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CHECK report for slalom on tokay1

This page was generated on 2018-04-12 13:30:40 -0400 (Thu, 12 Apr 2018).

Package 1309/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
slalom 1.0.0
Davis McCarthy
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/slalom
Branch: RELEASE_3_6
Last Commit: 8c29e0b
Last Changed Date: 2017-10-30 12:42:02 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: slalom
Version: 1.0.0
Command: rm -rf slalom.buildbin-libdir slalom.Rcheck && mkdir slalom.buildbin-libdir slalom.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=slalom.buildbin-libdir slalom_1.0.0.tar.gz >slalom.Rcheck\00install.out 2>&1 && cp slalom.Rcheck\00install.out slalom-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=slalom.buildbin-libdir --install="check:slalom-install.out" --force-multiarch --no-vignettes --timings slalom_1.0.0.tar.gz
StartedAt: 2018-04-12 03:15:28 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 03:23:52 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 503.5 seconds
RetCode: 0
Status:  OK  
CheckDir: slalom.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf slalom.buildbin-libdir slalom.Rcheck && mkdir slalom.buildbin-libdir slalom.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=slalom.buildbin-libdir slalom_1.0.0.tar.gz >slalom.Rcheck\00install.out 2>&1 && cp slalom.Rcheck\00install.out slalom-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=slalom.buildbin-libdir --install="check:slalom-install.out" --force-multiarch --no-vignettes --timings slalom_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/slalom.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'slalom/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'slalom' version '1.0.0'
* 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 'slalom' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 24.5Mb
  sub-directories of 1Mb or more:
    data      3.5Mb
    extdata  18.3Mb
    libs      1.9Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/slalom.buildbin-libdir/slalom/libs/i386/slalom.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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. 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/slalom.Rcheck/00check.log'
for details.

