MSnbase 1.99.1
Laurent Gatto
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase | | Last Changed Rev: 120944 / Revision: 121152 | | Last Changed Date: 2016-09-14 09:16:36 -0700 (Wed, 14 Sep 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | OK | OK | ERROR | | |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | [ OK ] | OK | OK | OK |  |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | 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://zin1/BBS/3.4/bioc/src/contrib/MSnbase_1.99.1.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=MSnbase.buildbin-libdir --merge-multiarch MSnbase_1.99.1.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL MSnbase_1.99.1.zip && rm MSnbase_1.99.1.tar.gz MSnbase_1.99.1.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
100 1574k 100 1574k 0 0 46.5M 0 --:--:-- --:--:-- --:--:-- 53.0M
install for i386
* installing *source* package 'MSnbase' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Spectrum1_class.c -o Spectrum1_class.o
C:/Rtools/mingw_32/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Spectrum2_class.c -o Spectrum2_class.o
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-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 -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/MSnbase.buildbin-libdir/MSnbase/libs/i386
** R
** data
*** moving datasets to lazyload DB
Warning in fun(libname, pkgname) :
mzR has been built against a different Rcpp version (0.12.6)
than is installed on your system (0.12.7). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
Creating a new generic function for 'smooth' in package 'MSnbase'
Creating a new generic function for 'trimws' in package 'MSnbase'
Creating a generic function for 't' from package 'base' in package 'MSnbase'
Creating a generic function for 'scale' from package 'base' in package 'MSnbase'
in method for 'coerce' with signature '"IBSpectra","MSnSet"': no definition for class "IBSpectra"
Creating a generic function for 'split' from package 'base' in package 'MSnbase'
Creating a generic function for 'all.equal' from package 'base' in package 'MSnbase'
** 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'
Creating a generic function for 't' from package 'base' in package 'MSnbase'
Creating a generic function for 'scale' from package 'base' in package 'MSnbase'
in method for 'coerce' with signature '"IBSpectra","MSnSet"': no definition for class "IBSpectra"
Creating a generic function for 'split' from package 'base' in package 'MSnbase'
Creating a generic function for 'all.equal' from package 'base' in package 'MSnbase'
** help
*** installing help indices
** building package indices
** installing vignettes
'benchmarking.Rmd'
'MSnbase-demo.Rnw'
'MSnbase-development.Rnw'
'MSnbase-io.Rnw'
** testing if installed package can be loaded
Warning in fun(libname, pkgname) :
mzR has been built against a different Rcpp version (0.12.6)
than is installed on your system (0.12.7). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
install for x64
* installing *source* package 'MSnbase' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Spectrum1_class.c -o Spectrum1_class.o
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Spectrum2_class.c -o Spectrum2_class.o
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-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 -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/MSnbase.buildbin-libdir/MSnbase/libs/x64
** testing if installed package can be loaded
Warning in fun(libname, pkgname) :
mzR has been built against a different Rcpp version (0.12.6)
than is installed on your system (0.12.7). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
* MD5 sums
packaged installation of 'MSnbase' as MSnbase_1.99.1.zip
* DONE (MSnbase)
* installing to library 'D:/biocbld/bbs-3.4-bioc/R/library'
package 'MSnbase' successfully unpacked and MD5 sums checked