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This page was generated on 2024-06-21 17:38 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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: 2024-06-19 14:00 -0400 (Wed, 19 Jun 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
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
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 nebbiolo1

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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings graper_1.20.0.tar.gz
StartedAt: 2024-06-19 23:50:36 -0400 (Wed, 19 Jun 2024)
EndedAt: 2024-06-19 23:51:58 -0400 (Wed, 19 Jun 2024)
EllapsedTime: 81.3 seconds
RetCode: 0
Status:   OK  
CheckDir: graper.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings graper_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/graper.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/graper.Rcheck/00check.log’
for details.


Installation output

graper.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL graper
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘graper’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c fit_graper.cpp -o fit_graper.o
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/math/special_functions/digamma.hpp:15,
                 from graper_linear_dense_ff.h:2,
                 from fit_graper.cpp:4:
/home/biocbuild/bbs-3.19-bioc/R/site-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++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -llapack -L/home/biocbuild/bbs-3.19-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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=-860.179
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-561.919
ELB improved by 298.26

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-504.869
ELB improved by 57.0502

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-468.135
ELB improved by 36.7338

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.2
ELB improved by 16.9356

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.74
ELB improved by 7.45986

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.235
ELB improved by 4.50468

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.232
ELB improved by 4.00305

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.995
ELB improved by 4.23701

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.237
ELB improved by 4.75823

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.943
ELB improved by 5.29423

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.445
ELB improved by 5.49725

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.373
ELB improved by 5.072

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.347
ELB improved by 4.02643

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.562
ELB improved by 2.78454

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.753
ELB improved by 1.80944

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.554
ELB improved by 1.19928

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.69
ELB improved by 0.86344

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.001
ELB improved by 0.688994

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.403
ELB improved by 0.598414

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.852
ELB improved by 0.550598

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.327
ELB improved by 0.524726

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.818
ELB improved by 0.509434

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.32
ELB improved by 0.497882

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.834
ELB improved by 0.485802

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.364
ELB improved by 0.470744

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.912
ELB improved by 0.451712

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.483
ELB improved by 0.428811

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.08
ELB improved by 0.402858

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.705
ELB improved by 0.374995

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.359
ELB improved by 0.346402

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.041
ELB improved by 0.318134

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.75
ELB improved by 0.291048

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.484
ELB improved by 0.265806

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.241
ELB improved by 0.242894

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.018
ELB improved by 0.222675

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.813
ELB improved by 0.20546

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.621
ELB improved by 0.19164

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.439
ELB improved by 0.181927

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.261
ELB improved by 0.177895

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.078
ELB improved by 0.183396

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.869
ELB improved by 0.208615

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.588
ELB improved by 0.281189

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.128
ELB improved by 0.459981

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.357
ELB improved by 0.771638

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.176
ELB improved by 1.18059

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.647
ELB improved by 1.52911

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.259
ELB improved by 1.38817

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.116
ELB improved by 1.1426

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.173
ELB improved by 0.942722

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.42
ELB improved by 0.753372

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.846
ELB improved by 0.573681

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.428
ELB improved by 0.418654

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.129
ELB improved by 0.298403

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.917
ELB improved by 0.212294

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.764
ELB improved by 0.153071

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.651
ELB improved by 0.112525

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.567
ELB improved by 0.0842938

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.503
ELB improved by 0.0641765

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.453
ELB improved by 0.0495444

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.415
ELB improved by 0.0387392

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.384
ELB improved by 0.030676

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.359
ELB improved by 0.0246139

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.339
ELB improved by 0.0200285

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.323
ELB improved by 0.0165385

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.309
ELB improved by 0.0138627

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.297
ELB improved by 0.0117927

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.287
ELB improved by 0.0101744

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.278
ELB improved by 0.00889404

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-860.772
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-579.591
ELB improved by 281.181

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-520.423
ELB improved by 59.1681

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-479.373
ELB improved by 41.0496

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.227
ELB improved by 18.1459

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.35
ELB improved by 7.87663

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.273
ELB improved by 5.07699

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.755
ELB improved by 4.5184

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.25
ELB improved by 4.50531

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-434.726
ELB improved by 4.5242

