Britta Velten
| Snapshot Date: 2025-10-24 13:45 -0400 (Fri, 24 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: 82b0592 |
| git_last_commit_date: 2025-06-24 03:15:40 -0400 (Tue, 24 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-25 12:04 -0400 (Sat, 25 Oct 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" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 1.25.2 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | NA | NA | ||||||||||
|
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: 1.25.2 |
| 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_1.25.2.tar.gz |
| StartedAt: 2025-10-24 21:39:49 -0400 (Fri, 24 Oct 2025) |
| EndedAt: 2025-10-24 21:41:08 -0400 (Fri, 24 Oct 2025) |
| EllapsedTime: 78.2 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_1.25.2.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: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.25.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* 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-x86_64/Resources/library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.25.2’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.1.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fit_graper.cpp -o fit_graper.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o graper.so RcppExports.o fit_graper.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-graper/00new/graper/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (graper)
graper.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(graper)
>
> test_check("graper")
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-859.04
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-558.238
ELB improved by 300.802
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-494.949
ELB improved by 63.2896
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.393
ELB improved by 35.5562
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.596
ELB improved by 13.7969
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.137
ELB improved by 5.45867
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.04
ELB improved by 3.09715
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.864
ELB improved by 2.17642
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.086
ELB improved by 1.778
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.485
ELB improved by 1.60102
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.965
ELB improved by 1.51947
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.492
ELB improved by 1.47348
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.061
ELB improved by 1.43048
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.691
ELB improved by 1.37055
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.409
ELB improved by 1.2821
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.246
ELB improved by 1.16266
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.227
ELB improved by 1.0193
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.361
ELB improved by 0.865192
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.647
ELB improved by 0.714097
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.071
ELB improved by 0.576657
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.611
ELB improved by 0.459238
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.247
ELB improved by 0.364076
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.957
ELB improved by 0.290035
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.723
ELB improved by 0.233916
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.531
ELB improved by 0.191859
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.371
ELB improved by 0.160314
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.235
ELB improved by 0.136445
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.117
ELB improved by 0.11815
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.013
ELB improved by 0.103924
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.92
ELB improved by 0.0926939
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.836
ELB improved by 0.0836946
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.76
ELB improved by 0.0763723
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.69
ELB improved by 0.0703245
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.624
ELB improved by 0.0652561
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.563
ELB improved by 0.0609493
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.506
ELB improved by 0.0572423
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.452
ELB improved by 0.0540136
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.401
ELB improved by 0.051171
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.352
ELB improved by 0.0486434
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.306
ELB improved by 0.0463752
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.262
ELB improved by 0.0443224
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.219
ELB improved by 0.0424497
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.178
ELB improved by 0.0407283
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.139
ELB improved by 0.0391343
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.102
ELB improved by 0.0376481
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.065
ELB improved by 0.0362534
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.03
ELB improved by 0.0349364
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.997
ELB improved by 0.0336857
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.964
ELB improved by 0.0324918
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.933
ELB improved by 0.031347
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.903
ELB improved by 0.0302449
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.873
ELB improved by 0.0291803
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.845
ELB improved by 0.0281492
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.818
ELB improved by 0.0271486
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.792
ELB improved by 0.0261762
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.767
ELB improved by 0.0252303
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.742
ELB improved by 0.0243101
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.719
ELB improved by 0.0234148
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.697
ELB improved by 0.0225443
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.675
ELB improved by 0.0216985
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.654
ELB improved by 0.0208776
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.634
ELB improved by 0.020082
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.615
ELB improved by 0.0193119
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.596
ELB improved by 0.0185677
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.578
ELB improved by 0.0178495
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.561
ELB improved by 0.0171575
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.544
ELB improved by 0.0164919
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.529
ELB improved by 0.0158525
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.513
ELB improved by 0.0152391
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.499
ELB improved by 0.0146514
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.485
ELB improved by 0.0140891
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.471
ELB improved by 0.0135515
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.458
ELB improved by 0.013038
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.445
ELB improved by 0.012548
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.433
ELB improved by 0.0120806
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.422
ELB improved by 0.0116351
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.411
ELB improved by 0.0112105
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.4
ELB improved by 0.010806
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.389
ELB improved by 0.0104207
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.379
ELB improved by 0.0100537
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.37
ELB improved by 0.00970417
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-871.993
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-583.317
ELB improved by 288.676
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-524.291
ELB improved by 59.0256
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-486.955
ELB improved by 37.336
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.601
ELB improved by 16.3539
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.29
ELB improved by 7.31137
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.253
ELB improved by 5.03655
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.783
ELB improved by 4.47051
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.431
ELB improved by 4.35204
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.178
ELB improved by 4.25322
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.241
ELB improved by 3.93619
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.908
