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CHECK report for LINC on merida2

This page was generated on 2018-10-17 08:57:05 -0400 (Wed, 17 Oct 2018).

Package 788/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LINC 1.8.0
Manuel Goepferich
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/LINC
Branch: RELEASE_3_7
Last Commit: fb436a1
Last Changed Date: 2018-04-30 10:35:43 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: LINC
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:LINC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings LINC_1.8.0.tar.gz
StartedAt: 2018-10-16 22:15:49 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 22:37:20 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 1291.3 seconds
RetCode: 0
Status:  OK 
CheckDir: LINC.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:LINC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings LINC_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/LINC.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LINC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘LINC’ version ‘1.8.0’
* 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 ‘LINC’ 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
justlinc,matrix: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
* 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 data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
              old_size new_size compress
  sysdata.rda    449Kb    299Kb       xz
* checking line endings in C/C++/Fortran sources/headers ... 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
getbio-methods      700.445 59.013 768.461
singlelinc-methods  181.642 14.453 199.034
clusterlinc-methods  21.031  0.455  21.569
linc-methods          7.867  0.493   8.425
plotlinc-methods      6.838  0.255   7.130
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/LINC.Rcheck/00check.log’
for details.



Installation output

LINC.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL LINC
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘LINC’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c Cppspear.cpp -o Cppspear.o
Cppspear.cpp:78:14: warning: unused variable 'qspear' [-Wunused-variable]
      double qspear;double nfraction;
             ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c LINC_init.c -o LINC_init.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c docdd.cpp -o docdd.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c doesd.cpp -o doesd.o
clang++ -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 LINC.so Cppspear.o LINC_init.o RcppExports.o docdd.o doesd.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/LINC/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘history’ in package ‘LINC’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (LINC)

Tests output

LINC.Rcheck/tests/runTests.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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.

> BiocGenerics:::testPackage("LINC")


This is LINC - Co-Expression Analysis of lincRNAs
 (Manuel Goepferich & Carl Herrmann)

Attaching package: 'LINC'

The following object is masked from 'package:utils':

    history

removed 4 zero variance genes from input
removed genes with duplicated names
linc: gene system(s) assumed:
ENTREZID
linc: Correlation function with 'everything' called
linc: Computation of correlation matrix started
clusterlinc: computation for the correlation test started
clusterlinc: distance matrix called with the method dicedist
clusterlinc: co-expressed genes selected based on 'pvalCutOff'
removed 4 zero variance genes from input
removed genes with duplicated names
linc: gene system(s) assumed:
ENTREZID
linc: Correlation function with 'everything' called
linc: Computation of correlation matrix started
singlelinc: no test conducted, genes selected based on correlation values
singlelinc: co-expression analysis yielded 9 genes
singlelinc: The function enrichGO will be called.
Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

removed 4 zero variance genes from input
removed genes with duplicated names
linc: gene system(s) assumed:
ENTREZID
linc: Correlation function with 'everything' called
linc: Computation of correlation matrix started
removed 4 zero variance genes from input
removed genes with duplicated names
linc: gene system(s) assumed:
ENTREZID
linc: Correlation function with 'everything' called
linc: Computation of correlation matrix started
clusterlinc: computation for the correlation test started
clusterlinc: distance matrix called with the method dicedist
clusterlinc: co-expressed genes selected based on 'pvalCutOff'


RUNIT TEST PROTOCOL -- Tue Oct 16 22:37:14 2018 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
LINC RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In linc(cor_test_mat, codingGenes = c(TRUE, FALSE, TRUE, TRUE, FALSE,  :
  Input 'object' contains infinite values
2: In linc(cor_test_mat, codingGenes = c(TRUE, FALSE, TRUE, TRUE, FALSE,  :
  Input 'object' contains infinite values
3: In singlelinc(linc_matrix, query = "17", onlycor = T, underth = F,  :
  'testFun' was supplied and 'onlycor' equals 'TRUE', here 'onlycor' has the higher priority
4: In linc(cor_test_mat, codingGenes = c(TRUE, FALSE, TRUE, TRUE, FALSE,  :
  Input 'object' contains infinite values
5: In linc(cor_test_mat, codingGenes = c(TRUE, FALSE, TRUE, TRUE, FALSE,  :
  Input 'object' contains infinite values
> 
> proc.time()
   user  system elapsed 
103.881   9.271 114.552 

Example timings

LINC.Rcheck/LINC-Ex.timings

nameusersystemelapsed
Arith-methods2.3460.1062.462
BRAIN_EXPR0.2280.0210.249
LINCbio-class0.0020.0000.003
LINCcluster-class0.0030.0010.003
LINCfeature-class0.0020.0000.002
LINCmatrix-class0.0020.0010.002
LINCsingle-class0.0020.0000.002
assignment-methods0.2360.0290.265
changeOrgDb0.5780.0160.597
clusterlinc-methods21.031 0.45521.569
correlation-methods0.2910.0800.372
express-methods0.3700.1710.543
feature1.9430.0542.001
getbio-methods700.445 59.013768.461
getcoexpr0.7950.1060.903
getlinc-methods0.2400.0210.261
history-methods0.2530.0230.276
justlinc-methods0.0040.0000.004
linCenvir-methods0.2430.0230.266
linc-methods7.8670.4938.425
linctable-methods0.0010.0000.002
plotlinc-methods6.8380.2557.130
querycluster0.5050.0280.534
results-methods0.2400.0230.263
singlelinc-methods181.642 14.453199.034