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.436
ELB improved by 4.28986

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.774
ELB improved by 3.66128

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.995
ELB improved by 2.77971

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.046
ELB improved by 1.94831

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.704
ELB improved by 1.34262

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.75
ELB improved by 0.953804

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.038
ELB improved by 0.711654

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.476
ELB improved by 0.562671

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418
ELB improved by 0.475845

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.572
ELB improved by 0.427915

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.178
ELB improved by 0.393899

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.827
ELB improved by 0.351376

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.531
ELB improved by 0.296119

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.286
ELB improved by 0.244278

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.077
ELB improved by 0.209554

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.884
ELB improved by 0.192388

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.696
ELB improved by 0.188321

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.503
ELB improved by 0.193315

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.3
ELB improved by 0.202283

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.094
ELB improved by 0.206014

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.901
ELB improved by 0.193339

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.739
ELB improved by 0.162076

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.615
ELB improved by 0.123928

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.523
ELB improved by 0.0919151

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.453
ELB improved by 0.0700914

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.397
ELB improved by 0.0562799

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.349
ELB improved by 0.0473118

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.308
ELB improved by 0.0410152

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.272
ELB improved by 0.0362148

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.24
ELB improved by 0.0323251

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.211
ELB improved by 0.0290525

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.185
ELB improved by 0.0262381

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.161
ELB improved by 0.0237863

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.139
ELB improved by 0.0216324

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.119
ELB improved by 0.0197292

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.101
ELB improved by 0.0180399

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.085
ELB improved by 0.0165348

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.07
ELB improved by 0.0151896

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.056
ELB improved by 0.0139838

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.043
ELB improved by 0.0129001

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.031
ELB improved by 0.0119239

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.02
ELB improved by 0.0110426

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.01
ELB improved by 0.0102453

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414
ELB improved by 0.00952258

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-861.131
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-581.519
ELB improved by 279.612

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-523.324
ELB improved by 58.1946

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-481.649
ELB improved by 41.6755

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-459.149
ELB improved by 22.4996

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.27
ELB improved by 9.8793

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.088
ELB improved by 5.1814

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.087
ELB improved by 4.00115

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.202
ELB improved by 3.88527

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.015
ELB improved by 4.18663

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.31
ELB improved by 4.70559

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.14
ELB improved by 5.16992

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.994
ELB improved by 5.14578

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.582
ELB improved by 4.41211

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.253
ELB improved by 3.32914

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.907
ELB improved by 2.34574

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.337
ELB improved by 1.57014

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.314
ELB improved by 1.02302

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.629
ELB improved by 0.684899

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.143
ELB improved by 0.486141

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.777
ELB improved by 0.366192

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.487
ELB improved by 0.289861

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.247
ELB improved by 0.239667

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.041
ELB improved by 0.206555

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.856
ELB improved by 0.184865

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.685
ELB improved by 0.170866

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.523
ELB improved by 0.162261

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.365
ELB improved by 0.157601

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.209
ELB improved by 0.155613

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.055
ELB improved by 0.154677

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.902
ELB improved by 0.15293

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.753
ELB improved by 0.14929

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.608
ELB improved by 0.144396

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.468
ELB improved by 0.139944

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.331
ELB improved by 0.137174

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.195
ELB improved by 0.136327

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.058
ELB improved by 0.137096

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.918
ELB improved by 0.139104

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.776
ELB improved by 0.142075

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.631
ELB improved by 0.145828

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.48
ELB improved by 0.15023

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.325
ELB improved by 0.15517

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.165
ELB improved by 0.160568

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.998
ELB improved by 0.16641

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.825
ELB improved by 0.172777

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.646
ELB improved by 0.179862

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.458
ELB improved by 0.187942

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.26
ELB improved by 0.197333

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.052
ELB improved by 0.208351

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.831
ELB improved by 0.221293

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.594
ELB improved by 0.236477

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.34
ELB improved by 0.25434

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.064
ELB improved by 0.275706

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.762
ELB improved by 0.302346

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.424
ELB improved by 0.338156

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.033
ELB improved by 0.390965

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.561
ELB improved by 0.471809

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.982
ELB improved by 0.578366

