Package: Linnorm

Version: 2.8.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Linnorm.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Linnorm_2.8.0.tar.gz

StartedAt: 2019-10-16 04:48:18 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:04:11 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 952.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Linnorm.Rcheck

Warnings: 1

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Linnorm.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Linnorm_2.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/Linnorm.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Linnorm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Linnorm' version '2.8.0'
* 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 '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
* 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
* 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 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/Linnorm/libs/i386/Linnorm.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/Linnorm/libs/x64/Linnorm.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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
RnaXSim           91.36   0.03   91.40
Linnorm.Norm      68.20   0.11   68.31
Linnorm           65.00   0.01   65.01
Linnorm.limma     58.23   0.10   58.33
Linnorm.Cor       53.11   0.50   53.61
Linnorm.tSNE      11.53   0.28   11.91
Linnorm.PCA        9.71   0.45   10.50
Linnorm.HClust     8.83   0.31    9.14
Linnorm.DataImput  7.03   0.39    7.43
Linnorm.HVar       5.61   0.13    5.73
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
RnaXSim           124.47   0.10  124.74
Linnorm            61.46   0.00   61.46
Linnorm.Norm       57.00   0.04   57.08
Linnorm.limma      48.75   0.00   48.76
Linnorm.Cor        34.03   0.20   34.41
Linnorm.PCA         9.57   0.49   10.79
Linnorm.tSNE        8.76   0.20    8.97
Linnorm.HClust      7.86   0.28    8.14
Linnorm.DataImput   6.55   0.38    6.92
Linnorm.HVar        5.16   0.19    5.35
* 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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/Linnorm.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/Linnorm_2.8.0.tar.gz && rm -rf Linnorm.buildbin-libdir && mkdir Linnorm.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Linnorm.buildbin-libdir Linnorm_2.8.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL Linnorm_2.8.0.zip && rm Linnorm_2.8.0.tar.gz Linnorm_2.8.0.zip
###
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100 2416k  100 2416k    0     0  28.8M      0 --:--:-- --:--:-- --:--:-- 31.4M

install for i386

* installing *source* package 'Linnorm' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Misc.cpp -o Misc.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o Linnorm.dll tmp.def Misc.o -std=c++11 -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -DARMA_64BIT_WORD=1 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/Linnorm.buildbin-libdir/00LOCK-Linnorm/00new/Linnorm/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Linnorm'
    finding HTML links ... done
    Islam2011                               html  
    LIHC                                    html  
    LinearRegression                        html  
    LinearRegressionFP                      html  
    Linnorm.Cor                             html  
    Linnorm.DataImput                       html  
    Linnorm.HClust                          html  
    Linnorm.HVar                            html  
    Linnorm.Norm                            html  
    Linnorm.PCA                             html  
    Linnorm                                 html  
    Linnorm.SGenes                          html  
    Linnorm.limma                           html  
    Linnorm.tSNE                            html  
    RnaXSim                                 html  
    SEQC                                    html  
** 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

install for x64

* installing *source* package 'Linnorm' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Misc.cpp -o Misc.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o Linnorm.dll tmp.def Misc.o -std=c++11 -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -DARMA_64BIT_WORD=1 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/Linnorm.buildbin-libdir/Linnorm/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Linnorm' as Linnorm_2.8.0.zip
* DONE (Linnorm)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'Linnorm' successfully unpacked and MD5 sums checked

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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.

> library(testthat)
> library(Linnorm)
> 
> test_check("Linnorm")
== testthat results  ===========================================================
[ OK: 26 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  31.50    0.75   32.23 

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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.

> library(testthat)
> library(Linnorm)
> 
> test_check("Linnorm")
== testthat results  ===========================================================
[ OK: 26 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  30.18    0.42   30.59