Multiple platform build/check report for BioC 3.9 - CHECK report for Linnorm on malbec2

Package: Linnorm

Version: 2.8.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Linnorm.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Linnorm_2.8.0.tar.gz

StartedAt: 2019-10-16 02:44:20 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:51:19 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 418.8 seconds

RetCode: 0

Status: WARNINGS

CheckDir: Linnorm.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Linnorm.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Linnorm_2.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/Linnorm.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘2.8.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
RnaXSim           100.396  0.252 100.693
Linnorm            43.204  0.000  43.247
Linnorm.Norm       42.869  0.000  42.963
Linnorm.Cor        34.748  0.112  34.872
Linnorm.limma      33.841  0.000  33.972
Linnorm.tSNE        9.723  0.032   9.757
Linnorm.HClust      8.476  0.044   7.868
Linnorm.PCA         8.011  0.032   8.042
Linnorm.DataImput   5.623  0.059   5.713
Linnorm.HVar        5.580  0.016   5.613
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/Linnorm.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL Linnorm
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘Linnorm’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c Misc.cpp -o Misc.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o Linnorm.so Misc.o -std=c++11 -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -DARMA_64BIT_WORD=1 -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-Linnorm/00new/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 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 (Linnorm)


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
 30.610   0.299  31.336

name	user	system	elapsed
LinearRegression	0	0	0
LinearRegressionFP	0	0	0
Linnorm.Cor	34.748	0.112	34.872
Linnorm.DataImput	5.623	0.059	5.713
Linnorm.HClust	8.476	0.044	7.868
Linnorm.HVar	5.580	0.016	5.613
Linnorm.Norm	42.869	0.000	42.963
Linnorm.PCA	8.011	0.032	8.042
Linnorm	43.204	0.000	43.247
Linnorm.SGenes	1.052	0.048	1.100
Linnorm.limma	33.841	0.000	33.972
Linnorm.tSNE	9.723	0.032	9.757
RnaXSim	100.396	0.252	100.693

CHECK report for Linnorm on malbec2

Summary

Command output

Installation output

Tests output

Example timings