Britta Velten
| Snapshot Date: 2026-05-18 13:45 -0400 (Mon, 18 May 2026) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: ba611e2 |
| git_last_commit_date: 2026-04-28 08:49:19 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-19 12:54 -0400 (Tue, 19 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4898 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There" | 4617 |
| 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 932/2377 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.29.0 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | 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: 1.29.0 |
| 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_1.29.0.tar.gz |
| StartedAt: 2026-05-18 21:54:24 -0400 (Mon, 18 May 2026) |
| EndedAt: 2026-05-18 21:54:54 -0400 (Mon, 18 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_1.29.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.24-bioc/meat/graper.Rcheck’
* using R version 4.6.0 Patched (2026-05-01 r89994)
* 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: 2026-05-19 01:54:24 UTC
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.29.0’
* 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-3.24-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 ‘1.29.0’ ** 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 (2026-05-01 r89994) -- "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=-831.495
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-561.88
ELB improved by 269.615
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-504.168
ELB improved by 57.712
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.028
ELB improved by 37.1401
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.466
ELB improved by 17.5616
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.69
ELB improved by 7.77627
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.433
ELB improved by 4.25676
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.442
ELB improved by 2.99108
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.933
ELB improved by 2.50965
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.682
ELB improved by 2.25076
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.641
ELB improved by 2.04059
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.805
ELB improved by 1.83623
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.175
ELB improved by 1.62976
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.752
ELB improved by 1.42334
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.529
ELB improved by 1.22262
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.495
ELB improved by 1.03396
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.633
ELB improved by 0.862657
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.921
ELB improved by 0.711926
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.338
ELB improved by 0.582817
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.863
ELB improved by 0.474699
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.477
ELB improved by 0.385923
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.163
ELB improved by 0.314298
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.906
ELB improved by 0.257352
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.693
ELB improved by 0.212516
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.516
ELB improved by 0.177335
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.366
ELB improved by 0.149648
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.238
ELB improved by 0.127688
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.128
ELB improved by 0.110081
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.033
ELB improved by 0.0957945
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.949
ELB improved by 0.0840623
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.874
ELB improved by 0.0743167
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.808
ELB improved by 0.066134
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.749
ELB improved by 0.059195
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.696
ELB improved by 0.0532565
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.648
ELB improved by 0.0481312
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.604
ELB improved by 0.0436738
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.564
ELB improved by 0.0397704
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.528
ELB improved by 0.0363305
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.494
ELB improved by 0.0332823
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.464
ELB improved by 0.0305675
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.436
ELB improved by 0.0281388
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.41
ELB improved by 0.0259575
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.386
ELB improved by 0.0239913
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.364
ELB improved by 0.0222134
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.343
ELB improved by 0.0206011
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.324
ELB improved by 0.0191351
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.306
ELB improved by 0.0177991
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.289
ELB improved by 0.0165789
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.274
ELB improved by 0.0154623
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.26
ELB improved by 0.0144386
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.246
ELB improved by 0.0134985
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.233
ELB improved by 0.0126338
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.222
ELB improved by 0.0118374
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.211
ELB improved by 0.0111027
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.2
ELB improved by 0.0104242
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.19
ELB improved by 0.00979681
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-839.44
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-547.58
ELB improved by 291.86
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-487.026
ELB improved by 60.554
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.058
ELB improved by 30.9675
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.158
ELB improved by 11.9001
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.124
ELB improved by 6.0341
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.986
ELB improved by 4.13809
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.343
ELB improved by 3.6431
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.709
ELB improved by 3.63334
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.897
ELB improved by 3.8121
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.861
ELB improved by 4.03609
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.794
ELB improved by 4.06766
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.141
ELB improved by 3.65312
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.323
ELB improved by 2.81761
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.421
ELB improved by 1.90162
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.216
ELB improved by 1.20517
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.436
ELB improved by 0.78008
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.893
ELB improved by 0.543173
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.483
ELB improved by 0.410176
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.152
ELB improved by 0.330672
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.873
ELB improved by 0.279228
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.629
ELB improved by 0.243505
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.412
ELB improved by 0.217355
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.214
ELB improved by 0.197513
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.032
ELB improved by 0.182109
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.862
ELB improved by 0.169979
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.702
ELB improved by 0.160354
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.549
ELB improved by 0.152692
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.403
ELB improved by 0.146605
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.261
ELB improved by 0.141805
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.123
ELB improved by 0.138079
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.988
ELB improved by 0.135275
