Britta Velten
| Snapshot Date: 2025-11-13 13:45 -0500 (Thu, 13 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/graper |
| git_branch: RELEASE_3_22 |
| git_last_commit: 76fc31b |
| git_last_commit_date: 2025-10-29 10:49:21 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-14 11:58 -0500 (Fri, 14 Nov 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" | 4903 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 922/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graper 1.26.0 (landing page) Britta Velten
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | 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: 1.26.0 |
| 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_1.26.0.tar.gz |
| StartedAt: 2025-11-14 00:21:50 -0500 (Fri, 14 Nov 2025) |
| EndedAt: 2025-11-14 00:23:20 -0500 (Fri, 14 Nov 2025) |
| EllapsedTime: 90.1 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_1.26.0.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 ‘1.26.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graper’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 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 ‘1.26.0’ ** 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=-877.677
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-579.524
ELB improved by 298.153
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-520.488
ELB improved by 59.036
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-481.822
ELB improved by 38.6657
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-465.338
ELB improved by 16.4844
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-457.992
ELB improved by 7.34617
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-452.833
ELB improved by 5.15828
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-448.062
ELB improved by 4.77156
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-442.959
ELB improved by 5.10247
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.997
ELB improved by 5.96215
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-429.727
ELB improved by 7.26971
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.282
ELB improved by 8.44592
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.291
ELB improved by 7.99104
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.513
ELB improved by 5.77787
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.857
ELB improved by 3.65568
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.402
ELB improved by 2.45461
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.572
ELB improved by 1.82994
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.082
ELB improved by 1.49024
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-396.79
ELB improved by 1.29251
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.597
ELB improved by 1.19263
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.417
ELB improved by 1.18012
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.192
ELB improved by 1.22534
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.888
ELB improved by 1.30312
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.486
ELB improved by 1.4026
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.966
ELB improved by 1.52027
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.315
ELB improved by 1.65069
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.538
ELB improved by 1.7767
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.676
ELB improved by 1.86232
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-381.818
ELB improved by 1.85793
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-380.09
ELB improved by 1.72827
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-378.589
ELB improved by 1.50078
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-377.315
ELB improved by 1.2736
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-376.253
ELB improved by 1.06246
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.502
ELB improved by 0.750645
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-375.042
ELB improved by 0.460293
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.742
ELB improved by 0.299485
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.521
ELB improved by 0.220977
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.339
ELB improved by 0.182823
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.171
ELB improved by 0.168051
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-374.005
ELB improved by 0.165737
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.846
ELB improved by 0.158848
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.714
ELB improved by 0.132364
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.62
ELB improved by 0.0939276
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.558
ELB improved by 0.0617005
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.516
ELB improved by 0.0415729
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.486
ELB improved by 0.0302786
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.462
ELB improved by 0.0238403
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.442
ELB improved by 0.0198508
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.425
ELB improved by 0.0171135
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.41
ELB improved by 0.0150669
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.397
ELB improved by 0.0134438
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.385
ELB improved by 0.0121081
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.374
ELB improved by 0.010983
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.364
ELB improved by 0.0100202
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-373.355
ELB improved by 0.00918675
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-827.343
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-570.455
ELB improved by 256.889
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-509.212
ELB improved by 61.2426
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-462.851
ELB improved by 46.3609
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-440.655
ELB improved by 22.1962
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.492
ELB improved by 9.16272
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-426.223
ELB improved by 5.26898
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-422.227
ELB improved by 3.99677
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.631
ELB improved by 3.59579
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.067
ELB improved by 3.56397
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.359
ELB improved by 3.70814
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.388
ELB improved by 3.97087
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.111
ELB improved by 4.2769
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-398.712
ELB improved by 4.39904
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-394.689
ELB improved by 4.02338
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.559
ELB improved by 3.13
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.426
ELB improved by 2.1325
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.036
ELB improved by 1.39038
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-387.129
ELB improved by 0.906284
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.547
ELB improved by 0.582485
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-386.16
ELB improved by 0.386711
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.881
ELB improved by 0.279568
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.661
ELB improved by 0.219584
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.478
ELB improved by 0.183189
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.319
