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CHECK report for oligo on malbec2

This page was generated on 2019-04-09 11:24:04 -0400 (Tue, 09 Apr 2019).

Package 1101/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oligo 1.47.0
Benilton Carvalho
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/oligo
Branch: master
Last Commit: f620294
Last Changed Date: 2018-10-30 11:54:26 -0400 (Tue, 30 Oct 2018)
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: oligo
Version: 1.47.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:oligo.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings oligo_1.47.0.tar.gz
StartedAt: 2019-04-09 02:25:13 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:32:13 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 420.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: oligo.Rcheck
Warnings: 4

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:oligo.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings oligo_1.47.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/oligo.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 ‘oligo/DESCRIPTION’ ... OK
* this is package ‘oligo’ version ‘1.47.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘doMPI’
* 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 ‘oligo’ can be installed ... WARNING
Found the following significant warnings:
  ParserGzXYS.c:18:17: warning: passing argument 1 of ‘gzeof’ from incompatible pointer type [-Wincompatible-pointer-types]
  ParserGzXYS.c:19:12: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types]
  ParserGzXYS.c:46:6: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  ParserGzXYS.c:50:10: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types]
  ParserGzXYS.c:51:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
  ParserGzXYS.c:134:6: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  ParserGzXYS.c:138:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/biocbuild/bbs-3.9-bioc/meat/oligo.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 17.0Mb
  sub-directories of 1Mb or more:
    scripts  15.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘biomaRt’ ‘AnnotationDbi’ ‘GenomeGraphs’ ‘RCurl’ ‘ff’
A package should be listed in only one of these fields.
* 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘oligo’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘Biobase:::annotatedDataFrameFromMatrix’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
  .Call("ReadHeader", ..., PACKAGE = "affyio")
  .Call("read_abatch", ..., PACKAGE = "affyio")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
image,FeatureSet: warning in matrix(NA, nr = geom[1], nc = geom[2]):
  partial argument match of 'nr' to 'nrow'
image,FeatureSet: warning in matrix(NA, nr = geom[1], nc = geom[2]):
  partial argument match of 'nc' to 'ncol'
NUSE: no visible global function definition for ‘abline’
RLE: no visible global function definition for ‘abline’
basicMvApairsPlot: no visible binding for global variable
  ‘smoothScatter’
basicMvApairsPlot: no visible global function definition for ‘frame’
basicMvApairsPlot: no visible global function definition for ‘text’
basicMvApairsPlot: no visible global function definition for ‘IQR’
basicMvApairsPlot: no visible global function definition for ‘mtext’
basicMvAplot: no visible binding for global variable ‘smoothScatter’
basicMvAplot: no visible global function definition for ‘IQR’
basicMvAplot: no visible global function definition for ‘loess’
basicMvAplot: no visible global function definition for ‘approx’
basicMvAplot: no visible global function definition for ‘abline’
basicMvAplot: no visible global function definition for ‘text’
fitAffySnpMixture: no visible global function definition for
  ‘aggregate’
getRefDABG: no visible global function definition for ‘data’
invariantsetV: no visible global function definition for
  ‘smooth.spline’
invariantsetV: no visible global function definition for ‘approx’
loessNormV: no visible global function definition for ‘loess’
loessNormV: no visible global function definition for ‘predict’
maplot: no visible binding for global variable ‘smoothScatter’
qsplineNorm: no visible global function definition for ‘smooth.spline’
qsplineNorm: no visible global function definition for ‘splinefun’
MAplot,ExpressionSet: no visible binding for global variable
  ‘smoothScatter’
MAplot,FeatureSet: no visible binding for global variable
  ‘smoothScatter’
MAplot,TilingFeatureSet: no visible binding for global variable
  ‘smoothScatter’
MAplot,TilingFeatureSet: no visible global function definition for
  ‘rnorm’
MAplot,matrix: no visible binding for global variable ‘smoothScatter’
backgroundCorrect,matrix: no visible binding for global variable
  ‘intensities’
pmFragmentLength,AffySNPPDInfo: no visible global function definition
  for ‘complete.cases’
pmindex,GenericPDInfo: no visible binding for global variable
  ‘man_fsetid’
Undefined global functions or variables:
  IQR abline aggregate approx complete.cases data frame intensities
  loess man_fsetid mtext predict rnorm smooth.spline smoothScatter
  splinefun text
Consider adding
  importFrom("graphics", "abline", "frame", "mtext", "smoothScatter",
             "text")
  importFrom("stats", "IQR", "aggregate", "approx", "complete.cases",
             "loess", "predict", "rnorm", "smooth.spline", "splinefun")
  importFrom("utils", "data")
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 ... WARNING
Codoc mismatches from documentation object 'boxplot':
\S4method{boxplot}{FeatureSet}
  Code: function(x, which = c("pm", "mm", "bg", "both", "all"), transfo
                 = log2, nsample = 10000, target = "mps1", ...)
  Docs: function(x, which = c("pm", "mm", "bg", "both", "all"), transfo
                 = log2, nsample = 10000, ...)
  Argument names in code not in docs:
    target
  Mismatches in argument names:
    Position: 5 Code: target Docs: ...

