xiaodfeng
commented
1 year ago As the latest version of MSnbase 2.27.1 (https://github.com/lgatto/MSnbase/blob/master/DESCRIPTION) has changed the the Spectra and Chromatograms class into MSpectra and MChromatograms class. Thus installing the XCMS 3.8.2.1 based on MSnbase 2.27.1 will result in an error. We need to stick to the MSnbase-2.14.2 which can be downloaded via https://code.bioconductor.org/browse/MSnbase/blob/RELEASE_3_11/DESCRIPTION. In the long run, the DynamicXCMS needs to be implanted based on the latest version of XCMS version 4. See below for the scripts and outputs.
library(devtools)
devtools::install("d:/OneDrive/github/PackageR/MSnbase-2.14.2",update = FALSE)
devtools::install("d:/OneDrive/github/DynamicXCMS",update = FALSE)
library(MSnbase)
library(xcms)
sessionInfo()devtools::install("d:/OneDrive/github/PackageR/MSnbase-2.14.2",update = FALSE) These packages have more recent versions available. It is recommended to update all of them. Which would you like to update?
1: All
2: CRAN packages only
3: None
4: rlang (1.1.0 -> 1.1.1 ) [CRAN]
5: vctrs (0.6.1 -> 0.6.3 ) [CRAN]
6: viridisLite (0.4.1 -> 0.4.2 ) [CRAN]
7: Rcpp (1.0.9 -> 1.0.11 ) [CRAN]
8: BiocManager (1.30.20 -> 1.30.21.1) [CRAN]
9: digest (0.6.31 -> 0.6.33 ) [CRAN]
Enter one or more numbers, or an empty line to skip updates: 3 -- R CMD build --------------------------------------------------------------------------------------------------------------------------------------------------- v checking for file 'D:\OneDrive\github\PackageR\MSnbase-2.14.2/DESCRIPTION' (630ms)
- preparing 'MSnbase': (6.1s) v checking DESCRIPTION meta-information ...
- cleaning src
- checking for LF line-endings in source and make files and shell scripts (1.9s)
- checking for empty or unneeded directories
- building 'MSnbase_2.14.2.tar.gz'
Running "D:/Program Files/R/R-4.1.2/bin/x64/Rcmd.exe" INSTALL "C:\Users\XA250~1.FEN\AppData\Local\Temp\RtmpoxDYUx/MSnbase_2.14.2.tar.gz" --install-tests
- installing to library 'D:/Program Files/R/R-4.1.2/library'
- installing source package 'MSnbase' ... using staged installation libs
** arch - i386
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -I'D:/Program Files/R/R-4.1.2/library/Rcpp/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -I'D:/Program Files/R/R-4.1.2/library/Rcpp/include' -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw32/bin/"gcc -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -I'D:/Program Files/R/R-4.1.2/library/Rcpp/include' -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -I'D:/Program Files/R/R-4.1.2/library/Rcpp/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -I'D:/Program Files/R/R-4.1.2/library/Rcpp/include' -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
^~~
At top level:
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)
^~~~~~~~
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)
^~~~~~~
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o MSnbase.dll tmp.def RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -LD:/Program Files/R/R-4.1.2/bin/i386 -lR
installing to D:/Program Files/R/R-4.1.2/library/00LOCK-MSnbase/00new/MSnbase/libs/i386
arch - x64
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -I'D:/Program Files/R/R-4.1.2/library/Rcpp/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -I'D:/Program Files/R/R-4.1.2/library/Rcpp/include' -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw64/bin/"gcc -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -I'D:/Program Files/R/R-4.1.2/library/Rcpp/include' -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -I'D:/Program Files/R/R-4.1.2/library/Rcpp/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -I'D:/Program Files/R/R-4.1.2/library/Rcpp/include' -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
^~~
At top level:
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)
^~~~~~~~
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)
^~~~~~~
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o MSnbase.dll tmp.def RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -LD:/Program Files/R/R-4.1.2/bin/x64 -lR
installing to D:/Program Files/R/R-4.1.2/library/00LOCK-MSnbase/00new/MSnbase/libs/x64
R
data
moving datasets to lazyload DB
Warning in fun(libname, pkgname) :
mzR has been built against a different Rcpp version (1.0.7)
than is installed on your system (1.0.9). 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 'bin' in package 'MSnbase'
Creating a new generic function for 'compareSpectra' in package 'MSnbase'
Creating a new generic function for 'trimws' in package 'MSnbase'
in method for 'coerce' with signature '"MSnSet","SummarizedExperiment"': no definition for class "SummarizedExperiment"
in method for 'coerce' with signature '"SummarizedExperiment","MSnSet"': no definition for class "SummarizedExperiment"
in method for 'coerce' with signature '"IBSpectra","MSnSet"': no definition for class "IBSpectra"
Warning: multiple methods tables found for 'bin'
Warning: multiple methods tables found for 'compareSpectra'
inst
tests
byte-compile and prepare package for lazy loading
Warning messages:
1: In fun(libname, pkgname) :
mzR has been built against a different Rcpp version (1.0.7)
than is installed on your system (1.0.9). 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.
