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BioC 3.5: INSTALL report for VariantFiltering on tokay2

This page was generated on 2017-08-16 13:23:11 -0400 (Wed, 16 Aug 2017).

Package 1357/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantFiltering 1.12.1
Robert Castelo
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/VariantFiltering
Last Changed Rev: 129348 / Revision: 131943
Last Changed Date: 2017-05-02 14:06:49 -0400 (Tue, 02 May 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: VariantFiltering
Version: 1.12.1
Command: rm -rf VariantFiltering.buildbin-libdir && mkdir VariantFiltering.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.5/bioc/src/contrib/VariantFiltering_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=VariantFiltering.buildbin-libdir --merge-multiarch VariantFiltering_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL VariantFiltering_1.12.1.zip && rm VariantFiltering_1.12.1.tar.gz VariantFiltering_1.12.1.zip
StartedAt: 2017-08-15 18:40:55 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 18:42:54 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 119.4 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf VariantFiltering.buildbin-libdir && mkdir VariantFiltering.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.5/bioc/src/contrib/VariantFiltering_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=VariantFiltering.buildbin-libdir --merge-multiarch VariantFiltering_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL VariantFiltering_1.12.1.zip  && rm VariantFiltering_1.12.1.tar.gz VariantFiltering_1.12.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3030k  100 3030k    0     0  22.7M      0 --:--:-- --:--:-- --:--:-- 22.9M

install for i386

* installing *source* package 'VariantFiltering' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_VariantFiltering.c -o R_init_VariantFiltering.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c methods-WeightMatrix.c -o methods-WeightMatrix.o
methods-WeightMatrix.c: In function 'scoss_wm_score':
methods-WeightMatrix.c:100:11: warning: unused variable 'scores' [-Wunused-variable]
   double* scores;
           ^
methods-WeightMatrix.c:99:7: warning: unused variable 'nsco' [-Wunused-variable]
   int nsco = INTEGER(nscoR)[0];
       ^
methods-WeightMatrix.c:96:13: warning: variable 'k' set but not used [-Wunused-but-set-variable]
   int i, j, k;
             ^
methods-WeightMatrix.c: In function 'scoss_wm_score_DNAStringSet':
methods-WeightMatrix.c:131:11: warning: unused variable 'scores' [-Wunused-variable]
   double* scores;
           ^
methods-WeightMatrix.c:129:7: warning: unused variable 'nsco' [-Wunused-variable]
   int nsco = INTEGER(nscoR)[0];
       ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o VariantFiltering.dll tmp.def Biostrings_stubs.o R_init_VariantFiltering.o methods-WeightMatrix.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/VariantFiltering.buildbin-libdir/VariantFiltering/libs/i386
** R
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery

install for x64

* installing *source* package 'VariantFiltering' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_VariantFiltering.c -o R_init_VariantFiltering.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c methods-WeightMatrix.c -o methods-WeightMatrix.o
methods-WeightMatrix.c: In function 'scoss_wm_score':
methods-WeightMatrix.c:100:11: warning: unused variable 'scores' [-Wunused-variable]
   double* scores;
           ^
methods-WeightMatrix.c:99:7: warning: unused variable 'nsco' [-Wunused-variable]
   int nsco = INTEGER(nscoR)[0];
       ^
methods-WeightMatrix.c:96:13: warning: variable 'k' set but not used [-Wunused-but-set-variable]
   int i, j, k;
             ^
methods-WeightMatrix.c: In function 'scoss_wm_score_DNAStringSet':
methods-WeightMatrix.c:131:11: warning: unused variable 'scores' [-Wunused-variable]
   double* scores;
           ^
methods-WeightMatrix.c:129:7: warning: unused variable 'nsco' [-Wunused-variable]
   int nsco = INTEGER(nscoR)[0];
       ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o VariantFiltering.dll tmp.def Biostrings_stubs.o R_init_VariantFiltering.o methods-WeightMatrix.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/VariantFiltering.buildbin-libdir/VariantFiltering/libs/x64
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* MD5 sums
packaged installation of 'VariantFiltering' as VariantFiltering_1.12.1.zip
* DONE (VariantFiltering)
* installing to library 'C:/Users/biocbuild/bbs-3.5-bioc/R/library'
package 'VariantFiltering' successfully unpacked and MD5 sums checked