Codoc mismatches from documentation object 'hist':
\S4method{hist}{FeatureSet}
  Code: function(x, transfo = log2, which = c("pm", "mm", "bg", "both",
                 "all"), nsample = 10000, target = "mps1", ...)
  Docs: function(x, transfo = log2, which = c("pm", "mm", "bg", "both",
                 "all"), nsample = 10000, ...)
  Argument names in code not in docs:
    target
  Mismatches in argument names:
    Position: 5 Code: target Docs: ...

S4 class codoc mismatches from documentation object 'oligoPLM-class':
Slots for class 'oligoPLM'
  Code: annotation chip.coefs description geometry manufacturer method
        narrays nprobes nprobesets phenoData probe.coefs protocolData
        residualSE residuals se.chip.coefs se.probe.coefs weights
  Docs: annotation chip.coefs geometry manufacturer method narrays
        nprobes nprobesets probe.coefs residualSE residuals
        se.chip.coefs se.probe.coefs weights

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... 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) ... WARNING
  apparently using $(BLAS_LIBS) without following $(FLIBS) in ‘src/Makevars’
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory newer than all files in 'inst/doc':
  ‘Makefile’
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
preprocessTools    28.255  0.104  28.382
getProbeInfo       17.040  1.236  19.327
fitProbeLevelModel  5.021  0.028   5.208
read.celfiles       4.420  0.119   5.573
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.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: 4 WARNINGs, 8 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/oligo.Rcheck/00check.log’
for details.



Installation output

oligo.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL oligo
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘oligo’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c DABG.c -o DABG.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c ParserGzXYS.c -o ParserGzXYS.o
ParserGzXYS.c: In function ‘gzcountLines’:
ParserGzXYS.c:18:17: warning: passing argument 1 of ‘gzeof’ from incompatible pointer type [-Wincompatible-pointer-types]
   while (!gzeof(file)){
                 ^˜˜˜
In file included from ParserGzXYS.c:4:0:
/usr/include/zlib.h:1595:21: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT gzeof OF((gzFile file));
                     ^˜˜˜˜
ParserGzXYS.c:19:12: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types]
     gzgets(file, buffer, 1000);
            ^˜˜˜
In file included from ParserGzXYS.c:4:0:
/usr/include/zlib.h:1492:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
                        ^˜˜˜˜˜
ParserGzXYS.c: In function ‘gzxys_header_field’:
ParserGzXYS.c:46:6: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   fp = gzopen(currentFile, "rb");
      ^
ParserGzXYS.c:50:10: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzgets(fp, buffer, LINEMAX);
          ^˜
In file included from ParserGzXYS.c:4:0:
/usr/include/zlib.h:1492:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
                        ^˜˜˜˜˜
ParserGzXYS.c:51:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzclose(fp);
           ^˜
In file included from ParserGzXYS.c:4:0:
/usr/include/zlib.h:1631:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                        ^˜˜˜˜˜˜
ParserGzXYS.c: In function ‘R_read_gzxys_files’:
ParserGzXYS.c:134:6: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   fp = gzopen(CHAR(STRING_ELT(filenames, 0)), "rb");
      ^
ParserGzXYS.c:138:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzclose(fp);
           ^˜
In file included from ParserGzXYS.c:4:0:
/usr/include/zlib.h:1631:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                        ^˜˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c ParserXYS.c -o ParserXYS.o
ParserXYS.c: In function ‘xys_header_field’:
ParserXYS.c:145:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
   fgets(buffer, LINEMAX, fp);
   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ParserXYS.c: In function ‘R_read_xys_header’:
ParserXYS.c:320:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
   fgets(buffer, LINEMAX, fp);
   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c baseProfile.c -o baseProfile.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c basecontent.c -o basecontent.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c chipbackground.c -o chipbackground.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c mas5calls.c -o mas5calls.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c rma2.c -o rma2.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c rma_common.c -o rma_common.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c trimmed.c -o trimmed.o
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o oligo.so DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lz -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-oligo/00new/oligo/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Note: in method for ‘pm<-’ with signature
‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’:
expanding the signature to include omitted arguments in definition: =
"missing"
Note: in method for ‘mm<-’ with signature
‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’:
expanding the signature to include omitted arguments in definition: =
"missing"
** 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 (oligo)

Tests output

oligo.Rcheck/tests/doRUnit.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.

