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This page was generated on 2023-10-16 11:36:40 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 1944/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
slalom 1.22.0  (landing page)
Davis McCarthy
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/slalom
git_branch: RELEASE_3_17
git_last_commit: 1e36ad4
git_last_commit_date: 2023-04-25 10:57:13 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  ERROR    ERROR  skippedskipped
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for slalom on palomino3


To the developers/maintainers of the slalom package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/slalom.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.

raw results


Summary

Package: slalom
Version: 1.22.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:slalom.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings slalom_1.22.0.tar.gz
StartedAt: 2023-10-16 06:59:32 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 07:04:26 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 293.8 seconds
RetCode: 0
Status:   OK  
CheckDir: slalom.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:slalom.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings slalom_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/slalom.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'slalom/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'slalom' version '1.22.0'
* 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
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* checking installed package size ... NOTE
  installed size is 21.5Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata  18.3Mb
    libs      1.2Mb
* 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
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... 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 for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/slalom/libs/x64/slalom.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes 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
  'F:/biocbuild/bbs-3.17-bioc/meat/slalom.Rcheck/00check.log'
for details.



Installation output

slalom.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL slalom
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'slalom' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c slalom-classes.cpp -o slalom-classes.o
In file included from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/lexical_cast.hpp:30,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/math/tools/convert_from_string.hpp:15,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/math/constants/constants.hpp:14,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:20,
                 from slalom-classes.cpp:20:
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
      |     -
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
      |     -
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::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 -s -static-libgcc -o slalom.dll tmp.def RcppExports.o slalom-classes.o -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-slalom/00new/slalom/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (slalom)

Tests output

slalom.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 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.
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 3 | SKIP 1 | PASS 38 ]

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

[ FAIL 0 | WARN 3 | SKIP 1 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
  55.90    0.84   57.32 

Example timings

slalom.Rcheck/slalom-Ex.timings

nameusersystemelapsed
addResultsToSingleCellExperiment2.530.002.53
initSlalom0.150.020.17
newSlalomModel1.120.001.37
plotLoadings1.930.011.94
plotRelevance2.090.052.14
plotTerms1.860.051.91
topTerms1.620.001.62
trainSlalom2.250.012.27
updateSlalom0.160.000.15