Multiple platform build/check report for BioC 3.20 - CHECK results for graper on palomino4

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"	4679
palomino4	Windows Server 2022 Datacenter	x64	4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"	4414
merida1	macOS 12.7.4 Monterey	x86_64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4441
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4394
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 palomino4

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: 1.21.0

Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:graper.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings graper_1.21.0.tar.gz

StartedAt: 2024-06-10 03:32:52 -0400 (Mon, 10 Jun 2024)

EndedAt: 2024-06-10 03:36:03 -0400 (Mon, 10 Jun 2024)

EllapsedTime: 191.2 seconds

RetCode: 0

Status: OK

CheckDir: graper.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:graper.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings graper_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/graper.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 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 '1.21.0'
* 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 'F:/biocbuild/bbs-3.20-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
  'F:/biocbuild/bbs-3.20-bioc/meat/graper.Rcheck/00check.log'
for details.

Installation output

graper.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL graper
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.20-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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.20-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 F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:15,
                 from graper_linear_dense_ff.h:2,
                 from fit_graper.cpp:4:
F:/biocbuild/bbs-3.20-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 -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.20-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 -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-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 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
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=-875.074
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-592.585
ELB improved by 282.489

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-534.663
ELB improved by 57.9225

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-490.836
ELB improved by 43.8267

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.137
ELB improved by 20.6984

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.425
ELB improved by 6.71253

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.824
ELB improved by 3.60072

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.885
ELB improved by 2.93897

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.115
ELB improved by 2.77068

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.305
ELB improved by 2.80971

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.35
ELB improved by 2.95512

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.174
ELB improved by 3.17545

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.725
ELB improved by 3.44938

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438
ELB improved by 3.72523

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.115
ELB improved by 3.8849

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.367
ELB improved by 3.74785

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.163
ELB improved by 3.20432

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.74
ELB improved by 2.42269

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.047
ELB improved by 1.69319

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.891
ELB improved by 1.15534

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.09
ELB improved by 0.801673

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.512
ELB improved by 0.578006

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.076
ELB improved by 0.435986

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.733
ELB improved by 0.342808

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.455
ELB improved by 0.278353

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.223
ELB improved by 0.231064

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.029
ELB improved by 0.194581

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.863
ELB improved by 0.165431

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.722
ELB improved by 0.141657

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.6
ELB improved by 0.122056

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.494
ELB improved by 0.105799

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.402
ELB improved by 0.092256

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.321
ELB improved by 0.0809167

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.249
ELB improved by 0.0713659

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.186
ELB improved by 0.0632679

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.13
ELB improved by 0.0563546

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.079
ELB improved by 0.0504136

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.034
ELB improved by 0.0452768

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.993
ELB improved by 0.0408103

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.956
ELB improved by 0.0369067

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.923
ELB improved by 0.0334795

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.892
ELB improved by 0.0304579

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.865
ELB improved by 0.0277836

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.839
ELB improved by 0.0254084

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.816
ELB improved by 0.023292

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.795
ELB improved by 0.0214006

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.775
ELB improved by 0.0197054

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.757
ELB improved by 0.0181821

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.74
ELB improved by 0.0168101

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.724
ELB improved by 0.0155714

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.71
ELB improved by 0.0144507

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.696
ELB improved by 0.0134347

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.684
ELB improved by 0.0125119

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.672
ELB improved by 0.0116723

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.661
ELB improved by 0.0109069

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.651
ELB improved by 0.0102082

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.642
ELB improved by 0.0095692

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-870.85
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-553.491
ELB improved by 317.359

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-494.727
ELB improved by 58.764

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-463.836
ELB improved by 30.8903

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.379
ELB improved by 12.457

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.173
ELB improved by 6.20677

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.448
ELB improved by 4.72456

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.882
ELB improved by 4.5657

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.121
ELB improved by 4.76183

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.306
ELB improved by 4.81427

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.905
ELB improved by 4.40107

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.369
ELB improved by 3.53589

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.794
ELB improved by 2.57527

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.934
ELB improved by 1.86051

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.462
ELB improved by 1.47119

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.141
ELB improved by 1.32158

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.841
ELB improved by 1.29974