> ## from xmapcore package
> if( require( "RUnit", quietly=TRUE ) ) {
+ 	pkg <- "oligo"
+         path <- ifelse(Sys.getenv( "RCMDCHECK" ) == "FALSE",
+                        file.path( getwd(), "..", "inst", "unitTests" ),
+                        system.file( package=pkg, "unitTests" ))
+         
+ 	cat( "\nRunning unit tests\n" )
+ 	print( list( pkg=pkg, getwd=getwd(), pathToUnitTests=path ) )
+ 	library( package=pkg, character.only=TRUE )
+ 
+ 	##Fail on warnings
+ 	##options( warn=2 )
+ 	options(warn=0)
+ 
+ 	## Get the pattern (if there is one?)
+ 	patt <- Sys.getenv( "RUNITFILEPATTERN" )
+         testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ),
+                                      dirs=path,
+                                      testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ))
+ 	tests <- runTestSuite( testSuite )
+ 
+ 	pathReport <- file.path( path, "report" )
+ 
+ 	cat( "------------------- UNIT TEST SUMMARY ---------------------\n\n" )
+ 	printTextProtocol( tests, showDetails=FALSE )
+ 	printTextProtocol( tests, showDetails=FALSE, fileName=paste( pathReport, "Summary.txt", sep="" ) )
+ 	printTextProtocol( tests, showDetails=TRUE,  fileName=paste( pathReport, ".txt", sep="" ) )
+ 
+ 	printHTMLProtocol( tests, fileName=paste( pathReport, ".html", sep="" ) )
+ 
+ 	tmp <- getErrors( tests )
+ 	if( tmp$nFail > 0 | tmp$nErr > 0 ){
+ 		stop( paste( "\n\nunit testing failed (#test failures: ", tmp$nFail, ", #R errors: ",  tmp$nErr, ")\n\n", sep=""))
+ 	}
+ } else {
+ 	warning( "cannot run unit tests -- package RUnit is not available" )
+ }

Running unit tests
$pkg
[1] "oligo"

$getwd
[1] "/home/biocbuild/bbs-3.9-bioc/meat/oligo.Rcheck/tests"

$pathToUnitTests
[1] "/home/biocbuild/bbs-3.9-bioc/R/library/oligo/unitTests"

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, 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: oligoClasses
Welcome to oligoClasses version 1.45.0
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: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

================================================================================
Welcome to oligo version 1.47.0
================================================================================


Executing test function test_rma  ... Getting sample dataset
Loading required package: pd.hg18.60mer.expr
Loading required package: RSQLite
Loading required package: DBI
Platform design info loaded.
Checking designs for each XYS file... Done.
Allocating memory... Done.
Reading /home/biocbuild/bbs-3.9-bioc/R/library/maqcExpression4plex/extdata/9868701_532.xys.
Reading /home/biocbuild/bbs-3.9-bioc/R/library/maqcExpression4plex/extdata/9868901_532.xys.
Reading /home/biocbuild/bbs-3.9-bioc/R/library/maqcExpression4plex/extdata/9869001_532.xys.
Reading /home/biocbuild/bbs-3.9-bioc/R/library/maqcExpression4plex/extdata/9870301_532.xys.
Reading /home/biocbuild/bbs-3.9-bioc/R/library/maqcExpression4plex/extdata/9870401_532.xys.
Reading /home/biocbuild/bbs-3.9-bioc/R/library/maqcExpression4plex/extdata/9870601_532.xys.
Running RMA
Background correcting
Normalizing
Calculating Expression
Getting reference results
 done successfully.



Executing test function test_selector  ... Loading reference data
Loading sample dataset: Exon
Getting probe info: core
Loading required package: pd.huex.1.0.st.v2
Getting probe info: probeset
Getting probe info: antigenomic backgroung probes
Loading sample dataset: Gene
Getting probe info: core
Loading required package: pd.hugene.1.0.st.v1
Getting probe info: probeset
Getting probe info: antigenomic backgroung probes
 done successfully.

------------------- UNIT TEST SUMMARY ---------------------

RUNIT TEST PROTOCOL -- Tue Apr  9 02:32:05 2019 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
oligo unit testing - 2 test functions, 0 errors, 0 failures
> 
> proc.time()
   user  system elapsed 
118.442   4.339 149.997 

Example timings

oligo.Rcheck/oligo-Ex.timings

nameusersystemelapsed
Index-methods000
IntensityMatrix-methods0.7700.0171.936
MAplot-methods1.8550.0321.905
basecontent0.0000.0000.001
basicPLM3.9330.0003.933
basicRMA3.5800.0073.589
colors0.0330.0040.037
coordinates0.0010.0000.000
fitProbeLevelModel5.0210.0285.208
getProbeInfo17.040 1.23619.327
image1.2060.0161.222
justSNPRMA0.0010.0000.000
list.xysfiles000
oligoPLM-class0.0000.0000.001
paCalls000
preprocessTools28.255 0.10428.382
read.celfiles4.4200.1195.573
read.xysfiles0.7660.0200.786
rma-methods2.5560.0082.565
sequenceDesignMatrix0.0130.0000.014