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This page was generated on 2024-07-16 17:41 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4742
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4484
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4513
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4462
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 908/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
graper 1.20.0  (landing page)
Britta Velten
Snapshot Date: 2024-07-14 14:00 -0400 (Sun, 14 Jul 2024)
git_url: https://git.bioconductor.org/packages/graper
git_branch: RELEASE_3_19
git_last_commit: a4dfa52
git_last_commit_date: 2024-04-30 11:11:42 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for graper on merida1

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.

raw results


Summary

Package: graper
Version: 1.20.0
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_1.20.0.tar.gz
StartedAt: 2024-07-15 05:31:10 -0400 (Mon, 15 Jul 2024)
EndedAt: 2024-07-15 05:33:24 -0400 (Mon, 15 Jul 2024)
EllapsedTime: 133.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: graper.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### 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_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/graper.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.20.0’
* 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 ... WARNING
Found the following significant warnings:
  /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
  #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
See ‘/Users/biocbuild/bbs-3.19-bioc/meat/graper.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/graper.Rcheck/00check.log’
for details.


Installation output

graper.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL graper
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘graper’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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
In file included from fit_graper.cpp:4:
In file included from ./graper_linear_dense_ff.h:2:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/digamma.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/math_fwd.hpp:29:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
#    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
     ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -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-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-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)

Tests output

graper.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 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=-884.449
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-587.751
ELB improved by 296.698

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-526.642
ELB improved by 61.1097

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-486.164
ELB improved by 40.4781

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.529
ELB improved by 17.6349

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.405
ELB improved by 7.12404

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.85
ELB improved by 4.5544

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.303
ELB improved by 4.54758

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.994
ELB improved by 5.30863

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.533
ELB improved by 6.46095

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.102
ELB improved by 7.43128

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.909
ELB improved by 7.19319

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.494
ELB improved by 5.41449

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.164
ELB improved by 3.32988

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.125
ELB improved by 2.03977

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.633
ELB improved by 1.49113

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.387
ELB improved by 1.24616

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.31
ELB improved by 1.07776

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.367
ELB improved by 0.942965

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.57
ELB improved by 0.796827

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.903
ELB improved by 0.666924

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.322
ELB improved by 0.580914

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.798
ELB improved by 0.523753

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.318
ELB improved by 0.480172

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.874
ELB improved by 0.443693

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.462
ELB improved by 0.412015

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.078
ELB improved by 0.384248

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.718
ELB improved by 0.359902

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.38
ELB improved by 0.338579

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.06
ELB improved by 0.319942

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.756
ELB improved by 0.30375

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.466
ELB improved by 0.289872

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.188
ELB improved by 0.278239

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.919
ELB improved by 0.268665

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.659
ELB improved by 0.260434

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.407
ELB improved by 0.251687

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.168
ELB improved by 0.23935

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.947
ELB improved by 0.221014

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.749
ELB improved by 0.197824

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.575
ELB improved by 0.173918

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.422
ELB improved by 0.152498

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.288
ELB improved by 0.134204

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.17
ELB improved by 0.11842

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.065
ELB improved by 0.104512

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.973
ELB improved by 0.0921143

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.892
ELB improved by 0.0810453

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.821
ELB improved by 0.0711955

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.758
ELB improved by 0.0624763

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.704
ELB improved by 0.0548009

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.656
ELB improved by 0.0480813

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.613
ELB improved by 0.0422281

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.576
ELB improved by 0.0371526

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.543
ELB improved by 0.0327682

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.514
ELB improved by 0.0289926

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.489
ELB improved by 0.0257487

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.466
ELB improved by 0.022966

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.445
ELB improved by 0.0205812

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.427
ELB improved by 0.0185385

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.41
ELB improved by 0.0167889

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.394
ELB improved by 0.0152908

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.38
ELB improved by 0.0140084

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.368
ELB improved by 0.0129122

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.356
ELB improved by 0.0119774

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.344
ELB improved by 0.0111843

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.334
ELB improved by 0.0105175

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.324
ELB improved by 0.00996579

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-885.607
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-587.762
ELB improved by 297.845

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-533.379
ELB improved by 54.3834

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-497.439
ELB improved by 35.9397

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-478.926
ELB improved by 18.5133

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.185
ELB improved by 8.74132

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.099
ELB improved by 5.08589

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.879
ELB improved by 4.21972