2: package 'S4Vectors' was built under R version 4.1.3
Creating a new generic function for 'bin' in package 'MSnbase'
Creating a new generic function for 'compareSpectra' in package 'MSnbase'
Creating a new generic function for 'trimws' in package 'MSnbase'
in method for 'coerce' with signature '"MSnSet","SummarizedExperiment"': no definition for class "SummarizedExperiment"
in method for 'coerce' with signature '"SummarizedExperiment","MSnSet"': no definition for class "SummarizedExperiment"
in method for 'coerce' with signature '"IBSpectra","MSnSet"': no definition for class "IBSpectra"
help
*** installing help indices
converting help for package 'MSnbase'
finding HTML links ... done
Chromatogram-class html
Chromatograms-class html
FeatComp-class html
FeaturesOfInterest-class html
finding level-2 HTML links ... done
MIAPE-class html
MSmap-class html REDIRECT:topic Previous alias or file overwritten by alias: D:/Program Files/R/R-4.1.2/library/00LOCK-MSnbase/00new/MSnbase/help/msMap.html
MSnExp-class html
MSnProcess-class html
MSnSet-class html
MSnSetList-class html
MSnbaseOptions html
MzTab-class html
OnDiskMSnExp-class html
ProcessingStep-class html
ReporterIons-class html
Spectra html
Spectrum-class html
Spectrum1-class html
Spectrum2-class html
TMT6 html
addIdentificationData-methods html
aggvar html
averageMSnSet html
bin-methods html
calculateFragments-methods html
chromatogram-MSnExp-method html
REDIRECT:topic Previous alias or file overwritten by alias: D:/Program Files/R/R-4.1.2/library/00LOCK-MSnbase/00new/MSnbase/help/chromatogram.html
clean-methods html
combineFeatures html
combineSpectra html
combineSpectraMovingWindow html
commonFeatureNames html
compareMSnSets html
compareSpectra-methods html
consensusSpectrum html
defunct html
estimateMzResolution html
estimateMzScattering html
estimateNoise-method html
extractPrecSpectra-methods html
fData-utils html
factorsAsStrings html
featureCV html
fillUp html
filterIdentificationDataFrame html
formatRt html
get.amino.acids html
get.atomic.mass html
getVariableName html
grepEcols html
hasSpectraOrChromatograms html
iPQF html
iTRAQ4 html
imageNA2 html
impute-methods html
isCentroidedFromFile html
itraqdata html
REDIRECT:topic Previous alias or file overwritten by alias: D:/Program Files/R/R-4.1.2/library/00LOCK-MSnbase/00new/MSnbase/help/msnset.html
listOf html
makeCamelCase html
makeNaData html
meanMzInts html
missing-data html
mzRident2dfr html
nFeatures html
nQuants html
naplot html
navMS html
normToReference html
normalise-methods html
npcv html
pSet-class html
REDIRECT:topic Previous alias or file overwritten by alias: D:/Program Files/R/R-4.1.2/library/00LOCK-MSnbase/00new/MSnbase/help/spectra.html
pickPeaks-method html
plot-methods html
plot2d-methods html
plotDensity-methods html
plotMzDelta-methods html
plotNA-methods html
plotSpectrumSpectrum-methods html
precSelection html
purityCorrect-methods html
quantify-methods html
readMSData html
readMSnSet html
readMgfData html
readMzIdData html
readMzTabData html
readMzTabData_v0.9 html
readSRMData html
reduce-data.frame-method html
removeNoId-methods html
removePeaks-methods html
removeReporters-methods html
selectFeatureData html
smooth-methods html
trimMz-methods html
updateObject-methods html
writeMSData html
writeMgfData-methods html
writeMzTabData html
building package indices
installing vignettes
testing if installed package can be loaded from temporary location
** arch - i386
Warning in fun(libname, pkgname) :
mzR has been built against a different Rcpp version (1.0.7)
than is installed on your system (1.0.9). 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.
