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This page was generated on 2022-01-17 13:06:42 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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 tokay2


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? here 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: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 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 -0500 (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: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:oligo.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings oligo_1.58.0.tar.gz
StartedAt: 2022-01-17 00:49:27 -0500 (Mon, 17 Jan 2022)
EndedAt: 2022-01-17 01:00:58 -0500 (Mon, 17 Jan 2022)
EllapsedTime: 690.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: oligo.Rcheck
Warnings: 4

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:oligo.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings oligo_1.58.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/oligo.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'oligo' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 17.6Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/oligo/libs/i386/oligo.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/oligo/libs/x64/oligo.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... WARNING
Files in the 'vignettes' directory newer than all files in 'inst/doc':
  'Makefile'
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
preprocessTools         40.21   1.39   41.61
getProbeInfo            14.03   2.39   20.69
read.celfiles            6.98   0.13    7.40
fitProbeLevelModel       6.31   0.13    8.17
basicRMA                 5.52   0.08    5.59
basicPLM                 5.09   0.21    5.49
IntensityMatrix-methods  2.41   0.09    8.54
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
preprocessTools 31.33   0.44   31.77
getProbeInfo    11.48   1.75   13.23
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'doRUnit.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/oligo.Rcheck/00check.log'
for details.



Installation output

oligo.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/oligo_1.58.0.tar.gz && rm -rf oligo.buildbin-libdir && mkdir oligo.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=oligo.buildbin-libdir oligo_1.58.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL oligo_1.58.0.zip && rm oligo_1.58.0.tar.gz oligo_1.58.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 13 14.9M   13 2044k    0     0  3326k      0  0:00:04 --:--:--  0:00:04 3324k
 50 14.9M   50 7652k    0     0  4769k      0  0:00:03  0:00:01  0:00:02 4771k
 99 14.9M   99 14.7M    0     0  5819k      0  0:00:02  0:00:02 --:--:-- 5819k
100 14.9M  100 14.9M    0     0  5834k      0  0:00:02  0:00:02 --:--:-- 5835k

install for i386

* installing *source* package 'oligo' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c DABG.c -o DABG.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ParserGzXYS.c -o ParserGzXYS.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ParserXYS.c -o ParserXYS.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c baseProfile.c -o baseProfile.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c basecontent.c -o basecontent.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c chipbackground.c -o chipbackground.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c mas5calls.c -o mas5calls.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c rma2.c -o rma2.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c rma_common.c -o rma_common.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c trimmed.c -o trimmed.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o oligo.dll tmp.def DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lgfortran -lm -lquadmath -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRblas -LC:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/oligo.buildbin-libdir/00LOCK-oligo/00new/oligo/libs/i386
** 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
  converting help for package 'oligo'
    finding HTML links ... done
    Index-methods                           html  
    IntensityMatrix-methods                 html  
    MAplot-methods                          html  
    Sequences-methods                       html  
    basecontent                             html  
    basicPLM                                html  
    basicRMA                                html  
    boxplot                                 html  
    chromosome                              html  
    colors                                  html  
    coordinates                             html  
    crlmm                                   html  
    fitProbeLevelModel                      html  
    getAffinitySplineCoefficients           html  
    getBaseProfile                          html  
    getContainer                            html  
    getCrlmmSummaries                       html  
    getNetAffx                              html  
    getNgsColorsInfo                        html  
    getPlatformDesign                       html  
    getProbeInfo                            html  
    hist                                    html  
    image                                   html  
    justSNPRMA                              html  
    list.xysfiles                           html  
    oligo-package                           html  
    oligoDefunct                            html  
    oligoPLM-class                          html  
    paCalls                                 html  
    plotM-methods                           html  
    pmAllele                                html  
    pmFragmentLength                        html  
    pmPosition                              html  
    pmStrand                                html  
    preprocessTools                         html  
    probeNames                              html  
    read.celfiles                           html  
    read.xysfiles                           html  
    readSummaries                           html  
    rma-methods                             html  
    runDate                                 html  
    sequenceDesignMatrix                    html  
    snprma                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'oligo' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c DABG.c -o DABG.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ParserGzXYS.c -o ParserGzXYS.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ParserXYS.c -o ParserXYS.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c baseProfile.c -o baseProfile.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c basecontent.c -o basecontent.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c chipbackground.c -o chipbackground.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c mas5calls.c -o mas5calls.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c rma2.c -o rma2.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c rma_common.c -o rma_common.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c trimmed.c -o trimmed.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o oligo.dll tmp.def DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lgfortran -lm -lquadmath -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRblas -LC:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/oligo.buildbin-libdir/oligo/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'oligo' as oligo_1.58.0.zip
* DONE (oligo)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'oligo' successfully unpacked and MD5 sums checked