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.597
ELB improved by 4.28232

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.889
ELB improved by 4.70795

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.732
ELB improved by 5.15623

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.605
ELB improved by 5.12736

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.299
ELB improved by 4.30581

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.268
ELB improved by 3.03099

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.366
ELB improved by 1.90204

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.198
ELB improved by 1.16792

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.444
ELB improved by 0.754214

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.918
ELB improved by 0.526486

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.523
ELB improved by 0.394669

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.211
ELB improved by 0.311423

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.958
ELB improved by 0.253795

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.747
ELB improved by 0.210885

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.569
ELB improved by 0.177451

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.419
ELB improved by 0.150809

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.289
ELB improved by 0.129372

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.177
ELB improved by 0.112023

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.079
ELB improved by 0.0978874

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.993
ELB improved by 0.0862666

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.916
ELB improved by 0.0766108

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.848
ELB improved by 0.068499

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.786
ELB improved by 0.0616128

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.731
ELB improved by 0.0557122

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.68
ELB improved by 0.0506145

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.634
ELB improved by 0.0461795

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.591
ELB improved by 0.0422972

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.553
ELB improved by 0.0388806

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.517
ELB improved by 0.0358593

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.484
ELB improved by 0.0331763

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.453
ELB improved by 0.0307844

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.424
ELB improved by 0.0286446

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.397
ELB improved by 0.0267241

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.372
ELB improved by 0.0249953

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.349
ELB improved by 0.0234347

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.327
ELB improved by 0.0220224

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.306
ELB improved by 0.0207412

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.287
ELB improved by 0.0195763

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.268
ELB improved by 0.0185149

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.251
ELB improved by 0.0175459

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.234
ELB improved by 0.0166596

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.218
ELB improved by 0.0158475

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.203
ELB improved by 0.0151021

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.189
ELB improved by 0.0144167

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.175
ELB improved by 0.0137856

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.162
ELB improved by 0.0132036

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.149
ELB improved by 0.0126661

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.137
ELB improved by 0.0121689

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.125
ELB improved by 0.0117084

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.114
ELB improved by 0.0112812

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.103
ELB improved by 0.0108845

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.092
ELB improved by 0.0105155

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.082
ELB improved by 0.0101719

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.072
ELB improved by 0.00985143

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-895.25
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-580.182
ELB improved by 315.069

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-519.775
ELB improved by 60.4062

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-483.153
ELB improved by 36.6224

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.7
ELB improved by 16.4527

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.456
ELB improved by 8.24411

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.353
ELB improved by 6.10341

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.554
ELB improved by 5.79922

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.795
ELB improved by 5.75864

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.433
ELB improved by 5.36179

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.957
ELB improved by 4.47635

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.584
ELB improved by 3.37244

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.178
ELB improved by 2.40593

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.452
ELB improved by 1.72698

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.162
ELB improved by 1.28967

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.163
ELB improved by 0.999257

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.369
ELB improved by 0.793104

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.734
ELB improved by 0.635972

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.228
ELB improved by 0.505556

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.831
ELB improved by 0.397331

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.516
ELB improved by 0.314989

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.259
ELB improved by 0.256735

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.043
ELB improved by 0.216319

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.855
ELB improved by 0.187793

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.688
ELB improved by 0.167092

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.536
ELB improved by 0.151765

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.396
ELB improved by 0.140381

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.263
ELB improved by 0.132098

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.137
ELB improved by 0.126418

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.014
ELB improved by 0.123069

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.892
ELB improved by 0.121953

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.769
ELB improved by 0.123132

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.642
ELB improved by 0.126829

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.509
ELB improved by 0.133426

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.365
ELB improved by 0.143405

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.208
ELB improved by 0.157149

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.034
ELB improved by 0.174534

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.839
ELB improved by 0.194484

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.624
ELB improved by 0.215156

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.389
ELB improved by 0.235238

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.133
ELB improved by 0.255303

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.856
ELB improved by 0.277596

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.551
ELB improved by 0.304856

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.211
ELB improved by 0.339568

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.828
ELB improved by 0.383308

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.393
ELB improved by 0.434754

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.906
ELB improved by 0.487216

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.375
ELB improved by 0.530933

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.815
ELB improved by 0.560356

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.24
ELB improved by 0.575159

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.664
ELB improved by 0.575154

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.105
ELB improved by 0.559155

