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This page was generated on 2024-06-18 17:58 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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

Package 1453/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oligo 1.68.2  (landing page)
Benilton Carvalho
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/oligo
git_branch: RELEASE_3_19
git_last_commit: e5caf22
git_last_commit_date: 2024-06-03 21:41:12 -0400 (Mon, 03 Jun 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for oligo on nebbiolo1

To the developers/maintainers of the oligo package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: oligo
Version: 1.68.2
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:oligo.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings oligo_1.68.2.tar.gz
StartedAt: 2024-06-17 01:51:37 -0400 (Mon, 17 Jun 2024)
EndedAt: 2024-06-17 01:56:59 -0400 (Mon, 17 Jun 2024)
EllapsedTime: 322.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: oligo.Rcheck
Warnings: 4

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:oligo.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings oligo_1.68.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/oligo.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘oligo/DESCRIPTION’ ... OK
* this is package ‘oligo’ version ‘1.68.2’
* 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 ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... NOTE
  installed size is 16.8Mb
  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 code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 Rd file 'boxplot.Rd'
  ‘target’

Undocumented arguments in Rd file 'hist.Rd'
  ‘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 14.624  0.155  14.779
getProbeInfo     9.912  1.401  11.369
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/oligo.Rcheck/00check.log’
for details.


Installation output

oligo.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL oligo
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘oligo’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c DABG.c -o DABG.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c ParserGzXYS.c -o ParserGzXYS.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c ParserXYS.c -o ParserXYS.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c baseProfile.c -o baseProfile.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c basecontent.c -o basecontent.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c chipbackground.c -o chipbackground.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c mas5calls.c -o mas5calls.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c rma2.c -o rma2.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c rma_common.c -o rma_common.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c trimmed.c -o trimmed.o
gcc -shared -L/home/biocbuild/bbs-3.19-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 -llapack -L/home/biocbuild/bbs-3.19-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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-3.19-bioc/meat/oligo.Rcheck/tests"

$pathToUnitTests
[1] "/tmp/RtmpGhOh5B/RLIBS_52a0c27b4d904/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, aperm, 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, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: oligoClasses
Welcome to oligoClasses version 1.66.0
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:utils':

    findMatches

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 1.68.2
================================================================================


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 /tmp/RtmpGhOh5B/RLIBS_52a0c27b4d904/maqcExpression4plex/extdata/9868701_532.xys.
Reading /tmp/RtmpGhOh5B/RLIBS_52a0c27b4d904/maqcExpression4plex/extdata/9868901_532.xys.
Reading /tmp/RtmpGhOh5B/RLIBS_52a0c27b4d904/maqcExpression4plex/extdata/9869001_532.xys.
Reading /tmp/RtmpGhOh5B/RLIBS_52a0c27b4d904/maqcExpression4plex/extdata/9870301_532.xys.
Reading /tmp/RtmpGhOh5B/RLIBS_52a0c27b4d904/maqcExpression4plex/extdata/9870401_532.xys.
Reading /tmp/RtmpGhOh5B/RLIBS_52a0c27b4d904/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 -- Mon Jun 17 01:56:54 2024 
*********************************************** 
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 
 89.906   6.051  96.435 

Example timings

oligo.Rcheck/oligo-Ex.timings

nameusersystemelapsed
Index-methods0.0010.0000.000
IntensityMatrix-methods0.6380.0360.685
MAplot-methods1.7300.0521.783
basecontent0.0000.0000.001
basicPLM1.2300.0081.238
basicRMA1.2360.0001.236
colors0.040.000.04
coordinates000
fitProbeLevelModel2.9840.1643.151
getProbeInfo 9.912 1.40111.369
image0.7000.0440.744
justSNPRMA000
list.xysfiles0.0000.0000.001
oligoPLM-class0.0010.0000.000
paCalls0.0010.0000.000
preprocessTools14.624 0.15514.779
read.celfiles3.4170.2923.713
read.xysfiles0.3710.0120.383
rma-methods1.3710.0161.386
sequenceDesignMatrix0.0110.0000.011