xcms 1.49.6
Steffen Neumann
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms | | Last Changed Rev: 120725 / Revision: 121152 | | Last Changed Date: 2016-09-05 04:13:31 -0700 (Mon, 05 Sep 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | [ OK ] | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf xcms.buildbin-libdir && mkdir xcms.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/xcms_1.49.6.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=xcms.buildbin-libdir --merge-multiarch xcms_1.49.6.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL xcms_1.49.6.zip && rm xcms_1.49.6.tar.gz xcms_1.49.6.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 318k 100 318k 0 0 16.2M 0 --:--:-- --:--:-- --:--:-- 22.2M
install for i386
* installing *source* package 'xcms' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
massifquant/xcms_massifquant.cpp: In function 'SEXPREC* massifquant(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
massifquant/xcms_massifquant.cpp:122:6: warning: unused variable 'scanLength' [-Wunused-variable]
int scanLength = int(featInfo.at(5) - featInfo.at(4) + 1);
^
massifquant/xcms_massifquant.cpp:33:58: warning: unused variable 'vstcenter' [-Wunused-variable]
SEXP peaklist,entrylist,list_names,vmz,vmzmin,vmzmax,vstcenter,vscmin,vscmax,vintensity,vintenmax, vlength;
^
massifquant/xcms_massifquant.cpp:33:93: warning: unused variable 'vintenmax' [-Wunused-variable]
SEXP peaklist,entrylist,list_names,vmz,vmzmin,vmzmax,vstcenter,vscmin,vscmax,vintensity,vintenmax, vlength;
^
massifquant/xcms_massifquant.cpp:76:12: warning: unused variable 'maxScanNums' [-Wunused-variable]
double maxScanNums = double(scanrangeTo);
^
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -c massifquant/Tracker.cpp -o massifquant/Tracker.o
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -c massifquant/SegProc.cpp -o massifquant/SegProc.o
massifquant/SegProc.cpp: In member function 'void SegProc::collapseSubsets()':
massifquant/SegProc.cpp:119:13: warning: variable 'combinedUnions' set but not used [-Wunused-but-set-variable]
int combinedUnions = 0;
^
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -c obiwarp/mat.cpp -o obiwarp/mat.o
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -c obiwarp/vec.cpp -o obiwarp/vec.o
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
obiwarp/xcms_dynprog.cpp: In member function 'void DynProg::find_path(VEC::MatF&, VEC::VecF&, int, float, float, int, float)':
obiwarp/xcms_dynprog.cpp:1113:9: warning: variable 'bestscore' set but not used [-Wunused-but-set-variable]
float bestscore;
^
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -c xcms_obiwarp.cpp -o xcms_obiwarp.o
C:/Rtools/mingw_32/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -fno-inline -c fastMatch.c -o fastMatch.o
C:/Rtools/mingw_32/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -fno-inline -c mzClust_hclust.c -o mzClust_hclust.o
C:/Rtools/mingw_32/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -fno-inline -c mzROI.c -o mzROI.o
mzROI.c: In function 'getMZ':
mzROI.c:486:17: warning: variable 'pintensity' set but not used [-Wunused-but-set-variable]
double *pmz, *pintensity,*p_res, mzrangeFrom,mzrangeTo;
^
mzROI.c: In function 'findmzROI':
mzROI.c:538:41: warning: variable 'mzrangeTo' set but not used [-Wunused-but-set-variable]
double *pmz, *pintensity, mzrangeFrom,mzrangeTo;
^
mzROI.c:538:29: warning: variable 'mzrangeFrom' set but not used [-Wunused-but-set-variable]
double *pmz, *pintensity, mzrangeFrom,mzrangeTo;
^
C:/Rtools/mingw_32/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -fno-inline -c util.c -o util.o
C:/Rtools/mingw_32/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -fno-inline -c xcms.c -o xcms.o
C:/Rtools/mingw_32/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -fno-inline -c binners.c -o binners.o
binners.c: In function '_impute_linearly_interpolate_base_x':
binners.c:707:12: warning: unused variable 'next_bin_value' [-Wunused-variable]
double next_bin_value = base_value;
^
binners.c:642:10: warning: unused variable 'new_value' [-Wunused-variable]
double new_value;
^
binners.c:641:10: warning: unused variable 'incrementer' [-Wunused-variable]
double incrementer = 0;
^
binners.c: In function 'binYonX':
binners.c:174:5: warning: 'index' may be used uninitialized in this function [-Wmaybe-uninitialized]
SET_VECTOR_ELT(ans_list, 2, index);
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o xcms.dll tmp.def massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o binners.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/xcms.buildbin-libdir/xcms/libs/i386
** R
** inst
** preparing package for lazy loading
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.