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.578
ELB improved by 0.527026

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.097
ELB improved by 0.480815

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.673
ELB improved by 0.424573

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.309
ELB improved by 0.363597

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.006
ELB improved by 0.303398

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.757
ELB improved by 0.248593

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.555
ELB improved by 0.202074

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.39
ELB improved by 0.164802

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.254
ELB improved by 0.136154

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.14
ELB improved by 0.11445

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.042
ELB improved by 0.0974441

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.959
ELB improved by 0.0829104

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.89
ELB improved by 0.0694202

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.833
ELB improved by 0.0568345

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.787
ELB improved by 0.0458758

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.75
ELB improved by 0.0371659

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.719
ELB improved by 0.0307202

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.693
ELB improved by 0.0261067

iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.671
ELB improved by 0.0227885

iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.65
ELB improved by 0.0203204

iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.632
ELB improved by 0.0183893

iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.615
ELB improved by 0.0167904

iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.6
ELB improved by 0.0153932

iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.586
ELB improved by 0.0141174

iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.573
ELB improved by 0.0129177

iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.561
ELB improved by 0.011774

iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.55
ELB improved by 0.0106834

iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.541
ELB improved by 0.00965327

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-855.692
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-573.863
ELB improved by 281.829

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-514.159
ELB improved by 59.7038

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-476.156
ELB improved by 38.0027

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.318
ELB improved by 17.8376

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.406
ELB improved by 7.91261

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.801
ELB improved by 4.60506

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.197
ELB improved by 3.60325

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.903
ELB improved by 3.29442

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.739
ELB improved by 3.16358

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.747
ELB improved by 2.99291

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.039
ELB improved by 2.70785

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.701
ELB improved by 2.33755

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.78
ELB improved by 1.92155

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.283
ELB improved by 1.49666

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.162
ELB improved by 1.12067

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.331
ELB improved by 0.830939

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.7
ELB improved by 0.631293

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.2
ELB improved by 0.500059

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.79
ELB improved by 0.410241

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.443
ELB improved by 0.34709

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.136
ELB improved by 0.306519

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.85
ELB improved by 0.286069

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.568
ELB improved by 0.282012

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.277
ELB improved by 0.290773

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.967
ELB improved by 0.309901

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.629
ELB improved by 0.337965

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.255
ELB improved by 0.374059

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.838
ELB improved by 0.417305

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.372
ELB improved by 0.46648

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.852
ELB improved by 0.519805

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.277
ELB improved by 0.57494

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.648
ELB improved by 0.629166

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.968
ELB improved by 0.679608

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.245
ELB improved by 0.723312

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.488
ELB improved by 0.757077

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.71
ELB improved by 0.777279

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.93
ELB improved by 0.780221

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.167
ELB improved by 0.763561

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.438
ELB improved by 0.728893

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.753
ELB improved by 0.684682

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.105
ELB improved by 0.648001

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.465
ELB improved by 0.64028

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.804
ELB improved by 0.660728

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.159
ELB improved by 0.64485

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.62
ELB improved by 0.538805

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.22
ELB improved by 0.400671

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.931
ELB improved by 0.288653

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.721
ELB improved by 0.209605

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.567
ELB improved by 0.154633

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.451
ELB improved by 0.115564

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.364
ELB improved by 0.0871445

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.298
ELB improved by 0.0662231

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.247
ELB improved by 0.0507929

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.208
ELB improved by 0.0394323

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.177
ELB improved by 0.031071

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.152
ELB improved by 0.0248977

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.131
ELB improved by 0.0203087

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.115
ELB improved by 0.0168642

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.1
ELB improved by 0.0142478

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.088
ELB improved by 0.0122343

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.077
ELB improved by 0.010663

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.068
ELB improved by 0.0094193

ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
> 
> proc.time()
   user  system elapsed 
  4.748   0.468   5.878 

Example timings

graper.Rcheck/graper-Ex.timings

nameusersystemelapsed
coef.graper0.0840.0410.143
getPIPs0.0780.0400.121
graper0.1280.0550.201
makeExampleData0.0210.0020.027
makeExampleDataWithUnequalGroups0.0440.0040.049
plotELBO0.4180.0440.530
plotGroupPenalties1.6930.0671.871
plotPosterior1.2380.0521.406
predict.graper3.1310.2193.761
print.graper0.0750.0340.117