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INSTALL report for simpleaffy on tokay2

This page was generated on 2019-10-16 12:19:03 -0400 (Wed, 16 Oct 2019).

Package 1528/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
simpleaffy 2.60.0
Crispin Miller
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/simpleaffy
Branch: RELEASE_3_9
Last Commit: b32b5e7
Last Changed Date: 2019-05-02 11:53:02 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: simpleaffy
Version: 2.60.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/simpleaffy_2.60.0.tar.gz && rm -rf simpleaffy.buildbin-libdir && mkdir simpleaffy.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=simpleaffy.buildbin-libdir simpleaffy_2.60.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL simpleaffy_2.60.0.zip && rm simpleaffy_2.60.0.tar.gz simpleaffy_2.60.0.zip
StartedAt: 2019-10-15 19:36:20 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 19:38:01 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 100.7 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/simpleaffy_2.60.0.tar.gz && rm -rf simpleaffy.buildbin-libdir && mkdir simpleaffy.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=simpleaffy.buildbin-libdir simpleaffy_2.60.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL simpleaffy_2.60.0.zip && rm simpleaffy_2.60.0.tar.gz simpleaffy_2.60.0.zip
###
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install for i386

* installing *source* package 'simpleaffy' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c simpleaffy.c -o simpleaffy.o
simpleaffy.c: In function 'bgmas':
simpleaffy.c:440:30: warning: passing argument 1 of 'REprintf' from incompatible pointer type
     if(gn >= ngrid) REprintf(stderr,"Really ouch! %d %d\n",gn,ends[gn]);
                              ^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/R.h:88:0,
                 from simpleaffy.c:5:
C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/R_ext/Print.h:43:6: note: expected 'const char *' but argument is of type 'struct FILE *'
 void REprintf(const char *, ...);
      ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o simpleaffy.dll tmp.def simpleaffy.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/simpleaffy.buildbin-libdir/00LOCK-simpleaffy/00new/simpleaffy/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'simpleaffy'
    finding HTML links ... done
    PairComp-class                          html  
    QCStats-class                           html  
    all.present                             html  
    all.present.in.group                    html  
    bg.correct.sa                           html  
    call.exprs                              html  
    detection.p.val                         html  
    get.annotation                          html  
    get.array.indices                       html  
    get.array.subset                        html  
    get.array.subset.affy                   html  
    get.fold.change.and.t.test              html  
    hmap.colors                             html  
    hmap.eset                               html  
    hmap.pc                                 html  
    journalpng                              html  
    justMAS                                 html  
    pairwise.comparison                     html  
    pairwise.filter                         html  
    plot.pairwise.comparison                html  
    plot.qc.stats                           html  
    qc                                      html  
    qc.affy                                 html  
    qc.get.alpha1                           html  
    qc.get.array                            html  
    qc.get.probes                           html  
    qc.get.ratios                           html  
    qc.get.spikes                           html  
    qc.have.params                          html  
    qc.ok                                   html  
    qc.read.file                            html  
    qc.stats                                html  
    read.affy                               html  
    read.affy.mixed                         html  
    setQCEnvironment                        html  
    simpleaffy-deprecated                   html  
    standard.pearson                        html  
    trad.scatter.plot                       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 'simpleaffy' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c simpleaffy.c -o simpleaffy.o
simpleaffy.c: In function 'bgmas':
simpleaffy.c:440:30: warning: passing argument 1 of 'REprintf' from incompatible pointer type
     if(gn >= ngrid) REprintf(stderr,"Really ouch! %d %d\n",gn,ends[gn]);
                              ^
In file included from C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/R.h:88:0,
                 from simpleaffy.c:5:
C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include/R_ext/Print.h:43:6: note: expected 'const char *' but argument is of type 'struct FILE *'
 void REprintf(const char *, ...);
      ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o simpleaffy.dll tmp.def simpleaffy.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/simpleaffy.buildbin-libdir/simpleaffy/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'simpleaffy' as simpleaffy_2.60.0.zip
* DONE (simpleaffy)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'simpleaffy' successfully unpacked and MD5 sums checked