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BioC 3.5: INSTALL report for biovizBase on tokay2

This page was generated on 2017-08-16 13:21:18 -0400 (Wed, 16 Aug 2017).

Package 138/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biovizBase 1.24.0
Michael Lawrence
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/biovizBase
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: biovizBase
Version: 1.24.0
Command: rm -rf biovizBase.buildbin-libdir && mkdir biovizBase.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.5/bioc/src/contrib/biovizBase_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=biovizBase.buildbin-libdir --merge-multiarch biovizBase_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL biovizBase_1.24.0.zip && rm biovizBase_1.24.0.tar.gz biovizBase_1.24.0.zip
StartedAt: 2017-08-15 18:39:03 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 18:39:56 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 53.1 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf biovizBase.buildbin-libdir && mkdir biovizBase.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.5/bioc/src/contrib/biovizBase_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=biovizBase.buildbin-libdir --merge-multiarch biovizBase_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL biovizBase_1.24.0.zip  && rm biovizBase_1.24.0.tar.gz biovizBase_1.24.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2133k  100 2133k    0     0  36.0M      0 --:--:-- --:--:-- --:--:-- 37.2M

install for i386

* installing *source* package 'biovizBase' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_biovizBase.c -o R_init_biovizBase.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c bin_offsets.c -o bin_offsets.o
bin_offsets.c: In function 'scan_bam_bin_offsets':
bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of 'strncmp' differ in signedness [-Wpointer-sign]
   if (strncmp(b, "BAI\1", 4))
               ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include/R_ext/RS.h:34:0,
                 from C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include/Rdefines.h:37,
                 from bin_offsets.h:1,
                 from bin_offsets.c:3:
C:/Rtools/mingw_32/i686-w64-mingw32/include/string.h:76:15: note: expected 'const char *' but argument is of type 'Rbyte *'
   int __cdecl strncmp(const char *_Str1,const char *_Str2,size_t _MaxCount);
               ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o biovizBase.dll tmp.def R_init_biovizBase.o bin_offsets.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/biovizBase.buildbin-libdir/biovizBase/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'biovizBase' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_biovizBase.c -o R_init_biovizBase.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c bin_offsets.c -o bin_offsets.o
bin_offsets.c: In function 'scan_bam_bin_offsets':
bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of 'strncmp' differ in signedness [-Wpointer-sign]
   if (strncmp(b, "BAI\1", 4))
               ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include/R_ext/RS.h:34:0,
                 from C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include/Rdefines.h:37,
                 from bin_offsets.h:1,
                 from bin_offsets.c:3:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/string.h:76:15: note: expected 'const char *' but argument is of type 'Rbyte *'
   int __cdecl strncmp(const char *_Str1,const char *_Str2,size_t _MaxCount);
               ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o biovizBase.dll tmp.def R_init_biovizBase.o bin_offsets.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/biovizBase.buildbin-libdir/biovizBase/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biovizBase' as biovizBase_1.24.0.zip
* DONE (biovizBase)
* installing to library 'C:/Users/biocbuild/bbs-3.5-bioc/R/library'
package 'biovizBase' successfully unpacked and MD5 sums checked