Britta Velten
| Snapshot Date: 2025-09-25 13:45 -0400 (Thu, 25 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: devel |
| git_last_commit: 82b0592 |
| git_last_commit_date: 2025-06-24 03:15:40 -0400 (Tue, 24 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-26 12:03 -0400 (Fri, 26 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4831 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4619 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4563 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
| 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 913/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.25.2 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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: 1.25.2 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings graper_1.25.2.tar.gz |
| StartedAt: 2025-09-26 00:21:14 -0400 (Fri, 26 Sep 2025) |
| EndedAt: 2025-09-26 00:22:45 -0400 (Fri, 26 Sep 2025) |
| EllapsedTime: 91.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:graper.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings graper_1.25.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘graper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘graper’ version ‘1.25.2’
* 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 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
installed size is 6.0Mb
sub-directories of 1Mb or more:
libs 5.8Mb
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/graper.Rcheck/00check.log’
for details.
graper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL graper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘graper’ ... ** this is package ‘graper’ version ‘1.25.2’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c fit_graper.cpp -o fit_graper.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -llapack -L/home/biocbuild/bbs-3.22-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.22-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)
graper.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 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=-873.554
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-559.253
ELB improved by 314.301
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-501.947
ELB improved by 57.3056
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-472.21
ELB improved by 29.7368
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-460.286
ELB improved by 11.9242
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.047
ELB improved by 5.23909
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-451.573
ELB improved by 3.47377
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.553
ELB improved by 3.01998
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-445.595
ELB improved by 2.95811
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.548
ELB improved by 3.04687
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.346
ELB improved by 3.20197
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.03
ELB improved by 3.31671
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.799
ELB improved by 3.23049
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.967
ELB improved by 2.83268
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.765
ELB improved by 2.20165
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.209
ELB improved by 1.55596
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.151
ELB improved by 1.05783
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.426
ELB improved by 0.725542
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.918
ELB improved by 0.507216
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.555
ELB improved by 0.363476
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.284
ELB improved by 0.270913
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.073
ELB improved by 0.210822
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.903
ELB improved by 0.170623
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.76
ELB improved by 0.14278
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.637
ELB improved by 0.122697
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.53
ELB improved by 0.10756
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.434
ELB improved by 0.0956724
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.348
ELB improved by 0.0860089
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.27
ELB improved by 0.0779388
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.199
ELB improved by 0.0710617
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.134
ELB improved by 0.0651126
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.074
ELB improved by 0.0599087
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.018
ELB improved by 0.0553176
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.967
ELB improved by 0.0512404
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.92
ELB improved by 0.0475997
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.875
ELB improved by 0.0443342
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.834
ELB improved by 0.0413936
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.795
ELB improved by 0.0387364
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.759
ELB improved by 0.0363276
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.725
ELB improved by 0.0341375
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.693
ELB improved by 0.0321409
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.662
ELB improved by 0.0303158
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.634
ELB improved by 0.0286435
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.607
ELB improved by 0.0271074
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.581
ELB improved by 0.0256931
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.556
ELB improved by 0.0243881
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.533
ELB improved by 0.0231812
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.511
ELB improved by 0.0220627
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.49
ELB improved by 0.0210239
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.47
ELB improved by 0.0200571
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.451
ELB improved by 0.0191554
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.433
ELB improved by 0.0183128
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.415
ELB improved by 0.0175239
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.398
ELB improved by 0.0167837
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.382
ELB improved by 0.016088
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.367
ELB improved by 0.0154328
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.352
ELB improved by 0.0148147
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.338
ELB improved by 0.0142305
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.324
ELB improved by 0.0136775
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.311
ELB improved by 0.013153
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.298
ELB improved by 0.0126549
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.286
ELB improved by 0.0121811
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.274
ELB improved by 0.0117298
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.263
ELB improved by 0.0112994
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.252
ELB improved by 0.0108883
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.242
ELB improved by 0.0104952
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.232
ELB improved by 0.010119
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.222
ELB improved by 0.00975862
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-840.251
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-549.751
ELB improved by 290.5
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-490.034
ELB improved by 59.7161
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-454.314
ELB improved by 35.7205
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-439.101
ELB improved by 15.2131
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-433.005
ELB improved by 6.09608
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.124
ELB improved by 2.8802
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.353
ELB improved by 1.77129
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.067
ELB improved by 1.28648
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.015
ELB improved by 1.05193
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.076
ELB improved by 0.939178
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.186
ELB improved by 0.889936