Warning: package 'S4Vectors' was built under R version 4.1.3
Warning: multiple methods tables found for 'bin'
Warning: multiple methods tables found for 'compareSpectra'
arch - x64
Warning in fun(libname, pkgname) :
mzR has been built against a different Rcpp version (1.0.7)
than is installed on your system (1.0.9). 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.
Warning: package 'S4Vectors' was built under R version 4.1.3
Warning: multiple methods tables found for 'bin'
Warning: multiple methods tables found for 'compareSpectra'
testing if installed package can be loaded from final location
** arch - i386
Warning in fun(libname, pkgname) :
mzR has been built against a different Rcpp version (1.0.7)
than is installed on your system (1.0.9). 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.
Warning: package 'S4Vectors' was built under R version 4.1.3
Warning: multiple methods tables found for 'bin'
Warning: multiple methods tables found for 'compareSpectra'
arch - x64
Warning in fun(libname, pkgname) :
mzR has been built against a different Rcpp version (1.0.7)
than is installed on your system (1.0.9). 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.
Warning: package 'S4Vectors' was built under R version 4.1.3
Warning: multiple methods tables found for 'bin'
Warning: multiple methods tables found for 'compareSpectra'
** testing if installed package keeps a record of temporary installation path
- DONE (MSnbase)
Making 'packages.html' ... done
Warning message:
In devtools::install("d:/OneDrive/github/PackageR/MSnbase-2.14.2", :
Arguments in
...must be used. x Problematic argument: -
update = FALSE i Did you misspell an argument name? devtools::install("d:/github/DynamicXCMS",update = FALSE) Error in
package_file(): ! d:/github/DynamicXCMS is not a directory. Runrlang::last_trace()to see where the error occurred. devtools::install("d:/OneDrive - NKI/github/DynamicXCMS",update = FALSE) These packages have more recent versions available. It is recommended to update all of them. Which would you like to update?1: All
2: CRAN packages only
3: None
4: viridisLite (0.4.1 -> 0.4.2 ) [CRAN] 5: rlang (1.1.0 -> 1.1.1 ) [CRAN] 6: vctrs (0.6.1 -> 0.6.3 ) [CRAN] 7: Rcpp (1.0.9 -> 1.0.11 ) [CRAN] 8: BiocManager (1.30.20 -> 1.30.21.1) [CRAN] 9: DEoptimR (1.0-12 -> 1.1-0 ) [CRAN] 10: digest (0.6.31 -> 0.6.33 ) [CRAN] 11: robustbase (0.95-1 -> 0.99-0 ) [CRAN] 12: MSnbase (2.14.2 -> 2.20.4 ) [CRAN]
Enter one or more numbers, or an empty line to skip updates: 3 -- R CMD build --------------------------------------------------------------------------------------------------------------------------------------------------- v checking for file 'D:\OneDrive - NKI\github\DynamicXCMS/DESCRIPTION' (493ms)
- preparing 'xcms': (6s) v checking DESCRIPTION meta-information ...
