improved by 0.0159024
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.904
ELB improved by 0.0147102
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.89
ELB improved by 0.0135861
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.878
ELB improved by 0.0125403
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.866
ELB improved by 0.0115829
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.856
ELB improved by 0.0107238
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.846
ELB improved by 0.00997397
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
3.166 0.252 4.850
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.036 | 0.020 | 0.098 | |
| getPIPs | 0.030 | 0.014 | 0.061 | |
| graper | 0.050 | 0.022 | 0.078 | |
| makeExampleData | 0.005 | 0.001 | 0.007 | |
| makeExampleDataWithUnequalGroups | 0.026 | 0.003 | 0.063 | |
| plotELBO | 0.355 | 0.026 | 0.560 | |
| plotGroupPenalties | 1.362 | 0.045 | 1.959 | |
| plotPosterior | 0.642 | 0.029 | 0.985 | |
| predict.graper | 0.425 | 0.072 | 0.740 | |
| print.graper | 0.033 | 0.013 | 0.088 | |