Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKLMN[O]PQRSTUVWXYZ

This page was generated on 2022-04-13 12:05:42 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for oligo on nebbiolo2


To the developers/maintainers of the oligo package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/oligo.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1317/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oligo 1.58.0  (landing page)
Benilton Carvalho
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/oligo
git_branch: RELEASE_3_14
git_last_commit: 24a02c2
git_last_commit_date: 2021-10-26 11:48:16 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: oligo
Version: 1.58.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:oligo.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings oligo_1.58.0.tar.gz
StartedAt: 2022-04-12 08:31:08 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 08:35:47 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 279.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: oligo.Rcheck
Warnings: 5

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:oligo.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings oligo_1.58.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/oligo.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.58.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  'doMC', '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 to ‘struct gzFile_s **’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-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 to ‘struct gzFile_s **’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-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-3.14-bioc/meat/oligo.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 17.1Mb
  sub-directories of 1Mb or more:
    scripts  15.7Mb
* 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 ... 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'
cloneFS: no visible global function definition for ‘clone’
rmaBgCorrectLDSmaster: no visible global function definition for
  ‘clone’
backgroundCorrect,matrix: no visible binding for global variable
  ‘intensities’
normalize,ff_matrix: no visible global function definition for ‘clone’
normalizeToTarget,ff_matrix: no visible global function definition for
  ‘clone’
pmindex,GenericPDInfo: no visible binding for global variable
  ‘man_fsetid’
Undefined global functions or variables:
  clone intensities man_fsetid
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'mm<-' and siglist 'TilingFeatureSet,missing,missing,array'
  generic 'pm<-' and siglist 'TilingFeatureSet,missing,missing,array'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'boxplot'
  ‘target’

Undocumented arguments in documentation object 'hist'
  ‘target’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 use of PKG_*FLAGS in Makefiles ... OK
* 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 (user + system) or elapsed time > 5s
                  user system elapsed
preprocessTools 14.784  0.220  15.005
getProbeInfo    10.028  0.944  11.089
* 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: 5 WARNINGs, 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/oligo.Rcheck/00check.log’
for details.



Installation output

oligo.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL oligo
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘oligo’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c DABG.c -o DABG.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-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]
   18 |   while (!gzeof(file)){
      |                 ^~~~
      |                 |
      |                 struct gzFile_s **
In file included from /usr/include/zlib.h:34,
                 from ParserGzXYS.c:4:
/usr/include/zlib.h:1595:27: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’
 1595 | ZEXTERN int ZEXPORT gzeof OF((gzFile file));
      |                           ^~
ParserGzXYS.c:19:12: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types]
   19 |     gzgets(file, buffer, 1000);
      |            ^~~~
      |            |
      |            struct gzFile_s **
In file included from ParserGzXYS.c:4:
/usr/include/zlib.h:1492:24: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’
 1492 | ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
      |                        ^~~~~~
ParserGzXYS.c: In function ‘gzxys_header_field’:
ParserGzXYS.c:46:6: warning: assignment to ‘struct gzFile_s **’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types]
   46 |   fp = gzopen(currentFile, "rb");
      |      ^
ParserGzXYS.c:50:10: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types]
   50 |   gzgets(fp, buffer, LINEMAX);
      |          ^~
      |          |
      |          struct gzFile_s **
In file included from ParserGzXYS.c:4:
/usr/include/zlib.h:1492:24: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’
 1492 | 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]
   51 |   gzclose(fp);
      |           ^~
      |           |
      |           struct gzFile_s **
In file included from /usr/include/zlib.h:34,
                 from ParserGzXYS.c:4:
/usr/include/zlib.h:1631:32: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’
 1631 | ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
      |                                ^~
ParserGzXYS.c: In function ‘R_read_gzxys_files’:
ParserGzXYS.c:134:6: warning: assignment to ‘struct gzFile_s **’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types]
  134 |   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]
  138 |   gzclose(fp);
      |           ^~
      |           |
      |           struct gzFile_s **
In file included from /usr/include/zlib.h:34,
                 from ParserGzXYS.c:4:
/usr/include/zlib.h:1631:32: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’
 1631 | ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
      |                                ^~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-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]
  145 |   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]
  320 |   fgets(buffer, LINEMAX, fp);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c baseProfile.c -o baseProfile.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c basecontent.c -o basecontent.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c chipbackground.c -o chipbackground.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c mas5calls.c -o mas5calls.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c rma2.c -o rma2.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-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-3.14-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-3.14-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.14-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-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:
subset = "missing", target = "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:
subset = "missing", target = "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 version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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-3.14-bioc/meat/oligo.Rcheck/tests"

$pathToUnitTests
[1] "/home/biocbuild/bbs-3.14-bioc/R/library/oligo/unitTests"

Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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.max, which.min

Loading required package: oligoClasses
Welcome to oligoClasses version 1.56.0
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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

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

    strsplit

================================================================================
Welcome to oligo version 1.58.0
================================================================================


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-3.14-bioc/R/library/maqcExpression4plex/extdata/9868701_532.xys.
Reading /home/biocbuild/bbs-3.14-bioc/R/library/maqcExpression4plex/extdata/9868901_532.xys.
Reading /home/biocbuild/bbs-3.14-bioc/R/library/maqcExpression4plex/extdata/9869001_532.xys.
Reading /home/biocbuild/bbs-3.14-bioc/R/library/maqcExpression4plex/extdata/9870301_532.xys.
Reading /home/biocbuild/bbs-3.14-bioc/R/library/maqcExpression4plex/extdata/9870401_532.xys.
Reading /home/biocbuild/bbs-3.14-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 12 08:35:43 2022 
*********************************************** 
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
Warning messages:
1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: Marsaglia-Multicarry has poor statistical properties
2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
3: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: Marsaglia-Multicarry has poor statistical properties
4: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
> 
> proc.time()
   user  system elapsed 
 80.532   4.241  85.582 

Example timings

oligo.Rcheck/oligo-Ex.timings

nameusersystemelapsed
Index-methods0.0010.0000.000
IntensityMatrix-methods0.6250.0110.643
MAplot-methods2.2610.0282.289
basecontent000
basicPLM1.1820.0041.185
basicRMA1.1650.0001.164
colors0.0290.0000.029
coordinates000
fitProbeLevelModel3.1660.0363.203
getProbeInfo10.028 0.94411.089
image0.7040.0240.728
justSNPRMA0.0010.0000.000
list.xysfiles000
oligoPLM-class000
paCalls000
preprocessTools14.784 0.22015.005
read.celfiles2.6400.1162.757
read.xysfiles0.3630.0040.366
rma-methods1.3520.0041.355
sequenceDesignMatrix0.0090.0000.008