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INSTALL report for geneXtendeR on tokay1

This page was generated on 2020-04-15 12:27:23 -0400 (Wed, 15 Apr 2020).

Package 670/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geneXtendeR 1.12.0
Bohdan Khomtchouk
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/geneXtendeR
Branch: RELEASE_3_10
Last Commit: 2b766f5
Last Changed Date: 2019-10-29 13:10:08 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: geneXtendeR
Version: 1.12.0
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/geneXtendeR_1.12.0.tar.gz && rm -rf geneXtendeR.buildbin-libdir && mkdir geneXtendeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=geneXtendeR.buildbin-libdir geneXtendeR_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL geneXtendeR_1.12.0.zip && rm geneXtendeR_1.12.0.tar.gz geneXtendeR_1.12.0.zip
StartedAt: 2020-04-14 19:50:45 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 19:52:27 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 101.7 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/geneXtendeR_1.12.0.tar.gz && rm -rf geneXtendeR.buildbin-libdir && mkdir geneXtendeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=geneXtendeR.buildbin-libdir geneXtendeR_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL geneXtendeR_1.12.0.zip && rm geneXtendeR_1.12.0.tar.gz geneXtendeR_1.12.0.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
 17 11.7M   17 2064k    0     0  3473k      0  0:00:03 --:--:--  0:00:03 3486k
 88 11.7M   88 10.3M    0     0  6767k      0  0:00:01  0:00:01 --:--:-- 6777k
100 11.7M  100 11.7M    0     0  7300k      0  0:00:01  0:00:01 --:--:-- 7313k

install for i386

* installing *source* package 'geneXtendeR' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c annotate.c -o annotate.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c extract_number.c -o extract_number.o
extract_number.c: In function 'extractnumber':
extract_number.c:72:10: warning: variable 'n_1' set but not used [-Wunused-but-set-variable]
     long n_1;
          ^
extract_number.c:66:10: warning: variable 'j_1' set but not used [-Wunused-but-set-variable]
     long j_1;
          ^
extract_number.c:54:12: warning: variable 'pvcfcol5_5' set but not used [-Wunused-but-set-variable]
     char * pvcfcol5_5;
            ^
extract_number.c:53:12: warning: variable 'pvcfcol4_4' set but not used [-Wunused-but-set-variable]
     char * pvcfcol4_4;
            ^
extract_number.c:52:12: warning: variable 'pvcfcol3_3' set but not used [-Wunused-but-set-variable]
     char * pvcfcol3_3;
            ^
extract_number.c:51:12: warning: variable 'pvcfcol2_2' set but not used [-Wunused-but-set-variable]
     char * pvcfcol2_2;
            ^
extract_number.c:50:12: warning: variable 'pvcfcol1_1' set but not used [-Wunused-but-set-variable]
     char * pvcfcol1_1;
            ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c extract_peaks.c -o extract_peaks.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o geneXtendeR.dll tmp.def annotate.o extract_number.o extract_peaks.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/geneXtendeR.buildbin-libdir/00LOCK-geneXtendeR/00new/geneXtendeR/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'geneXtendeR'
    finding HTML links ... done
    allPeakLengths                          html  
    annotate                                html  
    annotate_n                              html  
    barChart                                html  
    cumlinePlot                             html  
    diffGO                                  html  
    distinct                                html  
    dot-geneXtender                         html  
    gene_annotate                           html  
    gene_lookup                             html  
    hotspotPlot                             html  
    linePlot                                html  
    makeNetwork                             html  
    makeWordCloud                           html  
    meanPeakLength                          html  
    meanPeakLengthPlot                      html  
    peakLengthBoxplot                       html  
    peaksInput                              html  
    peaksMerge                              html  
    plotWordFreq                            html  
    rat                                     html  
    samplepeaksinput                        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 'geneXtendeR' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c annotate.c -o annotate.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c extract_number.c -o extract_number.o
extract_number.c: In function 'extractnumber':
extract_number.c:72:10: warning: variable 'n_1' set but not used [-Wunused-but-set-variable]
     long n_1;
          ^
extract_number.c:66:10: warning: variable 'j_1' set but not used [-Wunused-but-set-variable]
     long j_1;
          ^
extract_number.c:54:12: warning: variable 'pvcfcol5_5' set but not used [-Wunused-but-set-variable]
     char * pvcfcol5_5;
            ^
extract_number.c:53:12: warning: variable 'pvcfcol4_4' set but not used [-Wunused-but-set-variable]
     char * pvcfcol4_4;
            ^
extract_number.c:52:12: warning: variable 'pvcfcol3_3' set but not used [-Wunused-but-set-variable]
     char * pvcfcol3_3;
            ^
extract_number.c:51:12: warning: variable 'pvcfcol2_2' set but not used [-Wunused-but-set-variable]
     char * pvcfcol2_2;
            ^
extract_number.c:50:12: warning: variable 'pvcfcol1_1' set but not used [-Wunused-but-set-variable]
     char * pvcfcol1_1;
            ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c extract_peaks.c -o extract_peaks.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o geneXtendeR.dll tmp.def annotate.o extract_number.o extract_peaks.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/geneXtendeR.buildbin-libdir/geneXtendeR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'geneXtendeR' as geneXtendeR_1.12.0.zip
* DONE (geneXtendeR)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'geneXtendeR' successfully unpacked and MD5 sums checked