Britta Velten
| Snapshot Date: 2025-11-10 13:45 -0500 (Mon, 10 Nov 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 2025-11-11 12:03 -0500 (Tue, 11 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4902 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4638 |
| 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 | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the graper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: graper |
| Version: 1.26.0 |
| 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: 2025-11-10 20:23:27 -0500 (Mon, 10 Nov 2025) |
| EndedAt: 2025-11-10 20:23:55 -0500 (Mon, 10 Nov 2025) |
| EllapsedTime: 28.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graper_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 13.7.7
* 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-1500.1.0.2.5)’
* 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-1500.1.0.2.5)’ 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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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=-869.976
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-602.332
ELB improved by 267.644
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-545.646
ELB improved by 56.6851
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-500.253
ELB improved by 45.3935
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-476.23
ELB improved by 24.0235
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.122
ELB improved by 9.10797
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.92
ELB improved by 5.20151
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.938
ELB improved by 4.98248
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.129
ELB improved by 5.80898
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.983
ELB improved by 7.14564
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.617
ELB improved by 8.36602
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.098
ELB improved by 8.51911
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.777
ELB improved by 7.32055
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.126
ELB improved by 5.65143
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.838
ELB improved by 4.28774
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.649
ELB improved by 3.18915
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.511
ELB improved by 2.1382
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.116
ELB improved by 1.39495
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.168
ELB improved by 0.948136
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.49
ELB improved by 0.677637
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.984
ELB improved by 0.506237
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.592
ELB improved by 0.392013
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.28
ELB improved by 0.312198
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.025
ELB improved by 0.254136
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.815
ELB improved by 0.210518
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.638
ELB improved by 0.176904
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.488
ELB improved by 0.150463
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.358
ELB improved by 0.129309
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.246
ELB improved by 0.112139
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.148
ELB improved by 0.0980278
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.062
ELB improved by 0.0863012
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.985
ELB improved by 0.0764582
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.917
ELB improved by 0.06812
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.856
ELB improved by 0.0609953
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.801
ELB improved by 0.0548573
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.752
ELB improved by 0.0495278
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.707
ELB improved by 0.0448652
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.666
ELB improved by 0.0407568
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.629
ELB improved by 0.0371127
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.595
ELB improved by 0.0338612
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.564
ELB improved by 0.0309452
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.536
ELB improved by 0.0283198
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.51
ELB improved by 0.0259489
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.486
ELB improved by 0.0238038
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.464
ELB improved by 0.0218609
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.444
ELB improved by 0.0201004
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.426
ELB improved by 0.018505
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.409
ELB improved by 0.0170595
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.393
ELB improved by 0.0157499
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.378
ELB improved by 0.0145632
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.365
ELB improved by 0.0134878
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.352
ELB improved by 0.0125126
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.341
ELB improved by 0.0116275
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.33
ELB improved by 0.0108236
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.32
ELB improved by 0.0100925
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.31
ELB improved by 0.00942688
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-867.322
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-560.811
ELB improved by 306.511
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-503.5
ELB improved by 57.3117
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.632
ELB improved by 33.868
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.845
ELB improved by 14.7863
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.408
ELB improved by 6.43747
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.662
ELB improved by 3.74641
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.683
ELB improved by 2.97888
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.966
ELB improved by 2.71672
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.347
ELB improved by 2.61887
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.777
ELB improved by 2.5705
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.263
ELB improved by 2.5141
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.846
ELB improved by 2.41695
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.583
ELB improved by 2.26284
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.532
ELB improved by 2.05026
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.739
ELB improved by 1.79358
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.217
ELB improved by 1.52224
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.951
ELB improved by 1.26545
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.915
ELB improved by 1.03611
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.077
ELB improved by 0.837692
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.402
ELB improved by 0.675661
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.848
ELB improved by 0.553739
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.38
ELB improved by 0.467969
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.971
ELB improved by 0.409184
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.603
ELB improved by 0.368114
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.265
ELB improved by 0.337798
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.951
ELB improved by 0.313707
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.658
ELB improved by 0.293154
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.383
ELB improved by 0.27467
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.126
ELB improved by 0.257485
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.885
ELB improved by 0.241162
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.659
ELB improved by 0.225427