Installation output

slalom.Rcheck/00install.out


install for i386

* installing *source* package 'slalom' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c slalom-classes.cpp -o slalom-classes.o
slalom-classes.cpp: In constructor 'SlalomModel::SlalomModel(arma::mat, arma::mat, arma::mat, arma::mat, arma::vec, arma::vec)':
slalom-classes.cpp:85:15: warning: 'SlalomModel::Y' will be initialized after [-Wreorder]
     arma::mat Y;
               ^
slalom-classes.cpp:84:15: warning:   'arma::mat SlalomModel::Pi_E1' [-Wreorder]
     arma::mat Pi_E1;
               ^
slalom-classes.cpp:126:5: warning:   when initialized here [-Wreorder]
     SlalomModel(arma::mat Y_init, arma::mat pi_init, arma::mat X_init,
     ^
slalom-classes.cpp:84:15: warning: 'SlalomModel::Pi_E1' will be initialized after [-Wreorder]
     arma::mat Pi_E1;
               ^
slalom-classes.cpp:80:15: warning:   'arma::mat SlalomModel::I' [-Wreorder]
     arma::mat I;
               ^
slalom-classes.cpp:126:5: warning:   when initialized here [-Wreorder]
     SlalomModel(arma::mat Y_init, arma::mat pi_init, arma::mat X_init,
     ^
slalom-classes.cpp:80:15: warning: 'SlalomModel::I' will be initialized after [-Wreorder]
     arma::mat I;
               ^
slalom-classes.cpp:75:15: warning:   'arma::mat SlalomModel::W_gamma0' [-Wreorder]
     arma::mat W_gamma0;
               ^
slalom-classes.cpp:126:5: warning:   when initialized here [-Wreorder]
     SlalomModel(arma::mat Y_init, arma::mat pi_init, arma::mat X_init,
     ^
slalom-classes.cpp:75:15: warning: 'SlalomModel::W_gamma0' will be initialized after [-Wreorder]
     arma::mat W_gamma0;
               ^
slalom-classes.cpp:68:15: warning:   'arma::mat SlalomModel::X_E1' [-Wreorder]
     arma::mat X_E1;
               ^
slalom-classes.cpp:126:5: warning:   when initialized here [-Wreorder]
     SlalomModel(arma::mat Y_init, arma::mat pi_init, arma::mat X_init,
     ^
slalom-classes.cpp: In member function 'void SlalomModel::train()':
slalom-classes.cpp:221:20: warning: unused variable 'meanerr' [-Wunused-variable]
             double meanerr = arma::mean(error);
                    ^
slalom-classes.cpp:200:12: warning: unused variable 'meanerr' [-Wunused-variable]
     double meanerr = arma::mean(error);
            ^
slalom-classes.cpp: In member function 'void SlalomModel::updateEpsilon()':
slalom-classes.cpp:429:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < this->epsilon_E1.n_elem; i++) {
                       ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o slalom.dll tmp.def RcppExports.o slalom-classes.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/slalom.buildbin-libdir/slalom/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'slalom'
    finding HTML links ... done
    Rcpp_SlalomModel                        html  
    SlalomModel                             html  
    addResultsToSingleCellExperiment        html  
    initSlalom                              html  
    mesc                                    html  
    newSlalomModel                          html  
    plotLoadings                            html  
    plotRelevance                           html  
    plotTerms                               html  
    slalom                                  html  
    topTerms                                html  
    trainSlalom                             html  
    updateSlalom                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'slalom' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c slalom-classes.cpp -o slalom-classes.o
slalom-classes.cpp: In constructor 'SlalomModel::SlalomModel(arma::mat, arma::mat, arma::mat, arma::mat, arma::vec, arma::vec)':
slalom-classes.cpp:85:15: warning: 'SlalomModel::Y' will be initialized after [-Wreorder]
     arma::mat Y;
               ^
slalom-classes.cpp:84:15: warning:   'arma::mat SlalomModel::Pi_E1' [-Wreorder]
     arma::mat Pi_E1;
               ^
slalom-classes.cpp:126:5: warning:   when initialized here [-Wreorder]
     SlalomModel(arma::mat Y_init, arma::mat pi_init, arma::mat X_init,
     ^
slalom-classes.cpp:84:15: warning: 'SlalomModel::Pi_E1' will be initialized after [-Wreorder]
     arma::mat Pi_E1;
               ^
slalom-classes.cpp:80:15: warning:   'arma::mat SlalomModel::I' [-Wreorder]
     arma::mat I;
               ^
slalom-classes.cpp:126:5: warning:   when initialized here [-Wreorder]
     SlalomModel(arma::mat Y_init, arma::mat pi_init, arma::mat X_init,
     ^
slalom-classes.cpp:80:15: warning: 'SlalomModel::I' will be initialized after [-Wreorder]
     arma::mat I;
               ^
slalom-classes.cpp:75:15: warning:   'arma::mat SlalomModel::W_gamma0' [-Wreorder]
     arma::mat W_gamma0;
               ^
slalom-classes.cpp:126:5: warning:   when initialized here [-Wreorder]
     SlalomModel(arma::mat Y_init, arma::mat pi_init, arma::mat X_init,
     ^
slalom-classes.cpp:75:15: warning: 'SlalomModel::W_gamma0' will be initialized after [-Wreorder]
     arma::mat W_gamma0;
               ^
slalom-classes.cpp:68:15: warning:   'arma::mat SlalomModel::X_E1' [-Wreorder]
     arma::mat X_E1;
               ^
slalom-classes.cpp:126:5: warning:   when initialized here [-Wreorder]
     SlalomModel(arma::mat Y_init, arma::mat pi_init, arma::mat X_init,
     ^
slalom-classes.cpp: In member function 'void SlalomModel::train()':
slalom-classes.cpp:221:20: warning: unused variable 'meanerr' [-Wunused-variable]
             double meanerr = arma::mean(error);
                    ^
slalom-classes.cpp:200:12: warning: unused variable 'meanerr' [-Wunused-variable]
     double meanerr = arma::mean(error);
            ^
slalom-classes.cpp: In member function 'void SlalomModel::updateEpsilon()':
slalom-classes.cpp:429:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < this->epsilon_E1.n_elem; i++) {
                       ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o slalom.dll tmp.def RcppExports.o slalom-classes.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/slalom.buildbin-libdir/slalom/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'slalom' as slalom_1.0.0.zip
* DONE (slalom)
In R CMD INSTALL
In R CMD INSTALL