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.313
ELB improved by 0.669671

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.593
ELB improved by 0.72019

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.829
ELB improved by 0.763278

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.031
ELB improved by 0.798663

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.261
ELB improved by 0.769906

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.591
ELB improved by 0.669945

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.052
ELB improved by 0.539264

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.642
ELB improved by 0.409355

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.336
ELB improved by 0.305809

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.112
ELB improved by 0.224483

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.955
ELB improved by 0.156824

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.849
ELB improved by 0.106358

iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.775
ELB improved by 0.0734735

iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.722
ELB improved by 0.0529326

iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.683
ELB improved by 0.0397356

iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.652
ELB improved by 0.0308574

iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.627
ELB improved by 0.0246405

iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.607
ELB improved by 0.0201466

iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.59
ELB improved by 0.0168129

iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.576
ELB improved by 0.0142843

iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.564
ELB improved by 0.0123287

iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.553
ELB improved by 0.0107899

iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.543
ELB improved by 0.00955984

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-863.484
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-589.202
ELB improved by 274.282

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-528.898
ELB improved by 60.3037

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-484.881
ELB improved by 44.0175

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.22
ELB improved by 22.6612

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.327
ELB improved by 9.89296

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.437
ELB improved by 5.88986

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.447
ELB improved by 4.98999

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.576
ELB improved by 4.87116

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.639
ELB improved by 4.93648

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.637
ELB improved by 5.00168

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.582
ELB improved by 5.0554

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.715
ELB improved by 4.86751

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.644
ELB improved by 4.07048

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.653
ELB improved by 2.99095

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.549
ELB improved by 2.10406

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.04
ELB improved by 1.50884

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.917
ELB improved by 1.12294

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.033
ELB improved by 0.884313

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.282
ELB improved by 0.750841

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.601
ELB improved by 0.681276

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.955
ELB improved by 0.645393

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.327
ELB improved by 0.627974

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.703
ELB improved by 0.624452

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.069
ELB improved by 0.633996

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.416
ELB improved by 0.652668

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.748
ELB improved by 0.66885

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.076
ELB improved by 0.671542

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.41
ELB improved by 0.665635

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.745
ELB improved by 0.665076

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.068
ELB improved by 0.677115

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.367
ELB improved by 0.701177

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.634
ELB improved by 0.732774

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.869
ELB improved by 0.764975

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.08
ELB improved by 0.789107

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.284
ELB improved by 0.796374

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.504
ELB improved by 0.780171

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.766
ELB improved by 0.73792

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.094
ELB improved by 0.671924

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.504
ELB improved by 0.589384

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.004
ELB improved by 0.500415

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.59
ELB improved by 0.41367

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.257
ELB improved by 0.33374

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.994
ELB improved by 0.262992

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.79
ELB improved by 0.203615

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.633
ELB improved by 0.15669

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.512
ELB improved by 0.121203

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.417
ELB improved by 0.0948597

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.342
ELB improved by 0.0752851

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.281
ELB improved by 0.0605856

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.232
ELB improved by 0.0493978

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.191
ELB improved by 0.0407691

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.157
ELB improved by 0.0340322

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.128
ELB improved by 0.028713

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.104
ELB improved by 0.0244695

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.083
ELB improved by 0.0210512

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.065
ELB improved by 0.0182728

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.049
ELB improved by 0.015995

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.034
ELB improved by 0.0141127

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.022
ELB improved by 0.0125452

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.011
ELB improved by 0.0112307

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.001
ELB improved by 0.0101208

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.991
ELB improved by 0.00917785

ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
> 
> proc.time()
   user  system elapsed 
  1.952   0.194   2.135 

Example timings

graper.Rcheck/graper-Ex.timings

nameusersystemelapsed
coef.graper0.0700.0110.082
getPIPs0.0600.0040.065
graper0.0860.0210.105
makeExampleData0.0070.0030.011
makeExampleDataWithUnequalGroups0.0050.0070.013
plotELBO0.2240.0360.260
plotGroupPenalties0.8570.0800.936
plotPosterior0.4680.0120.479
predict.graper2.0580.0692.126
print.graper0.0500.0140.065