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.854
ELB improved by 0.133288
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.722
ELB improved by 0.132057
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.591
ELB improved by 0.131557
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.459
ELB improved by 0.1318
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.326
ELB improved by 0.132832
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.191
ELB improved by 0.134733
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.054
ELB improved by 0.137625
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.912
ELB improved by 0.141673
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.765
ELB improved by 0.1471
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.611
ELB improved by 0.154203
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.447
ELB improved by 0.163384
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.272
ELB improved by 0.17519
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.082
ELB improved by 0.190373
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.872
ELB improved by 0.209965
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.636
ELB improved by 0.235328
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.368
ELB improved by 0.268066
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.059
ELB improved by 0.30952
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.699
ELB improved by 0.359408
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.286
ELB improved by 0.4136
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.823
ELB improved by 0.462424
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.331
ELB improved by 0.492031
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.841
ELB improved by 0.490557
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.384
ELB improved by 0.456879
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.982
ELB improved by 0.401654
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.644
ELB improved by 0.338413
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.367
ELB improved by 0.276995
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.144
ELB improved by 0.222771
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.966
ELB improved by 0.177728
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.825
ELB improved by 0.141729
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.711
ELB improved by 0.113593
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.619
ELB improved by 0.0918257
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.544
ELB improved by 0.0750102
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.482
ELB improved by 0.0619592
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.431
ELB improved by 0.0517412
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.387
ELB improved by 0.0436525
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.35
ELB improved by 0.0371727
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.318
ELB improved by 0.0319206
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.29
ELB improved by 0.0276181
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.266
ELB improved by 0.0240603
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.245
ELB improved by 0.0210948
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.226
ELB improved by 0.0186062
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.21
ELB improved by 0.0165051
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.195
ELB improved by 0.0147218
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.182
ELB improved by 0.0132004
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.17
ELB improved by 0.0118963
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.159
ELB improved by 0.0107733
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.149
ELB improved by 0.00980175
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-871.548
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-577.017
ELB improved by 294.532
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-515.637
ELB improved by 61.3797
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-473.711
ELB improved by 41.926
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.021
ELB improved by 18.6896
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.732
ELB improved by 7.28943
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.39
ELB improved by 4.34195
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.819
ELB improved by 3.57045
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.432
ELB improved by 3.38717
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.984
ELB improved by 3.44829
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.344
ELB improved by 3.63958
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.391
ELB improved by 3.95317
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.974
ELB improved by 4.41713
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.006
ELB improved by 4.96813
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.677
ELB improved by 5.32927
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.57
ELB improved by 5.10709
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.399
ELB improved by 4.17074
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.442
ELB improved by 2.95652
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.459
ELB improved by 1.98357
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.096
ELB improved by 1.36266
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.112
ELB improved by 0.983735
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.386
ELB improved by 0.726167
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.853
ELB improved by 0.533684
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.453
ELB improved by 0.39948
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.139
ELB improved by 0.313644
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.88
ELB improved by 0.259065
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.658
ELB improved by 0.222902
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.46
ELB improved by 0.197888
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.279
ELB improved by 0.18017
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.112
ELB improved by 0.167677
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.953
ELB improved by 0.159262
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.798
ELB improved by 0.154284
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.646
ELB improved by 0.152401
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.492
ELB improved by 0.153472
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.335
ELB improved by 0.157487
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.17
ELB improved by 0.164522
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.996
ELB improved by 0.174685
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.808
ELB improved by 0.188059
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.603
ELB improved by 0.204632
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.379
ELB improved by 0.224248
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.132
ELB improved by 0.246598
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.861
ELB improved by 0.271252
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.563
ELB improved by 0.297678
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.238
ELB improved by 0.32519
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.885
ELB improved by 0.352753
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.507
ELB improved by 0.378718
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.106
ELB improved by 0.400619
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.691
ELB improved by 0.415257
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.271
ELB improved by 0.419252
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.861
ELB improved by 0.410043
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.474
ELB improved by 0.38698
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.122
ELB improved by 0.351938
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.813
ELB improved by 0.30899
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.55
ELB improved by 0.263197
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.331
ELB improved by 0.219175
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.151
ELB improved by 0.18014
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.003
ELB improved by 0.147708
