Multiple platform build/check report for BioC 3.19 - CHECK results for graper on palomino7

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4763
palomino7	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4500
merida1	macOS 12.7.5 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4530
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4480
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*

CHECK results for graper on palomino7

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: E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:graper.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings graper_1.20.0.tar.gz

StartedAt: 2024-10-17 02:06:01 -0400 (Thu, 17 Oct 2024)

EndedAt: 2024-10-17 02:07:24 -0400 (Thu, 17 Oct 2024)

EllapsedTime: 83.7 seconds

RetCode: 0

Status: OK

CheckDir: graper.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:graper.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings graper_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/graper.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 whether package 'graper' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* 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 for x64 is not available
File 'E:/biocbuild/bbs-3.19-bioc/R/library/graper/libs/x64/graper.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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: 3 NOTEs
See
  'E:/biocbuild/bbs-3.19-bioc/meat/graper.Rcheck/00check.log'
for details.

Installation output

graper.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL graper
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'graper' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
using C++11
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fit_graper.cpp -o fit_graper.o
In file included from E:/biocbuild/bbs-3.19-bioc/R/library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11,
                 from E:/biocbuild/bbs-3.19-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
                 from E:/biocbuild/bbs-3.19-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:15,
                 from graper_linear_dense_ff.h:2,
                 from fit_graper.cpp:4:
E:/biocbuild/bbs-3.19-bioc/R/library/BH/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
      |      ^~~~~~~
g++ -shared -s -static-libgcc -o graper.dll tmp.def RcppExports.o fit_graper.o -LE:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lRlapack -LE:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-graper/00new/graper/libs/x64
** 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
** 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 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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=-849.325
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-564.119
ELB improved by 285.206

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-506.445
ELB improved by 57.674

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-471.805
ELB improved by 34.6402

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.998
ELB improved by 14.8072

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.498
ELB improved by 6.50011

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.452
ELB improved by 4.04619

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.222
ELB improved by 3.23001

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.285
ELB improved by 2.93635

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.454
ELB improved by 2.83159

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.68
ELB improved by 2.77399

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.999
ELB improved by 2.68055

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.505
ELB improved by 2.49468

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.309
ELB improved by 2.19564

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.493
ELB improved by 1.81548

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.069
ELB improved by 1.42403

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.987
ELB improved by 1.08242

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.171
ELB improved by 0.816215

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.546
ELB improved by 0.6248

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.05
ELB improved by 0.495671

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.638
ELB improved by 0.412126

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.279
ELB improved by 0.359004

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.954
ELB improved by 0.325496

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.649
ELB improved by 0.304896

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.356
ELB improved by 0.293313

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.067
ELB improved by 0.288534

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.778
ELB improved by 0.289311

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.483
ELB improved by 0.294951

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.178
ELB improved by 0.305108

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.858
ELB improved by 0.319682

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.519
ELB improved by 0.338789

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.156
ELB improved by 0.362771

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.764
ELB improved by 0.39223

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.336
ELB improved by 0.428062

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.865
ELB improved by 0.471479

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.341
ELB improved by 0.524037

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.753
ELB improved by 0.587674

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.088
ELB improved by 0.664711

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.331
ELB improved by 0.757553

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.463
ELB improved by 0.867677

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.47
ELB improved by 0.993411

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.343
ELB improved by 1.12612

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.098
ELB improved by 1.24575

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.776
ELB improved by 1.32185

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.447
ELB improved by 1.32901

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.182
ELB improved by 1.26515

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.044
ELB improved by 1.13767

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.095
ELB improved by 0.948816

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.367
ELB improved by 0.728188

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.843
ELB improved by 0.523809

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.478
ELB improved by 0.365605

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.218
ELB improved by 0.259167

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.025
ELB improved by 0.193404

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.872
ELB improved by 0.152704

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.748
ELB improved by 0.124088

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.649
ELB improved by 0.0994989

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.572
ELB improved by 0.0765376

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.516
ELB improved by 0.0566123

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.474
ELB improved by 0.0413342

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.444
ELB improved by 0.0307156

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.42
ELB improved by 0.0236882

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.401
ELB improved by 0.0190512

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.385
ELB improved by 0.0158999

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.371
ELB improved by 0.0136581

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.359
ELB improved by 0.0119834

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.349
ELB improved by 0.0106769

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.339
ELB improved by 0.00962105

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-891.561
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-579.529
ELB improved by 312.032

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-524.45
ELB improved by 55.0791

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-491.349
ELB improved by 33.1016

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-476.915
ELB improved by 14.4339

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.17
ELB improved by 6.7449

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.333
ELB improved by 4.83674

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.804
ELB improved by 4.52886

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.102
ELB improved by 4.70182

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.042
ELB improved by 5.06067

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.692
ELB improved by 5.35012

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.47
ELB improved by 5.22119

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.054
ELB improved by 4.41596

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.857
ELB improved by 3.19703

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.717
ELB improved by 2.1407

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.244
ELB improved by 1.47262

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.171
ELB improved by 1.07316

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.378
ELB improved by 0.793082