- cleaning src
- checking for LF line-endings in source and make files and shell scripts (1.7s)
- checking for empty or unneeded directories (510ms)
- building 'xcms_3.8.2.1.tar.gz'
Running "D:/Program Files/R/R-4.1.2/bin/x64/Rcmd.exe" INSTALL "C:\Users\XA250~1.FEN\AppData\Local\Temp\RtmpoxDYUx/xcms_3.8.2.1.tar.gz" --install-tests
- installing to library 'D:/Program Files/R/R-4.1.2/library'
- installing source package 'xcms' ... using staged installation libs
*** arch - i386
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/Tracker.cpp -o massifquant/Tracker.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/SegProc.cpp -o massifquant/SegProc.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c obiwarp/mat.cpp -o obiwarp/mat.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c obiwarp/vec.cpp -o obiwarp/vec.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c xcms_obiwarp.cpp -o xcms_obiwarp.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c fastMatch.c -o fastMatch.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c mzClust_hclust.c -o mzClust_hclust.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c mzROI.c -o mzROI.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c util.c -o util.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c xcms.c -o xcms.o
"C:/rtools40/mingw32/bin/"gcc -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c binners.c -o binners.o
binners.c: In function '_breaks_on_binSize':
binners.c:357:7: warning: unused variable 'idx' [-Wunused-variable]
int idx = 0;
^~~
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -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 -LD:/Program Files/R/R-4.1.2/bin/i386 -lR
installing to D:/Program Files/R/R-4.1.2/library/00LOCK-xcms/00new/xcms/libs/i386
* arch - x64
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/Tracker.cpp -o massifquant/Tracker.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/SegProc.cpp -o massifquant/SegProc.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c obiwarp/mat.cpp -o obiwarp/mat.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c obiwarp/vec.cpp -o obiwarp/vec.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c xcms_obiwarp.cpp -o xcms_obiwarp.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c fastMatch.c -o fastMatch.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c mzClust_hclust.c -o mzClust_hclust.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c mzROI.c -o mzROI.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c util.c -o util.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c xcms.c -o xcms.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/Program Files/R/R-4.1.2/include" -DNDEBUG -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-inline -c binners.c -o binners.o
binners.c: In function '_breaks_on_binSize':
binners.c:357:7: warning: unused variable 'idx' [-Wunused-variable]
int idx = 0;
^~~
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -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 -LD:/Program Files/R/R-4.1.2/bin/x64 -lR
installing to D:/Program Files/R/R-4.1.2/library/00LOCK-xcms/00new/xcms/libs/x64
R
inst
tests
byte-compile and prepare package for lazy loading
Warning messages:
1: In fun(libname, pkgname) :
mzR has been built against a different Rcpp version (1.0.7)
than is installed on your system (1.0.9). 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.
2: package 'S4Vectors' was built under R version 4.1.3
3: multiple methods tables found for 'bin'
4: multiple methods tables found for 'compareSpectra'
Creating a new generic function for 'sigma' in package 'xcms'
Creating a generic function from function 'hasFilledChromPeaks' in package 'xcms'
* help
installing help indices
converting help for package 'xcms'
finding HTML links ... done
AutoLockMass-methods html
GenericParam html
ProcessHistory-class html
SSgauss html
XCMSnExp-class html
REDIRECT:topic Previous alias or file overwritten by alias: D:/Program Files/R/R-4.1.2/library/00LOCK-xcms/00new/xcms/help/processHistory.html
finding level-2 HTML links ... done
XCMSnExp-filter-methods html
XCMSnExp-inherited-methods html
XCMSnExp-peak-grouping-results html
XChromatogram html
absent-methods html
adjustRtime-obiwarp html
adjustRtime-peakGroups html
adjustRtime html
align-Chromatogram html
applyAdjustedRtime html
binYonX html
breaks_on_binSize html
breaks_on_nBins html