Tests output

oligo.Rcheck/tests_i386/doRUnit.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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] "C:/Users/biocbuild/bbs-3.14-bioc/meat/oligo.Rcheck/tests_i386"

$pathToUnitTests
[1] "C:/Users/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

Attaching package: 'IRanges'

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

    windows

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 C:/Users/biocbuild/bbs-3.14-bioc/R/library/maqcExpression4plex/extdata/9868701_532.xys.
Reading C:/Users/biocbuild/bbs-3.14-bioc/R/library/maqcExpression4plex/extdata/9868901_532.xys.
Reading C:/Users/biocbuild/bbs-3.14-bioc/R/library/maqcExpression4plex/extdata/9869001_532.xys.
Reading C:/Users/biocbuild/bbs-3.14-bioc/R/library/maqcExpression4plex/extdata/9870301_532.xys.
Reading C:/Users/biocbuild/bbs-3.14-bioc/R/library/maqcExpression4plex/extdata/9870401_532.xys.
Reading C:/Users/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 -- Mon Jan 17 00:59:18 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 
 105.90    9.04  167.93 

oligo.Rcheck/tests_x64/doRUnit.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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] "C:/Users/biocbuild/bbs-3.14-bioc/meat/oligo.Rcheck/tests_x64"

$pathToUnitTests
[1] "C:/Users/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

Attaching package: 'IRanges'

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

    windows

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 C:/Users/biocbuild/bbs-3.14-bioc/R/library/maqcExpression4plex/extdata/9868701_532.xys.
Reading C:/Users/biocbuild/bbs-3.14-bioc/R/library/maqcExpression4plex/extdata/9868901_532.xys.
Reading C:/Users/biocbuild/bbs-3.14-bioc/R/library/maqcExpression4plex/extdata/9869001_532.xys.
Reading C:/Users/biocbuild/bbs-3.14-bioc/R/library/maqcExpression4plex/extdata/9870301_532.xys.
Reading C:/Users/biocbuild/bbs-3.14-bioc/R/library/maqcExpression4plex/extdata/9870401_532.xys.
Reading C:/Users/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 -- Mon Jan 17 01:00:48 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 
  83.73    5.40   89.18 

Example timings

oligo.Rcheck/examples_i386/oligo-Ex.timings

nameusersystemelapsed
Index-methods000
IntensityMatrix-methods2.410.098.54
MAplot-methods2.700.103.64
basecontent000
basicPLM5.090.215.49
basicRMA5.520.085.59
colors0.030.000.03
coordinates000
fitProbeLevelModel6.310.138.17
getProbeInfo14.03 2.3920.69
image1.280.121.41
justSNPRMA000
list.xysfiles000
oligoPLM-class000
paCalls000
preprocessTools40.21 1.3941.61
read.celfiles6.980.137.40
read.xysfiles1.780.141.93
rma-methods4.590.254.85
sequenceDesignMatrix0.020.000.01

oligo.Rcheck/examples_x64/oligo-Ex.timings

nameusersystemelapsed
Index-methods000
IntensityMatrix-methods1.050.031.08
MAplot-methods1.640.071.70
basecontent000
basicPLM4.160.004.17
basicRMA4.580.004.58
colors0.030.000.03
coordinates000
fitProbeLevelModel4.720.064.94
getProbeInfo11.48 1.7513.23
image0.860.030.89
justSNPRMA000
list.xysfiles000
oligoPLM-class000
paCalls000
preprocessTools31.33 0.4431.77
read.celfiles3.780.193.96
read.xysfiles0.900.000.91
rma-methods3.350.003.34
sequenceDesignMatrix000