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.309
ELB improved by 0.87636
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.425
ELB improved by 0.884775
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.517
ELB improved by 0.907891
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-420.576
ELB improved by 0.940361
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.601
ELB improved by 0.975732
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.596
ELB improved by 1.00457
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.581
ELB improved by 1.01488
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.585
ELB improved by 0.9963
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.638
ELB improved by 0.947193
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.758
ELB improved by 0.879388
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.944
ELB improved by 0.81469
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.169
ELB improved by 0.77412
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.398
ELB improved by 0.771195
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.577
ELB improved by 0.820883
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.646
ELB improved by 0.930843
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.612
ELB improved by 1.03489
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.56
ELB improved by 1.05178
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.564
ELB improved by 0.995862
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.659
ELB improved by 0.905029
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.838
ELB improved by 0.820754
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.07
ELB improved by 0.768339
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.321
ELB improved by 0.749297
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.564
ELB improved by 0.756285
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.794
ELB improved by 0.770571
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.044
ELB improved by 0.74928
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.372
ELB improved by 0.672185
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.787
ELB improved by 0.584775
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.269
ELB improved by 0.518388
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.798
ELB improved by 0.471159
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.359
ELB improved by 0.438616
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.94
ELB improved by 0.419363
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.526
ELB improved by 0.413722
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.102
ELB improved by 0.424108
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.645
ELB improved by 0.457324
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.116
ELB improved by 0.528648
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.458
ELB improved by 0.657863
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.645
ELB improved by 0.813212
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.772
ELB improved by 0.872654
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.937
ELB improved by 0.835298
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.144
ELB improved by 0.793354
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.377
ELB improved by 0.766919
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.611
ELB improved by 0.766283
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.781
ELB improved by 0.829177
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.802
ELB improved by 0.979593
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.543
ELB improved by 1.25898
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.947
ELB improved by 1.5958
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.455
ELB improved by 1.49216
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.443
ELB improved by 1.01158
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.833
ELB improved by 0.61063
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.465
ELB improved by 0.367308
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.225
ELB improved by 0.240517
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.049
ELB improved by 0.176039
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.912
ELB improved by 0.137064
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.803
ELB improved by 0.109086
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.715
ELB improved by 0.0879128
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.643
ELB improved by 0.0717584
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.584
ELB improved by 0.0593642
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.534
ELB improved by 0.049858
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.491
ELB improved by 0.0426371
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.454
ELB improved by 0.0372545
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.42
ELB improved by 0.0333686
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.39
ELB improved by 0.0307274
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.361
ELB improved by 0.0291621
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.332
ELB improved by 0.0285812
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.303
ELB improved by 0.0289581
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.273
ELB improved by 0.0303039
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.24
ELB improved by 0.0326085
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.204
ELB improved by 0.0357261
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.165
ELB improved by 0.0392063
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.123
ELB improved by 0.0421582
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.08
ELB improved by 0.0433752
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.038
ELB improved by 0.041894
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382
ELB improved by 0.0376897
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.968
ELB improved by 0.031787
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.943
ELB improved by 0.0256013
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.922
ELB improved by 0.02018
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.907
ELB improved by 0.0159423
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.894
ELB improved by 0.0128466
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.883
ELB improved by 0.0106556
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.874
ELB improved by 0.00911101
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-857.792
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-554.744
ELB improved by 303.048
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-493.684
ELB improved by 61.0597
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-455.231
ELB improved by 38.4531
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.045
ELB improved by 17.1868
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-430.911
ELB improved by 7.13389
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.047
ELB improved by 3.86325
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.533
ELB improved by 2.5148
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.658
ELB improved by 1.87431
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.081
ELB improved by 1.577
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-419.615
ELB improved by 1.46595
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.147
ELB improved by 1.46838
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-416.597
ELB improved by 1.55034
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-414.903
ELB improved by 1.69412
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.021
ELB improved by 1.88189
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.941
ELB improved by 2.07994
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.713
ELB improved by 2.22788
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.462
ELB improved by 2.25131
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.351
ELB improved by 2.11037
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.507
ELB improved by 1.84442
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.96
ELB improved by 1.5467
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.67
ELB improved by 1.28998
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.575
ELB improved by 1.09547
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.617
ELB improved by 0.95811
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.743
ELB improved by 0.87307