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 'xcms' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
massifquant/xcms_massifquant.cpp: In function 'SEXPREC* massifquant(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
massifquant/xcms_massifquant.cpp:122:6: warning: unused variable 'scanLength' [-Wunused-variable]
int scanLength = int(featInfo.at(5) - featInfo.at(4) + 1);
^
massifquant/xcms_massifquant.cpp:33:58: warning: unused variable 'vstcenter' [-Wunused-variable]
SEXP peaklist,entrylist,list_names,vmz,vmzmin,vmzmax,vstcenter,vscmin,vscmax,vintensity,vintenmax, vlength;
^
massifquant/xcms_massifquant.cpp:33:93: warning: unused variable 'vintenmax' [-Wunused-variable]
SEXP peaklist,entrylist,list_names,vmz,vmzmin,vmzmax,vstcenter,vscmin,vscmax,vintensity,vintenmax, vlength;
^
massifquant/xcms_massifquant.cpp:76:12: warning: unused variable 'maxScanNums' [-Wunused-variable]
double maxScanNums = double(scanrangeTo);
^
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -c massifquant/Tracker.cpp -o massifquant/Tracker.o
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -c massifquant/SegProc.cpp -o massifquant/SegProc.o
massifquant/SegProc.cpp: In member function 'void SegProc::collapseSubsets()':
massifquant/SegProc.cpp:119:13: warning: variable 'combinedUnions' set but not used [-Wunused-but-set-variable]
int combinedUnions = 0;
^
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -c obiwarp/mat.cpp -o obiwarp/mat.o
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -c obiwarp/vec.cpp -o obiwarp/vec.o
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
obiwarp/xcms_dynprog.cpp: In member function 'void DynProg::find_path(VEC::MatF&, VEC::VecF&, int, float, float, int, float)':
obiwarp/xcms_dynprog.cpp:1113:9: warning: variable 'bestscore' set but not used [-Wunused-but-set-variable]
float bestscore;
^
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -c xcms_obiwarp.cpp -o xcms_obiwarp.o
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -fno-inline -c fastMatch.c -o fastMatch.o
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -fno-inline -c mzClust_hclust.c -o mzClust_hclust.o
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -fno-inline -c mzROI.c -o mzROI.o
mzROI.c: In function 'getMZ':
mzROI.c:486:17: warning: variable 'pintensity' set but not used [-Wunused-but-set-variable]
double *pmz, *pintensity,*p_res, mzrangeFrom,mzrangeTo;
^
mzROI.c: In function 'findmzROI':
mzROI.c:538:41: warning: variable 'mzrangeTo' set but not used [-Wunused-but-set-variable]
double *pmz, *pintensity, mzrangeFrom,mzrangeTo;
^
mzROI.c:538:29: warning: variable 'mzrangeFrom' set but not used [-Wunused-but-set-variable]
double *pmz, *pintensity, mzrangeFrom,mzrangeTo;
^
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -fno-inline -c util.c -o util.o
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -fno-inline -c xcms.c -o xcms.o
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -fno-inline -c binners.c -o binners.o
binners.c: In function '_impute_linearly_interpolate_base_x':
binners.c:707:12: warning: unused variable 'next_bin_value' [-Wunused-variable]
double next_bin_value = base_value;
^
binners.c:642:10: warning: unused variable 'new_value' [-Wunused-variable]
double new_value;
^
binners.c:641:10: warning: unused variable 'incrementer' [-Wunused-variable]
double incrementer = 0;
^
binners.c: In function 'binYonX':
binners.c:174:5: warning: 'index' may be used uninitialized in this function [-Wmaybe-uninitialized]
SET_VECTOR_ELT(ans_list, 2, index);
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o xcms.dll tmp.def massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o binners.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/xcms.buildbin-libdir/xcms/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 'xcms' as xcms_1.49.6.zip
* DONE (xcms)
* installing to library 'D:/biocbld/bbs-3.4-bioc/R/library'
package 'xcms' successfully unpacked and MD5 sums checked