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.789
ELB improved by 0.588741

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.336
ELB improved by 0.453505

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.97
ELB improved by 0.365957

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.664
ELB improved by 0.305659

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.403
ELB improved by 0.260852

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.178
ELB improved by 0.225613

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.981
ELB improved by 0.196939

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.807
ELB improved by 0.173206

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.654
ELB improved by 0.15343

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.517
ELB improved by 0.136916

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.394
ELB improved by 0.123114

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.282
ELB improved by 0.111567

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.18
ELB improved by 0.101897

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.087
ELB improved by 0.0937954

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424
ELB improved by 0.0870153

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.918
ELB improved by 0.0813606

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.842
ELB improved by 0.076676

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.769
ELB improved by 0.0728385

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.699
ELB improved by 0.069751

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.632
ELB improved by 0.0673368

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.566
ELB improved by 0.0655356

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.502
ELB improved by 0.0643004

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.438
ELB improved by 0.0635948

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.375
ELB improved by 0.0633915

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.311
ELB improved by 0.0636701

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.247
ELB improved by 0.0644162

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.181
ELB improved by 0.0656197

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.114
ELB improved by 0.0672744

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.044
ELB improved by 0.0693765

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.973
ELB improved by 0.0719241

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.898
ELB improved by 0.0749163

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.819
ELB improved by 0.0783531

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.737
ELB improved by 0.0822349

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.651
ELB improved by 0.0865634

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.559
ELB improved by 0.0913428

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.463
ELB improved by 0.0965836

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.36
ELB improved by 0.102309

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.252
ELB improved by 0.108569

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.136
ELB improved by 0.115459

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.013
ELB improved by 0.123171

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.881
ELB improved by 0.132072

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.738
ELB improved by 0.142871

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.581
ELB improved by 0.156934

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.404
ELB improved by 0.176814

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.198
ELB improved by 0.206747

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.946
ELB improved by 0.251221

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.639
ELB improved by 0.306926

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.286
ELB improved by 0.353225

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.916
ELB improved by 0.370691

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.549
ELB improved by 0.366244

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.199
ELB improved by 0.350535

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.879
ELB improved by 0.319829

iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.604
ELB improved by 0.27471

iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.375
ELB improved by 0.228935

iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.184
ELB improved by 0.191593

iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.021
ELB improved by 0.162541

iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.882
ELB improved by 0.139653

iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.76
ELB improved by 0.121443

iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.653
ELB improved by 0.106886

iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.558
ELB improved by 0.0951538

iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.473
ELB improved by 0.0855131

iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.395
ELB improved by 0.0772884

iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.325
ELB improved by 0.0698868

iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.262
ELB improved by 0.0628747

iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.206
ELB improved by 0.0560507

iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.157
ELB improved by 0.0494401

iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.114
ELB improved by 0.0432001

iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.076
ELB improved by 0.037498

iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.044
ELB improved by 0.032436

iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.016
ELB improved by 0.0280373

iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.992
ELB improved by 0.0242679

iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.97
ELB improved by 0.021064

iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.952
ELB improved by 0.0183523

iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.936
ELB improved by 0.0160615

iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.922
ELB improved by 0.0141274

iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.909
ELB improved by 0.0124945

iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.898
ELB improved by 0.0111159

iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.888
ELB improved by 0.00995221

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-885.78
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-589.28
ELB improved by 296.5

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-526.762
ELB improved by 62.5175

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-479.266
ELB improved by 47.496

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.33
ELB improved by 21.9365

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.156
ELB improved by 8.17417

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.113
ELB improved by 4.04272

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.329
ELB improved by 2.78338

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.034
ELB improved by 2.29547

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.935
ELB improved by 2.09944

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.906
ELB improved by 2.02815

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.896
ELB improved by 2.00995

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.883
ELB improved by 2.01377

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.86
ELB improved by 2.02241

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.842
ELB improved by 2.01831

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.864
ELB improved by 1.97813

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.986
ELB improved by 1.8781

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.278
ELB improved by 1.70728

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.802
ELB improved by 1.47682

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.585
ELB improved by 1.21705

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.62
ELB improved by 0.965086

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.871
ELB improved by 0.748884

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.29
ELB improved by 0.580442

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.83
ELB improved by 0.460108

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.449
ELB improved by 0.381559

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.113
ELB improved by 0.33551

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.8
ELB improved by 0.313231

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.491
ELB improved by 0.308544

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.173
ELB improved by 0.318111

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.832
ELB improved by 0.340992

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.454
ELB improved by 0.378136

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.022
ELB improved by 0.431924

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.517
ELB improved by 0.505404

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.916
ELB improved by 0.600746

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.199
ELB improved by 0.716736

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.353
ELB improved by 0.845812

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.382
ELB improved by 0.971372

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.313
ELB improved by 1.06853

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.2
ELB improved by 1.11371

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.103
ELB improved by 1.09694

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.08
ELB improved by 1.02289

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.175
ELB improved by 0.904597

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.415
ELB improved by 0.76042

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.804
ELB improved by 0.611229

