Package: oligo

Version: 1.48.0

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_1.48.0.tar.gz

StartedAt: 2019-10-16 03:36:59 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:43:46 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 407.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: oligo.Rcheck

Warnings: 4

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### 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_1.48.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/oligo.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 ‘oligo/DESCRIPTION’ ... OK
* this is package ‘oligo’ version ‘1.48.0’
* 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]
  ParserXYS.c:145:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  ParserXYS.c:320:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
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    29.716  0.136  29.882
getProbeInfo       13.592  1.104  15.248
fitProbeLevelModel  5.144  0.052   5.655
* 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.

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

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.

> ## 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, 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, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: oligoClasses
Welcome to oligoClasses version 1.46.0
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 1.48.0
================================================================================


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 -- Wed Oct 16 03:43:39 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 
116.075   4.246 150.614 

name	user	system	elapsed
Index-methods	0.001	0.000	0.000
IntensityMatrix-methods	1.063	0.028	1.646
MAplot-methods	1.976	0.088	2.069
basecontent	0.000	0.000	0.001
basicPLM	2.688	0.000	2.689
basicRMA	2.598	0.000	2.598
colors	0.031	0.000	0.031
coordinates	0	0	0
fitProbeLevelModel	5.144	0.052	5.655
getProbeInfo	13.592	1.104	15.248
image	1.015	0.004	1.020
justSNPRMA	0	0	0
list.xysfiles	0	0	0
oligoPLM-class	0	0	0
paCalls	0	0	0
preprocessTools	29.716	0.136	29.882
read.celfiles	3.148	0.088	3.686
read.xysfiles	0.411	0.000	0.411
rma-methods	2.365	0.004	2.369
sequenceDesignMatrix	0.016	0.000	0.015