ELB improved by 0.159128
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.177
ELB improved by 0.141961
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-385.048
ELB improved by 0.128931
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.929
ELB improved by 0.118566
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.819
ELB improved by 0.110037
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.716
ELB improved by 0.102845
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.62
ELB improved by 0.0966645
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.528
ELB improved by 0.0912706
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.442
ELB improved by 0.0864962
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.36
ELB improved by 0.0822125
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.281
ELB improved by 0.0783173
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.207
ELB improved by 0.0747281
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.135
ELB improved by 0.0713779
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.067
ELB improved by 0.0682131
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-384.002
ELB improved by 0.0651907
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.94
ELB improved by 0.0622779
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.88
ELB improved by 0.0594507
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.823
ELB improved by 0.0566929
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.769
ELB improved by 0.0539952
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.718
ELB improved by 0.0513544
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.669
ELB improved by 0.0487719
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.623
ELB improved by 0.0462532
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.579
ELB improved by 0.0438062
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.538
ELB improved by 0.0414404
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.499
ELB improved by 0.0391659
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.462
ELB improved by 0.0369922
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.427
ELB improved by 0.0349277
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.394
ELB improved by 0.0329793
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.363
ELB improved by 0.0311517
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.333
ELB improved by 0.0294473
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.305
ELB improved by 0.0278666
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.279
ELB improved by 0.0264078
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.254
ELB improved by 0.0250674
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.23
ELB improved by 0.0238407
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.207
ELB improved by 0.0227214
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.186
ELB improved by 0.021703
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.165
ELB improved by 0.0207783
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.145
ELB improved by 0.01994
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.126
ELB improved by 0.019181
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.107
ELB improved by 0.0184946
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.089
ELB improved by 0.0178743
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.072
ELB improved by 0.0173141
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.055
ELB improved by 0.0168088
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.039
ELB improved by 0.0163534
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.023
ELB improved by 0.0159433
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-383.007
ELB improved by 0.0155747
iteration 71
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.992
ELB improved by 0.0152436
iteration 72
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.977
ELB improved by 0.0149469
iteration 73
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.962
ELB improved by 0.0146814
iteration 74
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.948
ELB improved by 0.0144443
iteration 75
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.934
ELB improved by 0.0142329
iteration 76
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.92
ELB improved by 0.0140449
iteration 77
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.906
ELB improved by 0.0138779
iteration 78
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.892
ELB improved by 0.0137297
iteration 79
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.878
ELB improved by 0.0135985
iteration 80
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.865
ELB improved by 0.0134821
iteration 81
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.852
ELB improved by 0.0133789
iteration 82
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.838
ELB improved by 0.0132869
iteration 83
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.825
ELB improved by 0.0132046
iteration 84
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.812
ELB improved by 0.0131302
iteration 85
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.799
ELB improved by 0.0130622
iteration 86
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.786
ELB improved by 0.0129991
iteration 87
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.773
ELB improved by 0.0129393
iteration 88
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.76
ELB improved by 0.0128814
iteration 89
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.747
ELB improved by 0.012824
iteration 90
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.735
ELB improved by 0.0127658
iteration 91
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.722
ELB improved by 0.0127054
iteration 92
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.709
ELB improved by 0.0126417
iteration 93
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.697
ELB improved by 0.0125735
iteration 94
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.684
ELB improved by 0.0124997
iteration 95
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.672
ELB improved by 0.0124193
iteration 96
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.659
ELB improved by 0.0123315
iteration 97
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.647
ELB improved by 0.0122354
iteration 98
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.635
ELB improved by 0.0121304
iteration 99
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.623
ELB improved by 0.0120161
iteration 100
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.611
ELB improved by 0.0118918
iteration 101
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.599
ELB improved by 0.0117576
iteration 102
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.588
ELB improved by 0.0116131
iteration 103
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.576
ELB improved by 0.0114585
iteration 104
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.565
ELB improved by 0.0112938
iteration 105
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.554
ELB improved by 0.0111196
iteration 106
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.543
ELB improved by 0.0109361
iteration 107
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.532
ELB improved by 0.0107441
iteration 108
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.522
ELB improved by 0.0105441
iteration 109
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.511
ELB improved by 0.0103371
iteration 110
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.501
ELB improved by 0.0101239
iteration 111
Updating parameters of variational distributions...
Calculating ELB..
