Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:05:42 -0400 (Fri, 15 Oct 2021).

CHECK results for graper on nebbiolo1

To the developers/maintainers of the graper package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 804/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
graper 1.8.0  (landing page)
Britta Velten
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/graper
git_branch: RELEASE_3_13
git_last_commit: f94ff44
git_last_commit_date: 2021-05-19 12:40:09 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: graper
Version: 1.8.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings graper_1.8.0.tar.gz
StartedAt: 2021-10-14 10:05:04 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 10:05:52 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 48.0 seconds
RetCode: 0
Status:   OK  
CheckDir: graper.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings graper_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/graper.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.8.0’
* 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
* 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 R 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 ... OK
* 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/graper.Rcheck/00check.log’
for details.

Installation output

graper.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL graper
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘graper’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/find_if.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/find.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/contains.hpp:20,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/policies/policy.hpp:10,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
                 from /home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.13-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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=-866.134
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-593.987
ELB improved by 272.147

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-533.075
ELB improved by 60.9122

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-488.648
ELB improved by 44.4265

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-466.379
ELB improved by 22.2695

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.426
ELB improved by 9.9525

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.733
ELB improved by 5.693

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.604
ELB improved by 4.12869

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.948
ELB improved by 3.65598

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.475
ELB improved by 3.47389

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.147
ELB improved by 3.32766

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.021
ELB improved by 3.12576

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.182
ELB improved by 2.8389

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.685
ELB improved by 2.49764

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.544
ELB improved by 2.1404

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.813
ELB improved by 1.73099

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.539
ELB improved by 1.27428

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.645
ELB improved by 0.894212

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.002
ELB improved by 0.642609

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.517
ELB improved by 0.485314

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.132
ELB improved by 0.384349

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.814
ELB improved by 0.318309

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.538
ELB improved by 0.276335

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.287
ELB improved by 0.250845

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.051
ELB improved by 0.236107

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.822
ELB improved by 0.228476

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.596
ELB improved by 0.225903

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.369
ELB improved by 0.227282

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.137
ELB improved by 0.232029

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.897
ELB improved by 0.239907

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.646
ELB improved by 0.250991

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.381
ELB improved by 0.265721

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.096
ELB improved by 0.284992

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.785
ELB improved by 0.310194

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.442
ELB improved by 0.342964

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.058
ELB improved by 0.384302

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.625
ELB improved by 0.433303

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.137
ELB improved by 0.487791

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.588
ELB improved by 0.548911

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.963
ELB improved by 0.625402

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.229
ELB improved by 0.733191

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.335
ELB improved by 0.894106

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.202
ELB improved by 1.1335

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.739
ELB improved by 1.46265

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.929
ELB improved by 1.80986

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.928
ELB improved by 2.00176

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.95
ELB improved by 1.97808

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.147
ELB improved by 1.8023

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.579
ELB improved by 1.56867

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.179
ELB improved by 1.39924

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.871
ELB improved by 1.30789

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.845
ELB improved by 1.0264

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.192
ELB improved by 0.652718

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.785
ELB improved by 0.407734

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.508
ELB improved by 0.276884

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.297
ELB improved by 0.210826

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.124
ELB improved by 0.172472

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.984
ELB improved by 0.14029

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.876
ELB improved by 0.108583

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.795
ELB improved by 0.0800737

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.738
ELB improved by 0.057661

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.696
ELB improved by 0.0417832

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.665
ELB improved by 0.0311842

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.641
ELB improved by 0.0242069

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.621
ELB improved by 0.0195074

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.605
ELB improved by 0.0161991

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.591
ELB improved by 0.0137531

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.579
ELB improved by 0.0118658

iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.569
ELB improved by 0.0103625

iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.56
ELB improved by 0.00913866

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-861.928
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-576.572
ELB improved by 285.356

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-514.133
ELB improved by 62.4389

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.628
ELB improved by 41.5053

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.671
ELB improved by 16.9572

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.824
ELB improved by 6.84707

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.488
ELB improved by 4.33522

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.815
ELB improved by 3.67349

