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 | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
##############################################################################
##############################################################################
###
### 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