ELB=-382.491
ELB improved by 0.00990545
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-859.208
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-550.948
ELB improved by 308.26
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-488.918
ELB improved by 62.03
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-453.379
ELB improved by 35.5385
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-438.341
ELB improved by 15.038
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-431.639
ELB improved by 6.70235
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-427.395
ELB improved by 4.24383
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-424.046
ELB improved by 3.34873
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.115
ELB improved by 2.93149
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-418.424
ELB improved by 2.69097
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-415.911
ELB improved by 2.51288
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.559
ELB improved by 2.35231
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-411.373
ELB improved by 2.18578
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-409.378
ELB improved by 1.99472
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-407.613
ELB improved by 1.76499
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-406.117
ELB improved by 1.49566
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.91
ELB improved by 1.20714
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.976
ELB improved by 0.93472
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-403.267
ELB improved by 0.70874
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.726
ELB improved by 0.540522
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-402.302
ELB improved by 0.424287
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.955
ELB improved by 0.346885
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.66
ELB improved by 0.295125
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.402
ELB improved by 0.258434
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-401.172
ELB improved by 0.229138
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.97
ELB improved by 0.202489
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.793
ELB improved by 0.176751
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.641
ELB improved by 0.152475
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.51
ELB improved by 0.130916
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.397
ELB improved by 0.112779
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.299
ELB improved by 0.0979687
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.213
ELB improved by 0.0859409
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.137
ELB improved by 0.0760756
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.069
ELB improved by 0.0678525
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.008
ELB improved by 0.0608863
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.953
ELB improved by 0.0549034
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.904
ELB improved by 0.0497095
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.858
ELB improved by 0.0451633
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.817
ELB improved by 0.0411586
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.78
ELB improved by 0.0376128
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.745
ELB improved by 0.0344601
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.714
ELB improved by 0.0316468
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.684
ELB improved by 0.0291285
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.658
ELB improved by 0.0268676
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.633
ELB improved by 0.0248325
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.61
ELB improved by 0.0229962
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.588
ELB improved by 0.0213354
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.569
ELB improved by 0.0198303
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.55
ELB improved by 0.0184635
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.533
ELB improved by 0.0172199
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.517
ELB improved by 0.0160863
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.502
ELB improved by 0.0150514
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.488
ELB improved by 0.014105
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.474
ELB improved by 0.0132382
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.462
ELB improved by 0.0124432
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.45
ELB improved by 0.011713
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.439
ELB improved by 0.0110415
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.429
ELB improved by 0.0104231
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-399.419
ELB improved by 0.00985294
ELB converged
iteration 1
Updating parameters of variational distributions...
Calculating ELB..
ELB=-852.861
ELB improved by inf
iteration 2
Updating parameters of variational distributions...
Calculating ELB..
ELB=-566.104
ELB improved by 286.757
iteration 3
Updating parameters of variational distributions...
Calculating ELB..
ELB=-503.977
ELB improved by 62.1265
iteration 4
Updating parameters of variational distributions...
Calculating ELB..
ELB=-461.499
ELB improved by 42.4787
iteration 5
Updating parameters of variational distributions...
Calculating ELB..
ELB=-443.288
ELB improved by 18.2104
iteration 6
Updating parameters of variational distributions...
Calculating ELB..
ELB=-436.475
ELB improved by 6.81322
iteration 7
Updating parameters of variational distributions...
Calculating ELB..
ELB=-432.336
ELB improved by 4.13916
iteration 8
Updating parameters of variational distributions...
Calculating ELB..
ELB=-428.881
ELB improved by 3.45454
iteration 9
Updating parameters of variational distributions...
Calculating ELB..
ELB=-425.491
ELB improved by 3.38981
iteration 10
Updating parameters of variational distributions...
Calculating ELB..
ELB=-421.856
ELB improved by 3.6359
iteration 11
Updating parameters of variational distributions...
Calculating ELB..
ELB=-417.816
ELB improved by 4.03938
iteration 12
Updating parameters of variational distributions...
Calculating ELB..
ELB=-413.372
ELB improved by 4.44408
iteration 13
Updating parameters of variational distributions...
Calculating ELB..
ELB=-408.745
ELB improved by 4.62702
iteration 14
Updating parameters of variational distributions...
Calculating ELB..
ELB=-404.37
ELB improved by 4.37542
iteration 15
Updating parameters of variational distributions...
Calculating ELB..
ELB=-400.68
ELB improved by 3.68958
iteration 16
Updating parameters of variational distributions...
Calculating ELB..
ELB=-397.769
ELB improved by 2.91122
iteration 17
Updating parameters of variational distributions...