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.329
ELB improved by 0.474975

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.967
ELB improved by 0.361958

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.692
ELB improved by 0.274296

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.484
ELB improved by 0.208885

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.323
ELB improved by 0.160821

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.197
ELB improved by 0.125484

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.098
ELB improved by 0.0992588

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.018
ELB improved by 0.0795406

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.954
ELB improved by 0.0645076

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.901
ELB improved by 0.0528943

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.857
ELB improved by 0.0438163

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.821
ELB improved by 0.0366487

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.79
ELB improved by 0.0309425

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.763
ELB improved by 0.0263691

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.741
ELB improved by 0.0226829

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.721
ELB improved by 0.0196963

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.704
ELB improved by 0.0172638

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.688
ELB improved by 0.0152714

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.675
ELB improved by 0.013629

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.662
ELB improved by 0.0122657

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.651
ELB improved by 0.0111256

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.641
ELB improved by 0.0101643

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.632
ELB improved by 0.00934744

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-841.022
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-541.191
ELB improved by 299.83

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-486.358
ELB improved by 54.8329

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.086
ELB improved by 27.272

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.467
ELB improved by 11.6193

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.982
ELB improved by 5.48472

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.561
ELB improved by 3.42178

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.682
ELB improved by 2.87844

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.8
ELB improved by 2.88214

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.638
ELB improved by 3.16241

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.031
ELB improved by 3.60639

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.953
ELB improved by 4.07861

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.639
ELB improved by 4.31363

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.658
ELB improved by 3.98105

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.539
ELB improved by 3.11865

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.371
ELB improved by 2.16819

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.938
ELB improved by 1.43286

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.98
ELB improved by 0.9577

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.297
ELB improved by 0.68323

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.768
ELB improved by 0.528801

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.331
ELB improved by 0.437588

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.952
ELB improved by 0.37932

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.613
ELB improved by 0.338688

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.305
ELB improved by 0.307677

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.023
ELB improved by 0.281967

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.764
ELB improved by 0.259253

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.526
ELB improved by 0.238389

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.307
ELB improved by 0.218889

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.106
ELB improved by 0.200618

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.922
ELB improved by 0.183593

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.755
ELB improved by 0.167874

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.601
ELB improved by 0.153498

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.461
ELB improved by 0.140459

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.332
ELB improved by 0.128712

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.214
ELB improved by 0.118176

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.105
ELB improved by 0.108752

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.005
ELB improved by 0.100331

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.912
ELB improved by 0.092805

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.826
ELB improved by 0.0860699

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.746
ELB improved by 0.0800302

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.671
ELB improved by 0.0746003

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.601
ELB improved by 0.0697043

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.536
ELB improved by 0.065276

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.475
ELB improved by 0.0612577

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.417
ELB improved by 0.0575998

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.363
ELB improved by 0.0542594

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.312
ELB improved by 0.0511994

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.263
ELB improved by 0.0483877

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.218
ELB improved by 0.0457968

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.174
ELB improved by 0.0434027

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.133
ELB improved by 0.0411843

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.094
ELB improved by 0.0391235

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.057
ELB improved by 0.0372043

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.021
ELB improved by 0.0354125

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.988
ELB improved by 0.0337359

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.955
ELB improved by 0.0321634

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.925
ELB improved by 0.0306854

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.895
ELB improved by 0.0292932

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.867
ELB improved by 0.0279791

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.841
ELB improved by 0.0267363

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.815
ELB improved by 0.0255587

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.791
ELB improved by 0.0244408

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.767
ELB improved by 0.0233779

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.745
ELB improved by 0.0223656

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.724
ELB improved by 0.0214002

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.703
ELB improved by 0.0204781

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.684
ELB improved by 0.0195964

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.665
ELB improved by 0.0187525

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.647
ELB improved by 0.017944

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.63
ELB improved by 0.017169

iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.613
ELB improved by 0.0164255

iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.598
ELB improved by 0.0157122

iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.582
ELB improved by 0.0150275

iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.568
ELB improved by 0.0143705

iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.554
ELB improved by 0.01374

iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.541
ELB improved by 0.0131353

iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.529
ELB improved by 0.0125555

iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.517
ELB improved by 0.012

iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.505
ELB improved by 0.0114683

iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.494
ELB improved by 0.0109599

iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.484
ELB improved by 0.0104743

iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.474
ELB improved by 0.0100113

iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.464
ELB improved by 0.0095705

ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
> 
> proc.time()
   user  system elapsed 
   2.26    0.42    2.65

Example timings

graper.Rcheck/graper-Ex.timings

name	user	system	elapsed
coef.graper	0.08	0.00	0.07
getPIPs	0.06	0.00	0.06
graper	0.09	0.03	0.12
makeExampleData	0.02	0.00	0.02
makeExampleDataWithUnequalGroups	0	0	0
plotELBO	0.28	0.00	0.28
plotGroupPenalties	1.05	0.05	1.09
plotPosterior	0.56	0.01	0.58
predict.graper	1.89	0.08	1.97
print.graper	0.05	0.00	0.05