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.284
ELB improved by 3.53098

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.748
ELB improved by 3.53612

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.238
ELB improved by 3.50929

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.934
ELB improved by 3.30448

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.097
ELB improved by 2.83703

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.914
ELB improved by 2.18273

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.375
ELB improved by 1.539

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.33
ELB improved by 1.04483

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.625
ELB improved by 0.705505

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.151
ELB improved by 0.47434

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.83
ELB improved by 0.320888

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.605
ELB improved by 0.22511

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.437
ELB improved by 0.167235

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.306
ELB improved by 0.131588

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.197
ELB improved by 0.108444

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.105
ELB improved by 0.0924302

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.024
ELB improved by 0.0806529

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.953
ELB improved by 0.071522

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.889
ELB improved by 0.0641372

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.831
ELB improved by 0.057974

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.778
ELB improved by 0.0527197

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.73
ELB improved by 0.0481815

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.685
ELB improved by 0.0442327

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.645
ELB improved by 0.0407818

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.607
ELB improved by 0.0377557

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.572
ELB improved by 0.0350922

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.539
ELB improved by 0.0327366

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.508
ELB improved by 0.0306418

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.48
ELB improved by 0.0287678

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.453
ELB improved by 0.0270808

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.427
ELB improved by 0.0255532

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.403
ELB improved by 0.0241625

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.38
ELB improved by 0.0228902

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.358
ELB improved by 0.021721

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.338
ELB improved by 0.0206425

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.318
ELB improved by 0.019644

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.299
ELB improved by 0.0187169

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.281
ELB improved by 0.0178535

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.264
ELB improved by 0.0170473

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.248
ELB improved by 0.0162927

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.232
ELB improved by 0.0155848

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.218
ELB improved by 0.0149193

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.203
ELB improved by 0.0142924

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.19
ELB improved by 0.0137008

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.176
ELB improved by 0.0131416

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.164
ELB improved by 0.0126121

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.152
ELB improved by 0.0121099

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.14
ELB improved by 0.0116331

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.129
ELB improved by 0.0111797

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.118
ELB improved by 0.0107482

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.108
ELB improved by 0.010337

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.098
ELB improved by 0.00994482

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-892.641
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-589.251
ELB improved by 303.39

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-528.521
ELB improved by 60.7307

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-483.889
ELB improved by 44.6313

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.31
ELB improved by 22.5791

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.303
ELB improved by 9.00675

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-447.716
ELB improved by 4.58786

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.631
ELB improved by 3.08444

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.188
ELB improved by 2.44271

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.992
ELB improved by 2.19599

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.839
ELB improved by 2.15358

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.618
ELB improved by 2.22116

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.268
ELB improved by 2.35009

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.758
ELB improved by 2.50936

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.092
ELB improved by 2.66579

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.331
ELB improved by 2.7612

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.633
ELB improved by 2.69855

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.233
ELB improved by 2.39936

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.317
ELB improved by 1.91619

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.906
ELB improved by 1.41116

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.897
ELB improved by 1.0091

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.164
ELB improved by 0.732338

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.616
ELB improved by 0.548713

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.191
ELB improved by 0.424992

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.851
ELB improved by 0.33964

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.573
ELB improved by 0.278518

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.34
ELB improved by 0.232416

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.144
ELB improved by 0.196119

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.977
ELB improved by 0.166895

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.834
ELB improved by 0.143116

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.71
ELB improved by 0.123611

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.603
ELB improved by 0.107471

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.509
ELB improved by 0.0939999

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.426
ELB improved by 0.0826649

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.353
ELB improved by 0.0730578

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.288
ELB improved by 0.0648608

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.231
ELB improved by 0.0578237

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.179
ELB improved by 0.0517479

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.132
ELB improved by 0.0464743

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.09
ELB improved by 0.0418749

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.053
ELB improved by 0.0378456

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.018
ELB improved by 0.0343012

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.987
ELB improved by 0.0311717

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.959
ELB improved by 0.0283988

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.933
ELB improved by 0.0259342

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.909
ELB improved by 0.0237371

