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CHECK report for Linnorm on malbec2

This page was generated on 2019-04-09 11:45:42 -0400 (Tue, 09 Apr 2019).

Package 860/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Linnorm 2.7.2
Ken Shun Hang Yip
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/Linnorm
Branch: master
Last Commit: 28babbf
Last Changed Date: 2019-01-04 13:36:51 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: Linnorm
Version: 2.7.2
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_2.7.2.tar.gz
StartedAt: 2019-04-09 01:35:08 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:42:19 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 430.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: Linnorm.Rcheck
Warnings: 1

Command output

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### Running 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_2.7.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/Linnorm.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘2.7.2’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
RnaXSim           112.263  0.020 112.339
Linnorm            44.269  0.004  44.313
Linnorm.Norm       42.187  0.020  42.438
Linnorm.limma      36.451  0.000  36.472
Linnorm.Cor        34.736  0.172  34.925
Linnorm.tSNE       10.059  0.032  10.093
Linnorm.PCA         7.928  0.032   7.961
Linnorm.HClust      7.541  0.044   7.037
Linnorm.DataImput   5.487  0.076   5.561
Linnorm.HVar        5.416  0.036   5.466
* 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.

Installation output

Linnorm.Rcheck/00install.out

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###
### Running command:
###
###   /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)

Tests output

Linnorm.Rcheck/tests/testthat.Rout


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 32.132   0.334  32.784

Example timings

Linnorm.Rcheck/Linnorm-Ex.timings

nameusersystemelapsed
LinearRegression0.0010.0000.001
LinearRegressionFP0.0000.0000.001
Linnorm.Cor34.736 0.17234.925
Linnorm.DataImput5.4870.0765.561
Linnorm.HClust7.5410.0447.037
Linnorm.HVar5.4160.0365.466
Linnorm.Norm42.187 0.02042.438
Linnorm.PCA7.9280.0327.961
Linnorm44.269 0.00444.313
Linnorm.SGenes0.7730.0520.827
Linnorm.limma36.451 0.00036.472
Linnorm.tSNE10.059 0.03210.093
RnaXSim112.263 0.020112.339