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.449
ELB improved by 0.210119
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.254
ELB improved by 0.195186
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.073
ELB improved by 0.180666
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.907
ELB improved by 0.166651
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.753
ELB improved by 0.153254
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.613
ELB improved by 0.14058
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.484
ELB improved by 0.128707
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.366
ELB improved by 0.11768
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.259
ELB improved by 0.107515
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.161
ELB improved by 0.0981966
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.071
ELB improved by 0.0896937
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.989
ELB improved by 0.0819598
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.914
ELB improved by 0.0749406
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.846
ELB improved by 0.0685786
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.783
ELB improved by 0.0628161
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.725
ELB improved by 0.0575973
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.672
ELB improved by 0.0528695
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.624
ELB improved by 0.0485842
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.579
ELB improved by 0.0446968
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.538
ELB improved by 0.0411675
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.5
ELB improved by 0.0379599
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.465
ELB improved by 0.0350418
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.432
ELB improved by 0.0323843
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.403
ELB improved by 0.0299616
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.375
ELB improved by 0.0277507
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.349
ELB improved by 0.0257312
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.325
ELB improved by 0.0238847
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.303
ELB improved by 0.0221947
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.282
ELB improved by 0.0206468
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.263
ELB improved by 0.0192276
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.245
ELB improved by 0.0179254
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.228
ELB improved by 0.0167296
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.213
ELB improved by 0.0156306
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.198
ELB improved by 0.0146199
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.185
ELB improved by 0.0136896
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.172
ELB improved by 0.0128327
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.16
ELB improved by 0.012043
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.148
ELB improved by 0.0113145
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.138
ELB improved by 0.0106421
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.128
ELB improved by 0.0100211
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.118
ELB improved by 0.009447
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-798.717
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-558.789
ELB improved by 239.928
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-498.996
ELB improved by 59.793
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.81
ELB improved by 41.1861
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.171
ELB improved by 18.6385
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.978
ELB improved by 7.19286
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.899
ELB improved by 4.07951
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.358
ELB improved by 3.54072
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.761
ELB improved by 3.59767
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.846
ELB improved by 3.91456
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.49
ELB improved by 4.35553
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.824
ELB improved by 4.66667
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.37
ELB improved by 4.45416
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.79
ELB improved by 3.57979
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.346
ELB improved by 2.44375
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.817
ELB improved by 1.5295
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.843
ELB improved by 0.973355
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.163
ELB improved by 0.680356
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.633
ELB improved by 0.529733
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.186
ELB improved by 0.44737
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.785
ELB improved by 0.401017
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.408
ELB improved by 0.376673
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.042
ELB improved by 0.366533
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.676
ELB improved by 0.366042
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.303
ELB improved by 0.372625
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.918
ELB improved by 0.384823
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.516
ELB improved by 0.401974
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.092
ELB improved by 0.424179
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.64
ELB improved by 0.452262
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.152
ELB improved by 0.48765
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.62
ELB improved by 0.532091
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.033
ELB improved by 0.587194
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.379
ELB improved by 0.653749
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.648
ELB improved by 0.730849
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.833
ELB improved by 0.814889
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.935
ELB improved by 0.898507
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.965
ELB improved by 0.969845
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.952
ELB improved by 1.01312
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.94
ELB improved by 1.01207
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.983
ELB improved by 0.95674
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.132
ELB improved by 0.850847
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.419
ELB improved by 0.713294
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.849
ELB improved by 0.56994
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.408
ELB improved by 0.441229
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.071
ELB improved by 0.336374
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.815
ELB improved by 0.256096
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.618
ELB improved by 0.197242
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.463
ELB improved by 0.155325
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.337
ELB improved by 0.125677
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.233
ELB improved by 0.104129
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.146
ELB improved by 0.087305
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.073
ELB improved by 0.0727045
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.014
ELB improved by 0.0589173
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.968
ELB improved by 0.0458455
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.934
ELB improved by 0.0343286
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.909
ELB improved by 0.0251982
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.89
ELB improved by 0.018627
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.876
ELB improved by 0.0141961
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.864
ELB improved by 0.011285