Calculating ELB..
ELB=-395.336
ELB improved by 2.43271
iteration 18
Updating parameters of variational distributions...
Calculating ELB..
ELB=-393.28
ELB improved by 2.05621
iteration 19
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.873
ELB improved by 1.40716
iteration 20
Updating parameters of variational distributions...
Calculating ELB..
ELB=-391.036
ELB improved by 0.836626
iteration 21
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.537
ELB improved by 0.49953
iteration 22
Updating parameters of variational distributions...
Calculating ELB..
ELB=-390.215
ELB improved by 0.321328
iteration 23
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.99
ELB improved by 0.225196
iteration 24
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.821
ELB improved by 0.169281
iteration 25
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.687
ELB improved by 0.133896
iteration 26
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.577
ELB improved by 0.109794
iteration 27
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.485
ELB improved by 0.0923936
iteration 28
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.405
ELB improved by 0.079261
iteration 29
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.336
ELB improved by 0.0690113
iteration 30
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.276
ELB improved by 0.0608061
iteration 31
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.222
ELB improved by 0.0541096
iteration 32
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.173
ELB improved by 0.0485627
iteration 33
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.129
ELB improved by 0.0439144
iteration 34
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.089
ELB improved by 0.0399826
iteration 35
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.052
ELB improved by 0.0366314
iteration 36
Updating parameters of variational distributions...
Calculating ELB..
ELB=-389.019
ELB improved by 0.0337566
iteration 37
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.987
ELB improved by 0.0312767
iteration 38
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.958
ELB improved by 0.0291268
iteration 39
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.931
ELB improved by 0.0272546
iteration 40
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.905
ELB improved by 0.0256173
iteration 41
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.881
ELB improved by 0.0241796
iteration 42
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.858
ELB improved by 0.0229122
iteration 43
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.837
ELB improved by 0.0217905
iteration 44
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.816
ELB improved by 0.0207936
iteration 45
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.796
ELB improved by 0.0199039
iteration 46
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.777
ELB improved by 0.0191062
iteration 47
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.758
ELB improved by 0.0183875
iteration 48
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.741
ELB improved by 0.0177367
iteration 49
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.723
ELB improved by 0.017144
iteration 50
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.707
ELB improved by 0.0166011
iteration 51
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.691
ELB improved by 0.0161007
iteration 52
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.675
ELB improved by 0.0156363
iteration 53
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.66
ELB improved by 0.0152026
iteration 54
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.645
ELB improved by 0.0147946
iteration 55
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.631
ELB improved by 0.0144082
iteration 56
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.617
ELB improved by 0.0140398
iteration 57
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.603
ELB improved by 0.0136865
iteration 58
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.59
ELB improved by 0.0133455
iteration 59
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.577
ELB improved by 0.0130147
iteration 60
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.564
ELB improved by 0.0126923
iteration 61
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.552
ELB improved by 0.0123768
iteration 62
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.54
ELB improved by 0.0120671
iteration 63
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.528
ELB improved by 0.0117621
iteration 64
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.516
ELB improved by 0.0114612
iteration 65
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.505
ELB improved by 0.011164
iteration 66
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.494
ELB improved by 0.0108701
iteration 67
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.484
ELB improved by 0.0105793
iteration 68
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.473
ELB improved by 0.0102918
iteration 69
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.463
ELB improved by 0.0100074
iteration 70
Updating parameters of variational distributions...
Calculating ELB..
ELB=-388.454
ELB improved by 0.00972648
ELB converged
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
>
> proc.time()
user system elapsed
2.376 0.178 2.542
graper.Rcheck/graper-Ex.timings
| name | user | system | elapsed | |
| coef.graper | 0.051 | 0.002 | 0.054 | |
| getPIPs | 0.047 | 0.005 | 0.052 | |
| graper | 0.085 | 0.001 | 0.085 | |
| makeExampleData | 0.011 | 0.000 | 0.011 | |
| makeExampleDataWithUnequalGroups | 0.010 | 0.003 | 0.013 | |
| plotELBO | 0.319 | 0.025 | 0.345 | |
| plotGroupPenalties | 1.122 | 0.053 | 1.176 | |
| plotPosterior | 0.673 | 0.008 | 0.681 | |
| predict.graper | 2.085 | 0.016 | 2.102 | |
| print.graper | 0.049 | 0.004 | 0.051 | |