Tests output

slalom.Rcheck/tests_i386/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # test package
> library(testthat)
> library(slalom)
> 
> test_check("slalom")
14 annotated factors retained;  16 annotated factors dropped.
196  genes retained for analysis.
14 annotated factors retained;  16 annotated factors dropped.
196  genes retained for analysis.
14 annotated factors retained;  16 annotated factors dropped.
196  genes retained for analysis.
20 annotated factors retained;  3 annotated factors dropped.
500  genes retained for analysis.
iteration 0
Switched off factor 20
Switched off factor 17
Switched off factor 15
iteration 100
Switched off factor 10
Switched off factor 11
iteration 200
iteration 300
iteration 400
iteration 500
Model not converged after 500 iterations.
20 annotated factors retained;  3 annotated factors dropped.
500  genes retained for analysis.
pre-training model for faster convergence
iteration 0
Model not converged after 50 iterations.
iteration 0
Model not converged after 50 iterations.
iteration 0
Switched off factor 17
Switched off factor 20
Switched off factor 15
iteration 100
Switched off factor 11
Switched off factor 10
iteration 200
iteration 300
iteration 400
iteration 500
Model not converged after 500 iterations.
20 annotated factors retained;  3 annotated factors dropped.
500  genes retained for analysis.
pre-training model for faster convergence
iteration 0
Model not converged after 50 iterations.
iteration 0
Model not converged after 50 iterations.
iteration 0
Switched off factor 17
Switched off factor 20
Switched off factor 15
iteration 100
Switched off factor 11
Switched off factor 10
iteration 200
iteration 300
iteration 400
iteration 500
iteration 600
iteration 700
iteration 800
Switched off factor 16
iteration 900
iteration 1000
iteration 1100
iteration 1200
iteration 1300
iteration 1400
iteration 1500
iteration 1600
iteration 1700
iteration 1800
iteration 1900
iteration 2000
iteration 2100
iteration 2200
iteration 2300
iteration 2400
iteration 2500
iteration 2600
iteration 2700
Model converged after 2750 iterations.
20 annotated factors retained;  3 annotated factors dropped.
500  genes retained for analysis.
pre-training model for faster convergence
iteration 0
Model not converged after 50 iterations.
iteration 0
Model not converged after 50 iterations.
iteration 0
Switched off factor 20
Switched off factor 17
Switched off factor 10
Switched off factor 15
Switched off factor 16
iteration 100
iteration 200
iteration 300
Switched off factor 11
iteration 400
iteration 500
iteration 600
iteration 700
iteration 800
iteration 900
iteration 1000
Switched off factor 5
iteration 1100
iteration 1200
iteration 1300
iteration 1400
iteration 1500
iteration 1600
iteration 1700
iteration 1800
iteration 1900
iteration 2000
iteration 2100
iteration 2200
iteration 2300
iteration 2400
iteration 2500
iteration 2600
iteration 2700
iteration 2800
iteration 2900
iteration 3000
iteration 3100
iteration 3200
iteration 3300
iteration 3400
iteration 3500
iteration 3600
iteration 3700
iteration 3800
iteration 3900
iteration 4000
iteration 4100
iteration 4200
iteration 4300
iteration 4400
iteration 4500
Model converged after 4550 iterations.
25 annotated factors retained;  75 annotated factors dropped.
355  genes retained for analysis.
pre-training model for faster convergence
iteration 0
Model not converged after 50 iterations.
iteration 0
Model not converged after 50 iterations.
iteration 0
Switched off factor 15
Switched off factor 11
Switched off factor 18
Switched off factor 29
Switched off factor 12
Switched off factor 24
Switched off factor 26
Switched off factor 7
Switched off factor 28
Switched off factor 17
Switched off factor 23
Switched off factor 25
Switched off factor 27
Switched off factor 13
Switched off factor 22
Switched off factor 14
Switched off factor 20
Switched off factor 9
Switched off factor 21
Switched off factor 16
Switched off factor 5
Switched off factor 8
Switched off factor 6
Switched off factor 10
Switched off factor 19
iteration 100
Switched off factor 4
iteration 200
iteration 300
iteration 400
iteration 500
iteration 600
iteration 700
iteration 800
iteration 900
iteration 1000
Model converged after 1000 iterations.
== testthat results  ===========================================================
OK: 37 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  67.84    1.31   69.17