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.855
ELB improved by 0.00935218
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-866.693
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-557.033
ELB improved by 309.66
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-496.725
ELB improved by 60.3084
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.242
ELB improved by 36.4823
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.89
ELB improved by 14.3522
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.14
ELB improved by 5.75021
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.686
ELB improved by 3.45385
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.174
ELB improved by 2.51216
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.034
ELB improved by 2.1398
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.02
ELB improved by 2.01429
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.031
ELB improved by 1.98865
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.022
ELB improved by 2.00874
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.967
ELB improved by 2.05577
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.843
ELB improved by 2.12408
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.634
ELB improved by 2.20894
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.339
ELB improved by 2.29466
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.994
ELB improved by 2.34458
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.689
ELB improved by 2.30524
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.553
ELB improved by 2.13602
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.71
ELB improved by 1.8434
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.23
ELB improved by 1.47922
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.115
ELB improved by 1.11515
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.301
ELB improved by 0.81436
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.702
ELB improved by 0.599139
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.246
ELB improved by 0.456161
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.882
ELB improved by 0.36325
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.58
ELB improved by 0.302764
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.316
ELB improved by 0.263243
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.079
ELB improved by 0.237748
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.856
ELB improved by 0.222209
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.642
ELB improved by 0.214335
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.429
ELB improved by 0.212974
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.211
ELB improved by 0.217746
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.983
ELB improved by 0.228858
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.736
ELB improved by 0.246961
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.463
ELB improved by 0.272939
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.155
ELB improved by 0.307529
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.804
ELB improved by 0.350826
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.402
ELB improved by 0.40206
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.942
ELB improved by 0.460015
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.419
ELB improved by 0.52362
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.827
ELB improved by 0.591823
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.164
ELB improved by 0.662696
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.432
ELB improved by 0.732476
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.637
ELB improved by 0.795062
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.794
ELB improved by 0.842221
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.93
ELB improved by 0.864636
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.076
ELB improved by 0.854045
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.268
ELB improved by 0.807644
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.534
ELB improved by 0.733878
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.883
ELB improved by 0.650983
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.307
ELB improved by 0.57598
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.79
ELB improved by 0.51704
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.316
ELB improved by 0.474051
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.875
ELB improved by 0.441201
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.469
ELB improved by 0.406098
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.12
ELB improved by 0.348987
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.856
ELB improved by 0.26402
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.677
ELB improved by 0.178377
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.561
ELB improved by 0.116656
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.482
ELB improved by 0.0791445
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.424
ELB improved by 0.0571286
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.381
ELB improved by 0.0437446
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.346
ELB improved by 0.0351454
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.316
ELB improved by 0.0293402
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.291
ELB improved by 0.025281
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.269
ELB improved by 0.0223844
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.248
ELB improved by 0.020304
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.229
ELB improved by 0.018822
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.212
ELB improved by 0.0177947
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.195
ELB improved by 0.017123
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.178
ELB improved by 0.0167344
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.161
ELB improved by 0.016572
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.145
ELB improved by 0.0165877
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.128
ELB improved by 0.0167387
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.111
ELB improved by 0.016988
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.094
ELB improved by 0.0173077
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.076
ELB improved by 0.0176836
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.058
ELB improved by 0.018118
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.039
ELB improved by 0.0186274
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.02
ELB improved by 0.0192326
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388
ELB improved by 0.0199388
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.979
ELB improved by 0.0207073
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.958
ELB improved by 0.0214212
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.936
ELB improved by 0.0218665
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.914
ELB improved by 0.0217655
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.893
ELB improved by 0.0208906
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.874
ELB improved by 0.0192164
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.857
ELB improved by 0.0169874
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.843
ELB improved by 0.0146136
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.83
ELB improved by 0.0124682
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.819
ELB improved by 0.0107513
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.81
ELB improved by 0.00948668
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
1.022 0.092 1.111
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.029 | 0.007 | 0.035 | |
| getPIPs | 0.027 | 0.006 | 0.033 | |
| graper | 0.051 | 0.009 | 0.059 | |
| makeExampleData | 0.004 | 0.000 | 0.004 | |
| makeExampleDataWithUnequalGroups | 0.004 | 0.001 | 0.005 | |
| plotELBO | 0.123 | 0.008 | 0.131 | |
| plotGroupPenalties | 0.426 | 0.011 | 0.437 | |
| plotPosterior | 0.219 | 0.013 | 0.233 | |
| predict.graper | 1.028 | 0.022 | 1.051 | |
| print.graper | 0.027 | 0.005 | 0.032 | |