ELB improved by 3.33381
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.323
ELB improved by 2.58415
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.382
ELB improved by 1.9413
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.869
ELB improved by 1.51285
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.653
ELB improved by 1.21608
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.669
ELB improved by 0.983958
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.838
ELB improved by 0.831591
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.091
ELB improved by 0.746856
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.394
ELB improved by 0.69712
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.732
ELB improved by 0.661773
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.1
ELB improved by 0.631522
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.498
ELB improved by 0.602511
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.925
ELB improved by 0.572948
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.383
ELB improved by 0.541662
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.875
ELB improved by 0.508143
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.402
ELB improved by 0.473084
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.964
ELB improved by 0.438075
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.559
ELB improved by 0.404652
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.186
ELB improved by 0.373771
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.84
ELB improved by 0.345909
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.518
ELB improved by 0.321353
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.218
ELB improved by 0.300462
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.934
ELB improved by 0.28397
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.66
ELB improved by 0.273525
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.387
ELB improved by 0.272951
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.096
ELB improved by 0.291215
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.749
ELB improved by 0.347049
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.291
ELB improved by 0.45815
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.723
ELB improved by 0.567864
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.152
ELB improved by 0.571582
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.627
ELB improved by 0.52415
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.128
ELB improved by 0.499693
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.618
ELB improved by 0.509568
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.052
ELB improved by 0.56565
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.361
ELB improved by 0.691274
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.538
ELB improved by 0.823289
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.774
ELB improved by 0.763602
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.186
ELB improved by 0.588761
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.735
ELB improved by 0.450379
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.39
ELB improved by 0.344731
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.135
ELB improved by 0.255579
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.952
ELB improved by 0.183005
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.823
ELB improved by 0.128539
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.733
ELB improved by 0.0902813
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.669
ELB improved by 0.0645302
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.621
ELB improved by 0.0476011
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.584
ELB improved by 0.0365558
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.555
ELB improved by 0.0292709
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.531
ELB improved by 0.0242821
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.51
ELB improved by 0.0206145
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.493
ELB improved by 0.0176585
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.477
ELB improved by 0.0150844
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.465
ELB improved by 0.012764
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.454
ELB improved by 0.010689
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.445
ELB improved by 0.00889288
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-877.507
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-553.494
ELB improved by 324.013
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-495.842
ELB improved by 57.652
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-467.375
ELB improved by 28.4669
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.173
ELB improved by 10.2017
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.397
ELB improved by 4.77635
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.981
ELB improved by 3.41608
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.951
ELB improved by 3.03046
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.956
ELB improved by 2.9946
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.848
ELB improved by 3.10804
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.571
ELB improved by 3.27746
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.151
ELB improved by 3.41941
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.727
ELB improved by 3.42377
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.53
ELB improved by 3.19693
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.786
ELB improved by 2.74446
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.611
ELB improved by 2.17518
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.988
ELB improved by 1.62303
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.805
ELB improved by 1.18234
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.929
ELB improved by 0.876586
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.261
ELB improved by 0.667687
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.754
ELB improved by 0.507301
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.368
ELB improved by 0.386203
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.06
ELB improved by 0.307929
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.803
ELB improved by 0.25684
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.586
ELB improved by 0.216849
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.403
ELB improved by 0.182798
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.248
ELB improved by 0.155221
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.113
ELB improved by 0.134572
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.993
ELB improved by 0.119933
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.884
ELB improved by 0.109888
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.78
ELB improved by 0.103246
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.681
ELB improved by 0.0992092
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.584
ELB improved by 0.0972963
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.487
ELB improved by 0.0972438
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.388
ELB improved by 0.09894
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.285
ELB improved by 0.102393
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.178
ELB improved by 0.10772
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.062
ELB improved by 0.115153
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.937
ELB improved by 0.125043
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.799
ELB improved by 0.137879
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.645
ELB improved by 0.154274
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.47
ELB improved by 0.17493
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.27
ELB improved by 0.200535
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.038
ELB improved by 0.231605
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.77
ELB improved by 0.26834
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.459
ELB improved by 0.310671
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.101
ELB improved by 0.358581
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.688
ELB improved by 0.41268
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.213
ELB improved by 0.475071
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.662
ELB improved by 0.551191
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.007
ELB improved by 0.654195
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.195
ELB improved by 0.812586
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.126
ELB improved by 1.06907
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.703
ELB improved by 1.42263
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.974
ELB improved by 1.72864
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.106
ELB improved by 1.86832
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.163
ELB improved by 1.94323
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.176
