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INSTALL report for VegaMC on tokay1

This page was generated on 2020-04-15 12:20:35 -0400 (Wed, 15 Apr 2020).

Package 1791/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VegaMC 3.24.0
Sandro Morganella
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/VegaMC
Branch: RELEASE_3_10
Last Commit: 27f297a
Last Changed Date: 2019-10-29 13:08:30 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK 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  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: VegaMC
Version: 3.24.0
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/VegaMC_3.24.0.tar.gz && rm -rf VegaMC.buildbin-libdir && mkdir VegaMC.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VegaMC.buildbin-libdir VegaMC_3.24.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL VegaMC_3.24.0.zip && rm VegaMC_3.24.0.tar.gz VegaMC_3.24.0.zip
StartedAt: 2020-04-14 19:38:03 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 19:38:47 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 43.8 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/VegaMC_3.24.0.tar.gz && rm -rf VegaMC.buildbin-libdir && mkdir VegaMC.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VegaMC.buildbin-libdir VegaMC_3.24.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL VegaMC_3.24.0.zip && rm VegaMC_3.24.0.tar.gz VegaMC_3.24.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1613k  100 1613k    0     0  13.6M      0 --:--:-- --:--:-- --:--:-- 14.0M

install for i386

* installing *source* package 'VegaMC' ...
** 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 run_vegaMC.c -o run_vegaMC.o
run_vegaMC.c: In function 'read_params':
run_vegaMC.c:618:18: warning: unused variable 'brkt' [-Wunused-variable]
     char *elem, *brkt;
                  ^
run_vegaMC.c: In function 'call_VegaMC':
run_vegaMC.c:466:38: warning: 'first_seg' may be used uninitialized in this function [-Wmaybe-uninitialized]
             seg_chromosomes[j] = (tmp->chromosome) + 1;
                                      ^
run_vegaMC.c:435:32: warning: 'prev_seg' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 prev_seg->next = tmp;
                                ^
run_vegaMC.c: In function 'load_data':
run_vegaMC.c:534:32: warning: 'chr' may be used uninitialized in this function [-Wmaybe-uninitialized]
         temp_probe->chromosome = chr;
                                ^
run_vegaMC.c:535:30: warning: 'position' may be used uninitialized in this function [-Wmaybe-uninitialized]
         temp_probe->position = position;
                              ^
run_vegaMC.c:564:14: warning: 'first_probe' may be used uninitialized in this function [-Wmaybe-uninitialized]
     prev_chr = temp_probe->chromosome;
              ^
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 sort_data.c -o sort_data.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 vegaMC.c -o vegaMC.o
vegaMC.c: In function 'heap_delete':
vegaMC.c:235:10: warning: variable 'deleted' set but not used [-Wunused-but-set-variable]
     node deleted;
          ^
vegaMC.c: In function 'init_trivial_segmentation':
vegaMC.c:592:15: warning: variable 'index' set but not used [-Wunused-but-set-variable]
     int i, j, index;
               ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o VegaMC.dll tmp.def run_vegaMC.o sort_data.o vegaMC.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/VegaMC.buildbin-libdir/00LOCK-VegaMC/00new/VegaMC/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'VegaMC'
    finding HTML links ... done
    VegaMC-package                          html  
    sortData                                html  
    vegaMC-methods                          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 'VegaMC' ...
** 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 run_vegaMC.c -o run_vegaMC.o
run_vegaMC.c: In function 'read_params':
run_vegaMC.c:618:18: warning: unused variable 'brkt' [-Wunused-variable]
     char *elem, *brkt;
                  ^
run_vegaMC.c: In function 'load_data':
run_vegaMC.c:534:32: warning: 'chr' may be used uninitialized in this function [-Wmaybe-uninitialized]
         temp_probe->chromosome = chr;
                                ^
run_vegaMC.c:535:30: warning: 'position' may be used uninitialized in this function [-Wmaybe-uninitialized]
         temp_probe->position = position;
                              ^
run_vegaMC.c:564:14: warning: 'first_probe' may be used uninitialized in this function [-Wmaybe-uninitialized]
     prev_chr = temp_probe->chromosome;
              ^
run_vegaMC.c: In function 'call_VegaMC':
run_vegaMC.c:461:29: warning: 'first_seg' may be used uninitialized in this function [-Wmaybe-uninitialized]
         for (i = 0; i < (tmp->num_regions); i++) {
                             ^
run_vegaMC.c:435:32: warning: 'prev_seg' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 prev_seg->next = tmp;
                                ^
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 sort_data.c -o sort_data.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 vegaMC.c -o vegaMC.o
vegaMC.c: In function 'heap_delete':
vegaMC.c:235:10: warning: variable 'deleted' set but not used [-Wunused-but-set-variable]
     node deleted;
          ^
vegaMC.c: In function 'init_trivial_segmentation':
vegaMC.c:592:15: warning: variable 'index' set but not used [-Wunused-but-set-variable]
     int i, j, index;
               ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o VegaMC.dll tmp.def run_vegaMC.o sort_data.o vegaMC.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/VegaMC.buildbin-libdir/VegaMC/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'VegaMC' as VegaMC_3.24.0.zip
* DONE (VegaMC)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'VegaMC' successfully unpacked and MD5 sums checked