Multiple platform build/check report for BioC 3.9 - CHECK report for Linnorm on merida2

Package: Linnorm

Version: 2.7.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Linnorm.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Linnorm_2.7.2.tar.gz

StartedAt: 2019-04-09 01:50:41 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:58:38 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 476.6 seconds

RetCode: 0

Status: WARNINGS

CheckDir: Linnorm.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Linnorm.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Linnorm_2.7.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Linnorm.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Linnorm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Linnorm’ version ‘2.7.2’
* 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 ‘Linnorm’ can be installed ... OK
* checking installed package size ... OK
* 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 ... NOTE
Linnorm.HClust: no visible binding for global variable ‘x’
Linnorm.HClust: no visible binding for global variable ‘y’
Linnorm.HClust: no visible binding for global variable ‘xend’
Linnorm.HClust: no visible binding for global variable ‘yend’
Linnorm.HClust: no visible binding for global variable ‘cluster’
Linnorm.HClust: no visible binding for global variable ‘X1’
Linnorm.HClust: no visible binding for global variable ‘X2’
Linnorm.HVar: no visible binding for global variable ‘SD’
Linnorm.HVar: no visible binding for global variable ‘group’
Undefined global functions or variables:
  SD X1 X2 cluster group x xend y yend
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'Linnorm.Norm':
Linnorm.Norm
  Code: function(datamatrix, RowSamples = FALSE, spikein = NULL,
                 spikein_log2FC = NULL, showinfo = FALSE, output =
                 "XPM", minNonZeroPortion = 0.3, BE_F_p = 0.3173,
                 BE_F_LC_Genes = "Auto", BE_F_HC_Genes = 0.01,
                 BE_strength = 0.5, max_F_LC = 0.75)
  Docs: function(datamatrix, RowSamples = FALSE, spikein = NULL,
                 spikein_log2FC = NULL, showinfo = FALSE, output =
                 "XPM", minNonZeroPortion = 0.75, BE_F_p = 0.3173,
                 BE_F_LC_Genes = "Auto", BE_F_HC_Genes = 0.01,
                 BE_strength = 0.5, max_F_LC = 0.75)
  Mismatches in argument default values:
    Name: 'minNonZeroPortion' Code: 0.3 Docs: 0.75

Codoc mismatches from documentation object 'Linnorm':
Linnorm
  Code: function(datamatrix, RowSamples = FALSE, spikein = NULL,
                 spikein_log2FC = NULL, showinfo = FALSE, perturbation
                 = "Auto", Filter = FALSE, minNonZeroPortion = 0.3,
                 L_F_p = 0.3173, L_F_LC_Genes = "Auto", L_F_HC_Genes =
                 0.01, BE_F_p = 0.3173, BE_F_LC_Genes = "Auto",
                 BE_F_HC_Genes = 0.01, BE_strength = 0.5, max_F_LC =
                 0.75, DataImputation = FALSE, ...)
  Docs: function(datamatrix, RowSamples = FALSE, spikein = NULL,
                 spikein_log2FC = NULL, showinfo = FALSE, perturbation
                 = "Auto", Filter = FALSE, minNonZeroPortion = 0.75,
                 L_F_p = 0.3173, L_F_LC_Genes = "Auto", L_F_HC_Genes =
                 0.01, BE_F_p = 0.3173, BE_F_LC_Genes = "Auto",
                 BE_F_HC_Genes = 0.01, BE_strength = 0.5, max_F_LC =
                 0.75, DataImputation = FALSE, ...)
  Mismatches in argument default values:
    Name: 'minNonZeroPortion' Code: 0.3 Docs: 0.75

Codoc mismatches from documentation object 'Linnorm.SGenes':
Linnorm.SGenes
  Code: function(datamatrix, RowSamples = FALSE, showinfo = FALSE,
                 minNonZeroPortion = 0.3, F_p = 0.3173, F_LC_Genes =
                 "Auto", F_HC_Genes = 0.01, max_F_LC = 0.75)
  Docs: function(datamatrix, RowSamples = FALSE, showinfo = FALSE,
                 minNonZeroPortion = 0.75, F_p = 0.3173, F_LC_Genes =
                 "Auto", F_HC_Genes = 0.01, max_F_LC = 0.75)
  Mismatches in argument default values:
    Name: 'minNonZeroPortion' Code: 0.3 Docs: 0.75

* 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 is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
RnaXSim        129.754  2.522 133.413
Linnorm.Norm    49.003  0.206  49.643
Linnorm         45.533  0.163  46.085
Linnorm.limma   37.684  0.161  38.200
Linnorm.Cor     37.040  0.273  37.559
Linnorm.tSNE     8.941  0.192   9.216
Linnorm.PCA      7.947  0.279   8.273
Linnorm.HClust   6.922  0.290   6.549
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/Linnorm.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Linnorm
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘Linnorm’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c Misc.cpp -o Misc.o
In file included from Misc.cpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include/RcppArmadillo.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:26:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/RcppCommon.h:128:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion]
    inline void warning(const std::string& message) {        // #nocov start
                                                    ^
1 warning generated.
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Linnorm.so Misc.o -std=c++11 -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -DARMA_64BIT_WORD=1 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Linnorm/libs
** R
** data
** 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
* DONE (Linnorm)


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> library(testthat)
> library(Linnorm)
> 
> test_check("Linnorm")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 26 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 33.383   0.553  34.147

name	user	system	elapsed
LinearRegression	0.000	0.001	0.001
LinearRegressionFP	0	0	0
Linnorm.Cor	37.040	0.273	37.559
Linnorm.DataImput	4.678	0.216	4.916
Linnorm.HClust	6.922	0.290	6.549
Linnorm.HVar	4.453	0.121	4.604
Linnorm.Norm	49.003	0.206	49.643
Linnorm.PCA	7.947	0.279	8.273
Linnorm	45.533	0.163	46.085
Linnorm.SGenes	0.705	0.058	0.768
Linnorm.limma	37.684	0.161	38.200
Linnorm.tSNE	8.941	0.192	9.216
RnaXSim	129.754	2.522	133.413

CHECK report for Linnorm on merida2

Summary

Command output

Installation output

Tests output

Example timings