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.905
ELB improved by 0.838491
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.064
ELB improved by 0.840635
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.221
ELB improved by 0.843443
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.407
ELB improved by 0.813659
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.649
ELB improved by 0.758539
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.944
ELB improved by 0.704363
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.283
ELB improved by 0.661178
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.656
ELB improved by 0.626965
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.057
ELB improved by 0.59877
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.479
ELB improved by 0.578697
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.898
ELB improved by 0.580558
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.259
ELB improved by 0.639576
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.472
ELB improved by 0.786894
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.549
ELB improved by 0.922198
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.628
ELB improved by 0.921433
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.781
ELB improved by 0.846815
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.959
ELB improved by 0.822443
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.099
ELB improved by 0.860271
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.175
ELB improved by 0.923031
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.262
ELB improved by 0.913311
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.487
ELB improved by 0.774971
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.804
ELB improved by 0.683204
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-379.224
ELB improved by 0.580429
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.847
ELB improved by 0.376079
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.645
ELB improved by 0.202518
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.528
ELB improved by 0.116688
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.447
ELB improved by 0.0809591
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.382
ELB improved by 0.0652977
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.325
ELB improved by 0.0572345
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.273
ELB improved by 0.0520812
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.225
ELB improved by 0.0477665
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.182
ELB improved by 0.0431781
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.144
ELB improved by 0.0378982
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.112
ELB improved by 0.032193
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.085
ELB improved by 0.0267154
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.063
ELB improved by 0.0220282
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.045
ELB improved by 0.0183426
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.029
ELB improved by 0.0155718
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.016
ELB improved by 0.0135063
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.004
ELB improved by 0.0119396
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.993
ELB improved by 0.0107147
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.983
ELB improved by 0.00972603
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-884.956
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-583.076
ELB improved by 301.88
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-517.543
ELB improved by 65.5334
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-475.795
ELB improved by 41.7479
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-458.412
ELB improved by 17.3827
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-449.949
ELB improved by 8.46372
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.225
ELB improved by 6.72372
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.549
ELB improved by 6.67595
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.827
ELB improved by 6.72168
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-423.678
ELB improved by 6.14894
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.772
ELB improved by 4.90673
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.284
ELB improved by 3.48717
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-412.919
ELB improved by 2.36552
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.275
ELB improved by 1.64416
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-410.055
ELB improved by 1.21974
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.074
ELB improved by 0.980687
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.222
ELB improved by 0.852617
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.429
ELB improved by 0.792438
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.653
ELB improved by 0.776666
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.86
ELB improved by 0.792621
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-405.027
ELB improved by 0.833305
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.132
ELB improved by 0.89493
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.156
ELB improved by 0.975974
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.079
ELB improved by 1.07668
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.882
ELB improved by 1.19723
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.55
ELB improved by 1.33197
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.089
ELB improved by 1.46038
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.541
ELB improved by 1.54881
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.969
ELB improved by 1.57161
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.443
ELB improved by 1.5259
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-392.013
ELB improved by 1.42994
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.704
ELB improved by 1.30966
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.568
ELB improved by 1.13534
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.729
ELB improved by 0.838965
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.185
ELB improved by 0.544363
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.821
ELB improved by 0.364123
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.555
ELB improved by 0.266035
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.348
ELB improved by 0.206755
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.183
ELB improved by 0.16475
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.052
ELB improved by 0.131353
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.948
ELB improved by 0.104056
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.865
ELB improved by 0.0823984
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.8
ELB improved by 0.0657976
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.746
ELB improved by 0.0532463
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.703
ELB improved by 0.0437089
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.666
ELB improved by 0.0363628
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.636
ELB improved by 0.0306185
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.61
ELB improved by 0.0260635
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.587
ELB improved by 0.0224068
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.568
ELB improved by 0.0194388
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.551
ELB improved by 0.0170059
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.536
ELB improved by 0.0149936
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.522
ELB improved by 0.0133149
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.511
ELB improved by 0.0119036
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.5
ELB improved by 0.010708
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.49
ELB improved by 0.00968811
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.104 0.196 2.286
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.053 | 0.008 | 0.062 | |
| getPIPs | 0.050 | 0.002 | 0.051 | |
| graper | 0.083 | 0.002 | 0.086 | |
| makeExampleData | 0.009 | 0.001 | 0.011 | |
| makeExampleDataWithUnequalGroups | 0.013 | 0.002 | 0.013 | |
| plotELBO | 0.336 | 0.020 | 0.358 | |
| plotGroupPenalties | 1.202 | 0.049 | 1.251 | |
| plotPosterior | 0.657 | 0.011 | 0.668 | |
| predict.graper | 2.065 | 0.016 | 2.080 | |
| print.graper | 0.050 | 0.002 | 0.052 | |