Britta Velten
| Snapshot Date: 2024-05-21 14:00:15 -0400 (Tue, 21 May 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) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-22 11:35:43 -0400 (Wed, 22 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4751 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 3444 |
| 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 908/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.20.0 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: graper |
| Version: 1.20.0 |
| Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:graper.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings graper_1.20.0.tar.gz |
| StartedAt: 2024-05-22 02:36:12 -0400 (Wed, 22 May 2024) |
| EndedAt: 2024-05-22 02:37:41 -0400 (Wed, 22 May 2024) |
| EllapsedTime: 89.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:graper.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings graper_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/graper.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'graper/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'graper' version '1.20.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'graper' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) predict.graper.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.graper.Rd:23-24: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.19-bioc/R/library/graper/libs/x64/graper.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
'F:/biocbuild/bbs-3.19-bioc/meat/graper.Rcheck/00check.log'
for details.
graper.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL graper
###
##############################################################################
##############################################################################
* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'graper' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
using C++11
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BH/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BH/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fit_graper.cpp -o fit_graper.o
In file included from F:/biocbuild/bbs-3.19-bioc/R/library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11,
from F:/biocbuild/bbs-3.19-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
from F:/biocbuild/bbs-3.19-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:15,
from graper_linear_dense_ff.h:2,
from fit_graper.cpp:4:
F:/biocbuild/bbs-3.19-bioc/R/library/BH/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
| ^~~~~~~
g++ -shared -s -static-libgcc -o graper.dll tmp.def RcppExports.o fit_graper.o -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-graper/00new/graper/libs/x64
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (graper)
graper.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24 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=-902.902
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-580.546
ELB improved by 322.356
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-523.612
ELB improved by 56.9335
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-484.432
ELB improved by 39.1809
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.164
ELB improved by 19.2672
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-456.938
ELB improved by 8.22587
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.204
ELB improved by 4.73403
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.387
ELB improved by 3.81708
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-444.764
ELB improved by 3.62335
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-441.052
ELB improved by 3.71181
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.245
ELB improved by 3.80758
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.505
ELB improved by 3.73998
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.997
ELB improved by 3.50733
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.711
ELB improved by 3.28655
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.591
ELB improved by 3.11932
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.922
ELB improved by 2.66922
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.941
ELB improved by 1.98107
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.476
ELB improved by 1.46526
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.309
ELB improved by 1.16729
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.351
ELB improved by 0.957806
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.567
ELB improved by 0.783758
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.891
ELB improved by 0.67642
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.254
ELB improved by 0.636876
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.619
ELB improved by 0.634399
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.976
ELB improved by 0.643111
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.323
ELB improved by 0.653269
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.658
ELB improved by 0.664693
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.972
ELB improved by 0.68638
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.225
ELB improved by 0.746895
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.339
ELB improved by 0.885869
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.293
ELB improved by 1.04657
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.232
ELB improved by 1.06082
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.25
ELB improved by 0.981568
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.322
ELB improved by 0.927924
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.415
ELB improved by 0.906774
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.518
ELB improved by 0.897022
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.636
ELB improved by 0.882647
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.781
ELB improved by 0.854281
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.972
ELB improved by 0.809579
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.217
ELB improved by 0.755157
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.506
ELB improved by 0.711171
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.782
ELB improved by 0.72408
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.885
ELB improved by 0.896411
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.631
ELB improved by 1.25408
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.34
ELB improved by 1.29119
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.19
ELB improved by 1.15002
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.084
ELB improved by 1.10589
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.252
ELB improved by 0.831879
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.657
ELB improved by 0.594933
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.151
ELB improved by 0.506164
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.706
ELB improved by 0.445308
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.32
ELB improved by 0.385399
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.962
ELB improved by 0.358568
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.609
ELB improved by 0.352355
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.275
ELB improved by 0.334412
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.982
ELB improved by 0.293045
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.755
ELB improved by 0.227017
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.604
ELB improved by 0.150539
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.516
ELB improved by 0.0887964
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.465
ELB improved by 0.0500968
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.437
ELB improved by 0.0288611
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.419
ELB improved by 0.0178753
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.406
ELB improved by 0.0122646
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.397
ELB improved by 0.00932878
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-816.363
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-577.935
ELB improved by 238.429
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-517.562
ELB improved by 60.3725
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-470.71
ELB improved by 46.8525
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.11
ELB improved by 22.5995
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.872
ELB improved by 8.23845