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.881
ELB improved by 0.122221
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.778
ELB improved by 0.103185
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.688
ELB improved by 0.0895621
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.608
ELB improved by 0.0799111
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.536
ELB improved by 0.0725178
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.47
ELB improved by 0.0657273
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.412
ELB improved by 0.0584653
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.361
ELB improved by 0.0505748
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.318
ELB improved by 0.0426173
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.283
ELB improved by 0.0353184
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.254
ELB improved by 0.0291437
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.23
ELB improved by 0.0242127
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.209
ELB improved by 0.0204145
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.192
ELB improved by 0.0175484
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.176
ELB improved by 0.015411
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.163
ELB improved by 0.013833
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.15
ELB improved by 0.0126866
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.138
ELB improved by 0.0118812
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.127
ELB improved by 0.0113557
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.116
ELB improved by 0.0110725
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.105
ELB improved by 0.0110114
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.093
ELB improved by 0.0111658
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.082
ELB improved by 0.0115369
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.07
ELB improved by 0.0121275
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.057
ELB improved by 0.0129293
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.043
ELB improved by 0.0139048
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.028
ELB improved by 0.0149643
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.012
ELB improved by 0.0159464
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.995
ELB improved by 0.0166261
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.979
ELB improved by 0.0167714
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.962
ELB improved by 0.0162444
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.947
ELB improved by 0.0150865
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.934
ELB improved by 0.0135127
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.922
ELB improved by 0.0118094
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.912
ELB improved by 0.0102133
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.903
ELB improved by 0.00885249
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-892.489
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-591.496
ELB improved by 300.993
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-535.168
ELB improved by 56.3289
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-498.59
ELB improved by 36.5774
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-479.329
ELB improved by 19.2606
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.146
ELB improved by 12.1839
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.003
ELB improved by 11.1424
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.165
ELB improved by 10.8383
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.405
ELB improved by 8.76005
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.364
ELB improved by 6.04054
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.455
ELB improved by 3.90882
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.917
ELB improved by 2.5382
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.181
ELB improved by 1.73593
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.919
ELB improved by 1.26273
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.966
ELB improved by 0.952506
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.214
ELB improved by 0.751827
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.573
ELB improved by 0.641303
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.97
ELB improved by 0.60246
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.351
ELB improved by 0.619718
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.674
ELB improved by 0.67678
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.893
ELB improved by 0.781389
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.967
ELB improved by 0.925521
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.954
ELB improved by 1.01302
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.872
ELB improved by 1.08249
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.59
ELB improved by 1.2814
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.009
ELB improved by 1.58157
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.191
ELB improved by 1.81787
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.159
ELB improved by 2.03194
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.849
ELB improved by 2.30929
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.214
ELB improved by 2.63585
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.268
ELB improved by 2.9455
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.177
ELB improved by 3.0914
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.281
ELB improved by 2.89594
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.871
ELB improved by 2.40945
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.973
ELB improved by 1.89866
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.486
ELB improved by 1.48632
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.383
ELB improved by 1.10327
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.588
ELB improved by 0.794915
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.004
ELB improved by 0.584198
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.589
ELB improved by 0.415177
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.296
ELB improved by 0.293111
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.059
ELB improved by 0.237161
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.82
ELB improved by 0.238349
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.555
ELB improved by 0.265229
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.306
ELB improved by 0.249366
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.134
ELB improved by 0.171621
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.033
ELB improved by 0.100785
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.97
ELB improved by 0.0628873
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.926
ELB improved by 0.0445345
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.891
ELB improved by 0.0346825
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.862
ELB improved by 0.0285862
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.838
ELB improved by 0.0243541
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.817
ELB improved by 0.0211739
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.798
ELB improved by 0.0186582
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.782
ELB improved by 0.0166017
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.767
ELB improved by 0.0148844
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.753
ELB improved by 0.0134294
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.741
ELB improved by 0.0121842
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.73
ELB improved by 0.0111101
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.72
ELB improved by 0.0101779
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.711
ELB improved by 0.00936459
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
1.027 0.079 1.110
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.029 | 0.005 | 0.033 | |
| getPIPs | 0.026 | 0.004 | 0.030 | |
| graper | 0.044 | 0.006 | 0.050 | |
| makeExampleData | 0.004 | 0.001 | 0.004 | |
| makeExampleDataWithUnequalGroups | 0.005 | 0.000 | 0.005 | |
| plotELBO | 0.123 | 0.006 | 0.129 | |
| plotGroupPenalties | 0.327 | 0.005 | 0.333 | |
| plotPosterior | 0.250 | 0.004 | 0.256 | |
| predict.graper | 1.011 | 0.026 | 1.038 | |
| print.graper | 0.026 | 0.004 | 0.031 | |