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INSTALL report for oligo on tokay2

This page was generated on 2020-10-17 11:57:18 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE oligo PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1215/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oligo 1.52.1
Benilton Carvalho
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/oligo
Branch: RELEASE_3_11
Last Commit: cbd66c8
Last Changed Date: 2020-08-10 12:21:46 -0400 (Mon, 10 Aug 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: oligo
Version: 1.52.1
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/oligo_1.52.1.tar.gz && rm -rf oligo.buildbin-libdir && mkdir oligo.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=oligo.buildbin-libdir oligo_1.52.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL oligo_1.52.1.zip && rm oligo_1.52.1.tar.gz oligo_1.52.1.zip
StartedAt: 2020-10-16 17:58:30 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 18:00:16 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 106.9 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/oligo_1.52.1.tar.gz && rm -rf oligo.buildbin-libdir && mkdir oligo.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=oligo.buildbin-libdir oligo_1.52.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL oligo_1.52.1.zip && rm oligo_1.52.1.tar.gz oligo_1.52.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 59 14.9M   59 9104k    0     0  7392k      0  0:00:02  0:00:01  0:00:01 7425k
100 14.9M  100 14.9M    0     0  7835k      0  0:00:01  0:00:01 --:--:-- 7860k

install for i386

* installing *source* package 'oligo' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lRblas -LC:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/oligo.buildbin-libdir/00LOCK-oligo/00new/oligo/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'oligo'
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  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp6hXs3G/R.INSTALL169061a353d3/oligo/man/basicPLM.Rd:42: file link 'rcModelPLM' in package 'preprocessCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp6hXs3G/R.INSTALL169061a353d3/oligo/man/basicPLM.Rd:44: file link 'rcModelPLMrr' in package 'preprocessCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp6hXs3G/R.INSTALL169061a353d3/oligo/man/basicPLM.Rd:45: file link 'rcModelPLMrc' in package 'preprocessCore' does not exist and so has been treated as a topic
    basicRMA                                html  
    boxplot                                 html  
    chromosome                              html  
    colors                                  html  
    coordinates                             html  
    crlmm                                   html  
    fitProbeLevelModel                      html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp6hXs3G/R.INSTALL169061a353d3/oligo/man/fitProbeLevelModel.Rd:9: file link 'FeatureSet' in package 'oligoClasses' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp6hXs3G/R.INSTALL169061a353d3/oligo/man/fitProbeLevelModel.Rd:17: file link 'FeatureSet' in package 'oligoClasses' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp6hXs3G/R.INSTALL169061a353d3/oligo/man/fitProbeLevelModel.Rd:50: file link 'rma' in package 'oligo' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp6hXs3G/R.INSTALL169061a353d3/oligo/man/fitProbeLevelModel.Rd:50: file link 'summarizationMethods' in package 'oligo' does not exist and so has been treated as a topic
    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  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp6hXs3G/R.INSTALL169061a353d3/oligo/man/oligoPLM-class.Rd:131: file link 'rma' in package 'oligo' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp6hXs3G/R.INSTALL169061a353d3/oligo/man/oligoPLM-class.Rd:131: file link 'summarize' in package 'oligo' does not exist and so has been treated as a topic
    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
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'oligo'
** testing if installed package can be loaded from final location
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'oligo'
** 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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lRblas -LC:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/oligo.buildbin-libdir/oligo/libs/x64
** testing if installed package can be loaded
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'oligo'
* MD5 sums
packaged installation of 'oligo' as oligo_1.52.1.zip
* DONE (oligo)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'oligo' successfully unpacked and MD5 sums checked