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.539
ELB improved by 1.30173

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.263
ELB improved by 1.27614

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.011
ELB improved by 1.25268

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.746
ELB improved by 1.26419

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.416
ELB improved by 1.33071

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.94
ELB improved by 1.4757

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.285
ELB improved by 1.6554

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.556
ELB improved by 1.72845

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.846
ELB improved by 1.70972

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.167
ELB improved by 1.67971

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.536
ELB improved by 1.63036

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.007
ELB improved by 1.52906

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.645
ELB improved by 1.36271

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.497
ELB improved by 1.14705

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.583
ELB improved by 0.914383

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.885
ELB improved by 0.698478

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.363
ELB improved by 0.521439

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.977
ELB improved by 0.386313

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.692
ELB improved by 0.284935

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.482
ELB improved by 0.209831

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.326
ELB improved by 0.156029

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.207
ELB improved by 0.118588

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.115
ELB improved by 0.0926313

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.041
ELB improved by 0.0742987

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.98
ELB improved by 0.0609688

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.929
ELB improved by 0.0509794

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.885
ELB improved by 0.0432863

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.848
ELB improved by 0.0372211

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.816
ELB improved by 0.0323425

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.787
ELB improved by 0.0283505

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.762
ELB improved by 0.0250362

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.74
ELB improved by 0.0222503

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.72
ELB improved by 0.0198842

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.702
ELB improved by 0.0178572

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.686
ELB improved by 0.0161082

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.672
ELB improved by 0.01459

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.658
ELB improved by 0.0132656

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.646
ELB improved by 0.0121052

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.635
ELB improved by 0.0110849

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.625
ELB improved by 0.0101849

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.616
ELB improved by 0.00938884

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-855.691
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-566.233
ELB improved by 289.458

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-506.223
ELB improved by 60.0097

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.343
ELB improved by 33.8808

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.136
ELB improved by 13.2065

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.572
ELB improved by 6.56447

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.437
ELB improved by 5.13448

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.47
ELB improved by 4.96751

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.525
ELB improved by 4.94501

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.839
ELB improved by 4.68539

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.819
ELB improved by 4.02054

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.758
ELB improved by 3.061

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.649
ELB improved by 2.10822

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.265
ELB improved by 1.38393

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.348
ELB improved by 0.917749

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.709
ELB improved by 0.638649

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.238
ELB improved by 0.47151

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.871
ELB improved by 0.366749

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.574
ELB improved by 0.296719

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.327
ELB improved by 0.246854

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.118
ELB improved by 0.20945

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.938
ELB improved by 0.180265

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.781
ELB improved by 0.156824

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.643
ELB improved by 0.137592

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.522
ELB improved by 0.121558

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.414
ELB improved by 0.108023

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.317
ELB improved by 0.0964836

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.231
ELB improved by 0.0865644

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.153
ELB improved by 0.0779783

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.082
ELB improved by 0.0705009

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.018
ELB improved by 0.063954

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.96
ELB improved by 0.0581941

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.907
ELB improved by 0.0531044

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.858
ELB improved by 0.0485887

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.814
ELB improved by 0.0445676

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.773
ELB improved by 0.0409746

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.735
ELB improved by 0.0377539

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.7
ELB improved by 0.0348584

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.668
ELB improved by 0.0322481

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.638
ELB improved by 0.029889

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.61
ELB improved by 0.0277518

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.584
ELB improved by 0.0258112

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.56
ELB improved by 0.0240457

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.538
ELB improved by 0.0224362

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.517
ELB improved by 0.0209663

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.497
ELB improved by 0.0196216

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.479
ELB improved by 0.0183896

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.462
ELB improved by 0.0172591

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.445
ELB improved by 0.0162203

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.43
ELB improved by 0.0152645

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.416
ELB improved by 0.0143841

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.402
ELB improved by 0.0135721

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.389
ELB improved by 0.0128225

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.377
ELB improved by 0.0121297

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.366
ELB improved by 0.0114889

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.355
ELB improved by 0.0108957

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.344
ELB improved by 0.010346

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.335
ELB improved by 0.00983639

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-893.107
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-568.649
ELB improved by 324.457

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-512.714
ELB improved by 55.9356