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-435.242
ELB improved by 4.62923
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.245
ELB improved by 3.99746
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.95
ELB improved by 4.29514
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.856
ELB improved by 5.09369
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.772
ELB improved by 6.08401
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.207
ELB improved by 6.56521
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.398
ELB improved by 5.809
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.265
ELB improved by 4.13275
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.706
ELB improved by 2.55936
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.145
ELB improved by 1.56068
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.116
ELB improved by 1.0286
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.357
ELB improved by 0.75976
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.736
ELB improved by 0.620997
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.193
ELB improved by 0.543185
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.699
ELB improved by 0.493068
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.244
ELB improved by 0.455059
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.822
ELB improved by 0.422094
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.431
ELB improved by 0.391262
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.069
ELB improved by 0.361641
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.736
ELB improved by 0.333173
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.43
ELB improved by 0.306074
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.15
ELB improved by 0.280563
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.893
ELB improved by 0.256775
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.658
ELB improved by 0.234758
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.444
ELB improved by 0.214497
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.248
ELB improved by 0.195958
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.069
ELB improved by 0.179101
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.905
ELB improved by 0.163905
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.754
ELB improved by 0.150376
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.616
ELB improved by 0.138573
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.487
ELB improved by 0.128635
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.366
ELB improved by 0.120863
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.25
ELB improved by 0.115865
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.135
ELB improved by 0.114886
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.015
ELB improved by 0.12047
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.877
ELB improved by 0.1376
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.703
ELB improved by 0.173927
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.472
ELB improved by 0.230952
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.194
ELB improved by 0.277963
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.925
ELB improved by 0.269288
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.701
ELB improved by 0.223833
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.519
ELB improved by 0.182327
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.367
ELB improved by 0.152403
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.237
ELB improved by 0.130051
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.124
ELB improved by 0.112448
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.026
ELB improved by 0.098213
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.939
ELB improved by 0.0865587
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.862
ELB improved by 0.0769457
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.793
ELB improved by 0.0689549
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.731
ELB improved by 0.0622307
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.675
ELB improved by 0.056452
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.623
ELB improved by 0.0513282
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.577
ELB improved by 0.0466131
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.535
ELB improved by 0.0421289
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.497
ELB improved by 0.0377828
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.463
ELB improved by 0.0335634
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.434
ELB improved by 0.0295171
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.408
ELB improved by 0.025714
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.386
ELB improved by 0.0222185
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.367
ELB improved by 0.0190729
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.351
ELB improved by 0.0162934
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.337
ELB improved by 0.0138739
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.325
ELB improved by 0.0117933
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.315
ELB improved by 0.0100214
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.306
ELB improved by 0.00852413
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-840.681
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-571.803
ELB improved by 268.878
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-513.514
ELB improved by 58.2889
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-478.326
ELB improved by 35.1881
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.576
ELB improved by 16.7502
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.265
ELB improved by 7.31054
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.926
ELB improved by 4.339
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-446.356
ELB improved by 3.57035
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.031
ELB improved by 3.32471
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.797
ELB improved by 3.23375
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.602
ELB improved by 3.19513
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.478
ELB improved by 3.12452
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.558
ELB improved by 2.91997
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.049
ELB improved by 2.50863
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.108
ELB improved by 1.94066
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.73
ELB improved by 1.37863
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.782
ELB improved by 0.947413
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.116
ELB improved by 0.666163
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.619
ELB improved by 0.497424
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.22
ELB improved by 0.398716
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.88
ELB improved by 0.340358
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.575
ELB improved by 0.30506
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.291
ELB improved by 0.283491
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.02
ELB improved by 0.270735
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.756
ELB improved by 0.264202
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.494
ELB improved by 0.262547
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.228
ELB improved by 0.265176
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.956
ELB improved by 0.272079
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.673
ELB improved by 0.283837
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.371
ELB improved by 0.30172
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.043
ELB improved by 0.327646
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.68
ELB improved by 0.363541
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.27
ELB improved by 0.409651
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.807
ELB improved by 0.463103
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.287
ELB improved by 0.520334
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.704
ELB improved by 0.582346
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.048
ELB improved by 0.655927
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.296
ELB improved by 0.751761
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.416
ELB improved by 0.880977