ELB improved by 1.98661
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.427
ELB improved by 1.74901
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.098
ELB improved by 1.32903
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.125
ELB improved by 0.973453
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.519
ELB improved by 0.606133
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.182
ELB improved by 0.336776
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.987
ELB improved by 0.194588
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.862
ELB improved by 0.124989
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.773
ELB improved by 0.0891106
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.704
ELB improved by 0.0687442
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.648
ELB improved by 0.0560942
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.601
ELB improved by 0.0477464
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.558
ELB improved by 0.0421077
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.52
ELB improved by 0.0383701
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.484
ELB improved by 0.0360635
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.449
ELB improved by 0.0348224
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.415
ELB improved by 0.0342228
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.381
ELB improved by 0.0336726
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.349
ELB improved by 0.0324463
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.319
ELB improved by 0.0299659
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.293
ELB improved by 0.0261992
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.271
ELB improved by 0.0217571
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.253
ELB improved by 0.0174928
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.239
ELB improved by 0.0139923
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.228
ELB improved by 0.0114047
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.218
ELB improved by 0.00958912
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-877.251
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-591.604
ELB improved by 285.647
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-531.595
ELB improved by 60.0087
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-488.932
ELB improved by 42.6627
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.376
ELB improved by 20.5567
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.046
ELB improved by 8.32977
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.524
ELB improved by 4.52235
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.046
ELB improved by 3.47801
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.89
ELB improved by 3.15556
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.822
ELB improved by 3.06761
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.794
ELB improved by 3.02836
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.864
ELB improved by 2.93046
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.15
ELB improved by 2.714
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.77
ELB improved by 2.37978
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.787
ELB improved by 1.98321
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.208
ELB improved by 1.57877
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.001
ELB improved by 1.20723
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.085
ELB improved by 0.915641
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.368
ELB improved by 0.716649
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.777
ELB improved by 0.591207
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.259
ELB improved by 0.517932
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.779
ELB improved by 0.480423
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.315
ELB improved by 0.464134
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.862
ELB improved by 0.453002
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.426
ELB improved by 0.435256
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.017
ELB improved by 0.40974
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.635
ELB improved by 0.381308
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.277
ELB improved by 0.357883
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.932
ELB improved by 0.345023
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.59
ELB improved by 0.3421
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.244
ELB improved by 0.345746
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.891
ELB improved by 0.353148
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.529
ELB improved by 0.362722
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.155
ELB improved by 0.373851
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.768
ELB improved by 0.386645
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.366
ELB improved by 0.40182
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.946
ELB improved by 0.420667
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.501
ELB improved by 0.445079
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.023
ELB improved by 0.477593
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.502
ELB improved by 0.520963
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.927
ELB improved by 0.57541
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.295
ELB improved by 0.631369
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.628
ELB improved by 0.667079
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.958
ELB improved by 0.670376
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.306
ELB improved by 0.651644
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.686
ELB improved by 0.619813
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.112
ELB improved by 0.574719
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.595
ELB improved by 0.516305
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.148
ELB improved by 0.44762
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.774
ELB improved by 0.373932
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.472
ELB improved by 0.301384
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.237
ELB improved by 0.23548
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.057
ELB improved by 0.179784
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.922
ELB improved by 0.13549
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.82
ELB improved by 0.101904
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.742
ELB improved by 0.0773163
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.683
ELB improved by 0.0597547
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.635
ELB improved by 0.0474236
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.596
ELB improved by 0.0388709
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.563
ELB improved by 0.0329947
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.534
ELB improved by 0.0289855
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.508
ELB improved by 0.0262555
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.484
ELB improved by 0.0243797
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.461
ELB improved by 0.0230524
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.439
ELB improved by 0.0220567
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.417
ELB improved by 0.0212426
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.397
ELB improved by 0.020508
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.377
ELB improved by 0.019785
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.358
ELB improved by 0.0190286
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.34
ELB improved by 0.0182114
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.323
ELB improved by 0.0173211
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.306
ELB improved by 0.0163598
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.291
ELB improved by 0.0153426
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.277
ELB improved by 0.0142935
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.263
ELB improved by 0.0132405
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.251
ELB improved by 0.0122106
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.24
ELB improved by 0.0112256
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.23
ELB improved by 0.010301
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.22
ELB improved by 0.00944554
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.740 0.272 3.020
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.048 | 0.013 | 0.061 | |
| getPIPs | 0.047 | 0.013 | 0.060 | |
| graper | 0.076 | 0.018 | 0.095 | |
| makeExampleData | 0.024 | 0.004 | 0.029 | |
| makeExampleDataWithUnequalGroups | 0.009 | 0.000 | 0.011 | |
| plotELBO | 0.319 | 0.017 | 0.337 | |
| plotGroupPenalties | 1.319 | 0.051 | 1.376 | |
| plotPosterior | 0.744 | 0.022 | 0.770 | |
| predict.graper | 1.897 | 0.084 | 1.991 | |
| print.graper | 0.047 | 0.013 | 0.060 | |