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.887
ELB improved by 0.0217731

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.867
ELB improved by 0.0200129

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.849
ELB improved by 0.0184316

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.832
ELB improved by 0.017008

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.816
ELB improved by 0.0157235

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.802
ELB improved by 0.0145624

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.788
ELB improved by 0.0135108

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.776
ELB improved by 0.0125566

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.764
ELB improved by 0.0116896

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.753
ELB improved by 0.0109003

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.743
ELB improved by 0.0101808

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.733
ELB improved by 0.0095239

ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-841.395
ELB improved by inf

iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-566.154
ELB improved by 275.241

iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-508.587
ELB improved by 57.5668

iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-469.646
ELB improved by 38.9412

iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-450.126
ELB improved by 19.52

iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.913
ELB improved by 9.2126

iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.673
ELB improved by 5.23974

iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.571
ELB improved by 4.10255

iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.642
ELB improved by 3.92936

iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.58
ELB improved by 4.06148

iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.326
ELB improved by 4.25459

iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.012
ELB improved by 4.31394

iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.942
ELB improved by 4.07001

iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.396
ELB improved by 3.54584

iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.404
ELB improved by 2.99157

iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.908
ELB improved by 2.49596

iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.015
ELB improved by 1.89359

iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.703
ELB improved by 1.31157

iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.808
ELB improved by 0.894709

iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.173
ELB improved by 0.634893

iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.692
ELB improved by 0.481499

iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.301
ELB improved by 0.390735

iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.966
ELB improved by 0.335243

iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.666
ELB improved by 0.300102

iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.388
ELB improved by 0.277433

iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.126
ELB improved by 0.262837

iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.872
ELB improved by 0.2535

iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.625
ELB improved by 0.247523

iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.38
ELB improved by 0.244204

iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.136
ELB improved by 0.244543

iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.885
ELB improved by 0.251158

iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.617
ELB improved by 0.267668

iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.319
ELB improved by 0.29839

iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.968
ELB improved by 0.350142

iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.53
ELB improved by 0.438885

iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.943
ELB improved by 0.586782

iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.186
ELB improved by 0.757093

iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.343
ELB improved by 0.842957

iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.472
ELB improved by 0.87062

iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.569
ELB improved by 0.903053

iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.63
ELB improved by 0.939331

iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.657
ELB improved by 0.973004

iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.663
ELB improved by 0.993848

iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.677
ELB improved by 0.985995

iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.74
ELB improved by 0.936579

iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.897
ELB improved by 0.843058

iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.181
ELB improved by 0.716483

iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.603
ELB improved by 0.577827

iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.154
ELB improved by 0.448502

iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.812
ELB improved by 0.341934

iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.551
ELB improved by 0.261559

iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.347
ELB improved by 0.204078

iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.183
ELB improved by 0.163697

iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.048
ELB improved by 0.134721

iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.936
ELB improved by 0.112461

iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.842
ELB improved by 0.0935531

iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.766
ELB improved by 0.0763355

iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.705
ELB improved by 0.0607977

iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.658
ELB improved by 0.0476513

iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.62
ELB improved by 0.0372938

iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.591
ELB improved by 0.0295236

iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.567
ELB improved by 0.0238156

iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.547
ELB improved by 0.0196197

iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.531
ELB improved by 0.0164923

iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.517
ELB improved by 0.0141128

iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.505
ELB improved by 0.0122605

iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.494
ELB improved by 0.0107859

iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.484
ELB improved by 0.00958764

ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
> 
> proc.time()
   user  system elapsed 
  2.072   0.134   2.189

Example timings

graper.Rcheck/graper-Ex.timings

nameusersystemelapsed
coef.graper0.0490.0190.071
getPIPs0.0490.0160.064
graper0.0840.0200.104
makeExampleData0.0110.0000.011
makeExampleDataWithUnequalGroups0.0080.0040.012
plotELBO0.1780.0160.194
plotGroupPenalties0.5410.0160.557
plotPosterior0.6580.0320.690
predict.graper1.9310.0681.999
print.graper0.0500.0110.062