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.38
ELB improved by 1.03563
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.224
ELB improved by 1.15542
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.05
ELB improved by 1.17404
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.952
ELB improved by 1.09825
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.992
ELB improved by 0.960119
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.204
ELB improved by 0.787928
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.59
ELB improved by 0.613793
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.125
ELB improved by 0.465017
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.77
ELB improved by 0.355337
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.483
ELB improved by 0.286979
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.226
ELB improved by 0.256667
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.97
ELB improved by 0.256033
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.705
ELB improved by 0.264947
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.451
ELB improved by 0.254711
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.237
ELB improved by 0.213926
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.077
ELB improved by 0.159262
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.966
ELB improved by 0.111388
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.889
ELB improved by 0.0775757
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.833
ELB improved by 0.0558154
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.791
ELB improved by 0.0421243
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.757
ELB improved by 0.0333627
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.73
ELB improved by 0.027528
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.706
ELB improved by 0.023438
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.686
ELB improved by 0.0204147
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.668
ELB improved by 0.0180709
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.652
ELB improved by 0.0161826
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.637
ELB improved by 0.0146166
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.624
ELB improved by 0.0132909
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.612
ELB improved by 0.0121523
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.6
ELB improved by 0.0111647
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.59
ELB improved by 0.0103023
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.58
ELB improved by 0.0095457
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-854.448
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-558.363
ELB improved by 296.085
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-497.977
ELB improved by 60.3859
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.234
ELB improved by 36.7431
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.077
ELB improved by 16.1572
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-437.695
ELB improved by 7.38122
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.011
ELB improved by 4.68446
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.142
ELB improved by 3.8687
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.477
ELB improved by 3.66526
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.745
ELB improved by 3.73181
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.779
ELB improved by 3.96643
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.484
ELB improved by 4.29427
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.96
ELB improved by 4.52466
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.619
ELB improved by 4.34077
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.015
ELB improved by 3.60412
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.411
ELB improved by 2.6034
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.659
ELB improved by 1.75257
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.451
ELB improved by 1.20791
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.542
ELB improved by 0.909245
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.782
ELB improved by 0.759234
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.091
ELB improved by 0.691017
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.424
ELB improved by 0.667126
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.757
ELB improved by 0.667699
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.074
ELB improved by 0.682552
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.366
ELB improved by 0.707628
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.622
ELB improved by 0.744589
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.819
ELB improved by 0.80253
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.921
ELB improved by 0.898392
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.878
ELB improved by 1.04317
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.667
ELB improved by 1.21099
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.304
ELB improved by 1.36265
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.795
ELB improved by 1.50961
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.125
ELB improved by 1.66979
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.313
ELB improved by 1.81174
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.446
ELB improved by 1.8671
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.67
ELB improved by 1.77562
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.137
ELB improved by 1.53326
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.933
ELB improved by 1.20386
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-372.059
ELB improved by 0.87432
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.455
ELB improved by 0.603752
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-371.045
ELB improved by 0.410131
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.762
ELB improved by 0.282896
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.56
ELB improved by 0.201711
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.411
ELB improved by 0.148919
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.298
ELB improved by 0.113208
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.21
ELB improved by 0.0885296
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.138
ELB improved by 0.0718237
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.077
ELB improved by 0.061291
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-370.021
ELB improved by 0.0555739
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.968
ELB improved by 0.053393
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.914
ELB improved by 0.0531906
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.862
ELB improved by 0.052896
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.811
ELB improved by 0.050498
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.765
ELB improved by 0.0455654
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.726
ELB improved by 0.0399419
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.689
ELB improved by 0.0361983
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.654
ELB improved by 0.0357313
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.615
ELB improved by 0.0383442
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.573
ELB improved by 0.0423811
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.528
ELB improved by 0.0447331
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.486
ELB improved by 0.042176
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.452
ELB improved by 0.034398
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.427
ELB improved by 0.0246451
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.411
ELB improved by 0.0163443
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.4
ELB improved by 0.0106914
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-369.393
ELB improved by 0.00727469
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.15 0.32 2.68
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.06 | 0.02 | 0.95 | |
| getPIPs | 0.05 | 0.01 | 0.06 | |
| graper | 0.07 | 0.00 | 0.08 | |
| makeExampleData | 0.02 | 0.00 | 0.01 | |
| makeExampleDataWithUnequalGroups | 0.02 | 0.00 | 0.02 | |
| plotELBO | 0.23 | 0.02 | 0.25 | |
| plotGroupPenalties | 0.87 | 0.12 | 1.00 | |
| plotPosterior | 0.44 | 0.05 | 0.48 | |
| predict.graper | 1.75 | 0.03 | 1.78 | |
| print.graper | 0.08 | 0.00 | 0.08 | |