MSnbase 2.2.0
Laurent Gatto
| 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/MSnbase | | 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 | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK | |
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### Running command:
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### rm -rf MSnbase.buildbin-libdir && mkdir MSnbase.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.5/bioc/src/contrib/MSnbase_2.2.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=MSnbase.buildbin-libdir --merge-multiarch MSnbase_2.2.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL MSnbase_2.2.0.zip && rm MSnbase_2.2.0.tar.gz MSnbase_2.2.0.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
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1626k 100 1626k 0 0 2856k 0 --:--:-- --:--:-- --:--:-- 2858k
install for i386
* installing *source* package 'MSnbase' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.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/Rcpp/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Spectrum1_class.c -o Spectrum1_class.o
Spectrum1_class.c:8:13: warning: '_new_Spectrum1' defined but not used [-Wunused-function]
static SEXP _new_Spectrum1(SEXP msLevel, SEXP peaksCount, SEXP rt,
^
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/Rcpp/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Spectrum2_class.c -o Spectrum2_class.o
Spectrum2_class.c:9:13: warning: '_new_Spectrum2' defined but not used [-Wunused-function]
static SEXP _new_Spectrum2(SEXP msLevel, SEXP peaksCount, SEXP rt,
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c imp_neighbour_avg.cpp -o imp_neighbour_avg.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/Rcpp/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c utils.c -o utils.o
utils.c: In function 'compar_double_dd_for_stable_asc_order':
utils.c:92:15: warning: unused variable 'ret' [-Wunused-variable]
int i1, i2, ret;
^
utils.c: In function 'compar_double_dd_for_stable_desc_order':
utils.c:107:15: warning: unused variable 'ret' [-Wunused-variable]
int i1, i2, ret;
^
utils.c: In function 'compar_double_asc_order':
utils.c:123:18: warning: unused variable 'ret' [-Wunused-variable]
double d1, d2, ret;
^
utils.c: In function 'compar_double_desc_order':
utils.c:133:18: warning: unused variable 'ret' [-Wunused-variable]
double d1, d2, ret;
^
utils.c: At top level:
utils.c:121:12: warning: 'compar_double_asc_order' defined but not used [-Wunused-function]
static int compar_double_asc_order(const void *p1, const void *p2)
^
utils.c:131:12: warning: 'compar_double_desc_order' defined but not used [-Wunused-function]
static int compar_double_desc_order(const void *p1, const void *p2)
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o MSnbase.dll tmp.def RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.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/MSnbase.buildbin-libdir/MSnbase/libs/i386
** R
** data
*** moving datasets to lazyload DB
Creating a new generic function for 'smooth' in package 'MSnbase'
Creating a new generic function for 'trimws' in package 'MSnbase'
in method for 'coerce' with signature '"IBSpectra","MSnSet"': no definition for class "IBSpectra"
** inst
** preparing package for lazy loading
Creating a new generic function for 'smooth' in package 'MSnbase'
Creating a new generic function for 'trimws' in package 'MSnbase'
in method for 'coerce' with signature '"IBSpectra","MSnSet"': no definition for class "IBSpectra"
** help
*** installing help indices
** building package indices
** installing vignettes
'MSnbase-development.Rmd' using 'UTF-8'
'MSnbase-io.Rmd' using 'UTF-8'
'benchmarking.Rmd' using 'UTF-8'
'MSnbase-demo.Rnw'
** testing if installed package can be loaded
install for x64
* installing *source* package 'MSnbase' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.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/Rcpp/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Spectrum1_class.c -o Spectrum1_class.o
Spectrum1_class.c:8:13: warning: '_new_Spectrum1' defined but not used [-Wunused-function]
static SEXP _new_Spectrum1(SEXP msLevel, SEXP peaksCount, SEXP rt,
^
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/Rcpp/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Spectrum2_class.c -o Spectrum2_class.o
Spectrum2_class.c:9:13: warning: '_new_Spectrum2' defined but not used [-Wunused-function]
static SEXP _new_Spectrum2(SEXP msLevel, SEXP peaksCount, SEXP rt,
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c imp_neighbour_avg.cpp -o imp_neighbour_avg.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/Rcpp/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c utils.c -o utils.o
utils.c: In function 'compar_double_dd_for_stable_asc_order':
utils.c:92:15: warning: unused variable 'ret' [-Wunused-variable]
int i1, i2, ret;
^
utils.c: In function 'compar_double_dd_for_stable_desc_order':
utils.c:107:15: warning: unused variable 'ret' [-Wunused-variable]
int i1, i2, ret;
^
utils.c: In function 'compar_double_asc_order':
utils.c:123:18: warning: unused variable 'ret' [-Wunused-variable]
double d1, d2, ret;
^
utils.c: In function 'compar_double_desc_order':
utils.c:133:18: warning: unused variable 'ret' [-Wunused-variable]
double d1, d2, ret;
^
utils.c: At top level:
utils.c:121:12: warning: 'compar_double_asc_order' defined but not used [-Wunused-function]
static int compar_double_asc_order(const void *p1, const void *p2)
^
utils.c:131:12: warning: 'compar_double_desc_order' defined but not used [-Wunused-function]
static int compar_double_desc_order(const void *p1, const void *p2)
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o MSnbase.dll tmp.def RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.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/MSnbase.buildbin-libdir/MSnbase/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSnbase' as MSnbase_2.2.0.zip
* DONE (MSnbase)
* installing to library 'C:/Users/biocbuild/bbs-3.5-bioc/R/library'
package 'MSnbase' successfully unpacked and MD5 sums checked