slalom.Rcheck/tests_x64/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # test package
> library(testthat)
> library(slalom)
> 
> test_check("slalom")
14 annotated factors retained;  16 annotated factors dropped.
196  genes retained for analysis.
14 annotated factors retained;  16 annotated factors dropped.
196  genes retained for analysis.
14 annotated factors retained;  16 annotated factors dropped.
196  genes retained for analysis.
20 annotated factors retained;  3 annotated factors dropped.
500  genes retained for analysis.
iteration 0
Switched off factor 20
Switched off factor 17
Switched off factor 15
iteration 100
Switched off factor 10
Switched off factor 11
iteration 200
iteration 300
iteration 400
iteration 500
Model not converged after 500 iterations.
20 annotated factors retained;  3 annotated factors dropped.
500  genes retained for analysis.
pre-training model for faster convergence
iteration 0
Model not converged after 50 iterations.
iteration 0
Model not converged after 50 iterations.
iteration 0
Switched off factor 17
Switched off factor 20
Switched off factor 15
iteration 100
Switched off factor 11
Switched off factor 10
iteration 200
iteration 300
iteration 400
iteration 500
Model not converged after 500 iterations.
20 annotated factors retained;  3 annotated factors dropped.
500  genes retained for analysis.
pre-training model for faster convergence
iteration 0
Model not converged after 50 iterations.
iteration 0
Model not converged after 50 iterations.
iteration 0
Switched off factor 17
Switched off factor 20
Switched off factor 15
iteration 100
Switched off factor 11
Switched off factor 10
iteration 200
iteration 300
iteration 400
iteration 500
iteration 600
iteration 700
iteration 800
Switched off factor 16
iteration 900
iteration 1000
iteration 1100
iteration 1200
iteration 1300
iteration 1400
iteration 1500
iteration 1600
iteration 1700
iteration 1800
iteration 1900
iteration 2000
iteration 2100
iteration 2200
iteration 2300
iteration 2400
iteration 2500
iteration 2600
iteration 2700
Model converged after 2750 iterations.
20 annotated factors retained;  3 annotated factors dropped.
500  genes retained for analysis.
pre-training model for faster convergence
iteration 0
Model not converged after 50 iterations.
iteration 0
Model not converged after 50 iterations.
iteration 0
Switched off factor 20
Switched off factor 17
Switched off factor 10
Switched off factor 15
Switched off factor 16
iteration 100
iteration 200
iteration 300
Switched off factor 11
iteration 400
iteration 500
iteration 600
iteration 700
iteration 800
iteration 900
iteration 1000
Switched off factor 5
iteration 1100
iteration 1200
iteration 1300
iteration 1400
iteration 1500
iteration 1600
iteration 1700
iteration 1800
iteration 1900
iteration 2000
iteration 2100
iteration 2200
iteration 2300
iteration 2400
iteration 2500
iteration 2600
iteration 2700
iteration 2800
iteration 2900
iteration 3000
iteration 3100
iteration 3200
iteration 3300
iteration 3400
iteration 3500
iteration 3600
iteration 3700
iteration 3800
iteration 3900
iteration 4000
iteration 4100
iteration 4200
iteration 4300
iteration 4400
iteration 4500
Model converged after 4550 iterations.
25 annotated factors retained;  75 annotated factors dropped.
355  genes retained for analysis.
pre-training model for faster convergence
iteration 0
Model not converged after 50 iterations.
iteration 0
Model not converged after 50 iterations.
iteration 0
Switched off factor 15
Switched off factor 11
Switched off factor 18
Switched off factor 29
Switched off factor 12
Switched off factor 24
Switched off factor 26
Switched off factor 7
Switched off factor 28
Switched off factor 17
Switched off factor 23
Switched off factor 25
Switched off factor 27
Switched off factor 13
Switched off factor 22
Switched off factor 14
Switched off factor 20
Switched off factor 9
Switched off factor 21
Switched off factor 16
Switched off factor 5
Switched off factor 8
Switched off factor 6
Switched off factor 10
Switched off factor 19
iteration 100
Switched off factor 4
iteration 200
iteration 300
iteration 400
iteration 500
iteration 600
iteration 700
iteration 800
iteration 900
iteration 1000
Model converged after 1000 iterations.
== testthat results  ===========================================================
OK: 37 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  59.62    0.42   60.03

Example timings

slalom.Rcheck/examples_i386/slalom-Ex.timings

nameusersystemelapsed
addResultsToSingleCellExperiment4.040.014.07
initSlalom1.240.031.26
newSlalomModel0.910.050.95
plotLoadings4.700.094.79
plotRelevance3.920.023.94
plotTerms2.910.032.94
topTerms2.230.052.28
trainSlalom2.50.02.5
updateSlalom0.420.040.47

slalom.Rcheck/examples_x64/slalom-Ex.timings

nameusersystemelapsed
addResultsToSingleCellExperiment3.470.033.50
initSlalom0.940.010.95
newSlalomModel0.960.051.00
plotLoadings3.090.063.15
plotRelevance2.750.052.80
plotTerms2.310.002.31
topTerms2.140.002.14
trainSlalom1.450.031.48
updateSlalom0.740.050.78