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-480.586
ELB improved by 32.1282

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-464.636
ELB improved by 15.9492

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.827
ELB improved by 7.80975

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.009
ELB improved by 4.81722

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.076
ELB improved by 3.93303

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.278
ELB improved by 3.79779

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.344
ELB improved by 3.93449

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.211
ELB improved by 4.13347

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.989
ELB improved by 4.22121

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.955
ELB improved by 4.03405

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.445
ELB improved by 3.51027

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.719
ELB improved by 2.72602

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.795
ELB improved by 1.92427

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.488
ELB improved by 1.30644

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.597
ELB improved by 0.89146

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.97
ELB improved by 0.626508

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.514
ELB improved by 0.45606

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.17
ELB improved by 0.344531

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.898
ELB improved by 0.271418

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.676
ELB improved by 0.222597

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.487
ELB improved by 0.18854

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.324
ELB improved by 0.1636

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.179
ELB improved by 0.144624

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.049
ELB improved by 0.12981

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.931
ELB improved by 0.118061

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.822
ELB improved by 0.108668

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.721
ELB improved by 0.101144

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.626
ELB improved by 0.0951519

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.536
ELB improved by 0.0904468

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.449
ELB improved by 0.0868536

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.365
ELB improved by 0.0842446

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.282
ELB improved by 0.0825227

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.2
ELB improved by 0.0816055

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.119
ELB improved by 0.0814082

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.037
ELB improved by 0.0818287

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.954
ELB improved by 0.0827396

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.87
ELB improved by 0.083999

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.785
ELB improved by 0.0854866

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.698
ELB improved by 0.0871561

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.609
ELB improved by 0.0890776

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.517
ELB improved by 0.0914352

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.423
ELB improved by 0.0944781

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.324
ELB improved by 0.098457

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.221
ELB improved by 0.103593

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.111
ELB improved by 0.110102

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.992
ELB improved by 0.118259

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.864
ELB improved by 0.128491

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.722
ELB improved by 0.141416

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.565
ELB improved by 0.157717

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.387
ELB improved by 0.177688

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.187
ELB improved by 0.200544

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.962
ELB improved by 0.224374

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.714
ELB improved by 0.247689

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.443
ELB improved by 0.27105

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.147
ELB improved by 0.296184

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.824
ELB improved by 0.323709

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.471
ELB improved by 0.352177

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.093
ELB improved by 0.378595

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.693
ELB improved by 0.399505

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.281
ELB improved by 0.411997

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.867
ELB improved by 0.414227

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.462
ELB improved by 0.40545

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.076
ELB improved by 0.385926

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.719
ELB improved by 0.356939

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.398
ELB improved by 0.320777

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.117
ELB improved by 0.28046

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.878
ELB improved by 0.239181

iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.679
ELB improved by 0.19972

iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.515
ELB improved by 0.164039

iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.381
ELB improved by 0.133178

iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.274
ELB improved by 0.107386

iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.188
ELB improved by 0.0863672

iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.118
ELB improved by 0.0695281

iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.062
ELB improved by 0.0561736

iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.016
ELB improved by 0.0456281

iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.979
ELB improved by 0.0372994

iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.948
ELB improved by 0.0306999

iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.923
ELB improved by 0.0254447

iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.902
ELB improved by 0.021238

iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.884
ELB improved by 0.0178546

iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.869
ELB improved by 0.0151231

iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.856
ELB improved by 0.0129118

iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.845
ELB improved by 0.0111177

iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.835
ELB improved by 0.00965954

ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
> 
> proc.time()
   user  system elapsed 
   2.07    3.57    6.23

Example timings

graper.Rcheck/graper-Ex.timings

name	user	system	elapsed
coef.graper	0.04	0.00	1.94
getPIPs	0.06	0.00	0.06
graper	0.09	0.00	0.10
makeExampleData	0	0	0
makeExampleDataWithUnequalGroups	0.00	0.02	0.01
plotELBO	0.27	0.06	0.33
plotGroupPenalties	0.88	0.08	0.97
plotPosterior	0.47	0.01	0.48
predict.graper	1.76	0.00	1.77
print.graper	0.06	0.00	0.06