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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:slalom.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings slalom_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/slalom.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘slalom/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘slalom’ version ‘1.28.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘slalom’ can be installed ... WARNING
Found the following significant warnings:
  slalom-classes.cpp:262:28: warning: ‘void std::random_shuffle(_RAIter, _RAIter, _Generator&&) [with _RAIter = unsigned int*; _Generator = int (&)(int)]’ is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations]
See ‘/home/biocbuild/bbs-3.20-bioc/meat/slalom.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* checking installed package size ... NOTE
  installed size is 25.5Mb
  sub-directories of 1Mb or more:
    data      1.8Mb
    extdata  18.3Mb
    libs      5.1Mb
* 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 ... 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 LazyData ... 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 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: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/slalom.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL slalom
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘slalom’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c slalom-classes.cpp -o slalom-classes.o
slalom-classes.cpp: In member function ‘void SlalomModel::train()’:
slalom-classes.cpp:223:20: warning: unused variable ‘meanerr’ [-Wunused-variable]
  223 |             double meanerr = arma::mean(error);
      |                    ^~~~~~~
slalom-classes.cpp:202:12: warning: unused variable ‘meanerr’ [-Wunused-variable]
  202 |     double meanerr = arma::mean(error);
      |            ^~~~~~~
slalom-classes.cpp: In member function ‘void SlalomModel::update()’:
slalom-classes.cpp:262:28: warning: ‘void std::random_shuffle(_RAIter, _RAIter, _Generator&&) [with _RAIter = unsigned int*; _Generator = int (&)(int)]’ is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations]
  262 |         std::random_shuffle(kunfix.begin(), kunfix.end(), randWrapper);
      |         ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/functional:67,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include/RcppCommon.h:63,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from slalom-classes.cpp:10:
/usr/include/c++/13/bits/stl_algo.h:4620:5: note: declared here
 4620 |     random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last,
      |     ^~~~~~~~~~~~~~
slalom-classes.cpp: In member function ‘void SlalomModel::updateEpsilon()’:
slalom-classes.cpp:431:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  431 |     for (int i = 0; i < this->epsilon_E1.n_elem; i++) {
      |                     ~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o slalom.so RcppExports.o slalom-classes.o -llapack -L/home/biocbuild/bbs-3.20-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-slalom/00new/slalom/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** 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 (slalom)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 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.

> # 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.
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.
[ FAIL 0 | WARN 4 | SKIP 1 | PASS 38 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-SlalomModel-methods.R:262:1'

[ FAIL 0 | WARN 4 | SKIP 1 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
 53.078   0.773  53.843