c.xcmsSet html
calibrate-calibrant-mass html
calibrate html
chromPeakSpectra html
chromatogram-method html
chromatographic-peak-detection html
colMax html
collect-methods html
correlate-Chromatogram html
descendZero html
diffreport-methods html
dirname html
do_adjustRtime_peakGroups html
do_findChromPeaks_centWave html
do_findChromPeaks_centWaveWithPredIsoROIs
html
do_findChromPeaks_massifquant html
do_findChromPeaks_matchedFilter html
do_findPeaks_MSW html
do_groupChromPeaks_density html
do_groupChromPeaks_nearest html
do_groupPeaks_mzClust html
doubleMatrix html
etg html
exportMetaboAnalyst html
extractMsData-method html
featureChromatograms html
featureSpectra html
featureSummary html
fillChromPeaks html
fillPeaks-methods html
fillPeaks.MSW-methods html
fillPeaks.chrom-methods html
filtfft html
findChromPeaks-Chromatogram-CentWaveParam
html
findChromPeaks-Chromatogram-MatchedFilter
html
findChromPeaks-centWave html
findChromPeaks-centWaveWithPredIsoROIs
html
findChromPeaks-massifquant html
findChromPeaks-matchedFilter html
findChromPeaksIsolationWindow html
findEqualGreater html
findMZ html
findPeaks-MSW html
findPeaks-methods html
findPeaks.MS1-methods html
findPeaks.MSW-xcmsRaw-method html
findPeaks.addPredictedIsotopeFeatures-methods
html
findPeaks.centWave-methods html
findPeaks.centWaveWithPredictedIsotopeROIs-methods
html
findPeaks.massifquant-methods html
findPeaks.matchedFilter-xcmsRaw-method
html
findneutral html
getEIC-methods html
getPeaks-methods html
getScan-methods html
getSpec-methods html
getXcmsRaw-methods html
group-methods html
group.density html
group.mzClust html
group.nearest html
groupChromPeaks-density html
groupChromPeaks-mzClust html
groupChromPeaks-nearest html
groupChromPeaks html
groupnames-XCMSnExp html
groupnames-methods html
groupval-methods html
highlightChromPeaks html
image.xcmsRaw html
imputeLinInterpol html
imputeRowMin html
imputeRowMinRand html
isolationWindowTargetMz-OnDiskMSnExp-method
html
levelplot.xcmsRaw html
loadRaw-methods html
medianFilter html
msn2xcmsRaw html
na.flatfill html
overlappingFeatures html
panel.cor html
peakPlots-methods html
peakTable-methods html
peaksWithCentWave html
peaksWithMatchedFilter html
phenoDataFromPaths html
plot.xcmsEIC html
plotAdjustedRtime html
plotChrom-methods html
plotChromPeakDensity html
plotChromPeaks html
plotEIC-methods html
plotMsData html
plotPeaks-methods html
plotQC html
plotRaw-methods html
plotScan-methods html
plotSpec-methods html
plotSurf-methods html
plotTIC-methods html
plotrt-methods html
profGenerate html
profMat-xcmsSet html
profMedFilt-methods html
profMethod-methods html
profRange-methods html
profStep-methods html
pval html
rawEIC-methods html
rawMat-methods html
reconstructChromPeakSpectra html
rectUnique html
retcor-methods html
retcor.obiwarp-methods html
retcor.peakgroups-methods html
retexp html
rla html
sampnames-methods html
showError-xcmsSet-method html
specDist-methods html
specDist.cosine-methods html
specDist.meanMZmatch-methods html
specDist.peakCount-methods html
specNoise html
specPeaks html
split.xcmsRaw html
split.xcmsSet html
stitch-methods html
sub-xcmsRaw-logicalOrNumeric-missing-missing-method
html
updateObject-xcmsSet-method html
useOriginalCode html
verify.mzQuantML html
write.cdf-methods html
write.mzQuantML html
write.mzdata-methods html
writeMSData-XCMSnExp-character-method html
writeMzTab html
xcms-deprecated html
xcmsEIC-class html
xcmsFileSource-class html
xcmsFragments-class html
xcmsFragments html
xcmsPapply html
xcmsPeaks-class html
xcmsRaw-class html
xcmsRaw html
xcmsSet-class html
xcmsSet html
xcmsSource-class html
xcmsSource-methods html building package indices installing vignettes testing if installed package can be loaded from temporary location ** arch - i386 Warning in fun(libname, pkgname) : mzR has been built against a different Rcpp version (1.0.7) than is installed on your system (1.0.9). 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. Warning: package 'S4Vectors' was built under R version 4.1.3 Warning: multiple methods tables found for 'bin' Warning: multiple methods tables found for 'compareSpectra' arch - x64 Warning in fun(libname, pkgname) : mzR has been built against a different Rcpp version (1.0.7) than is installed on your system (1.0.9). 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. Warning: package 'S4Vectors' was built under R version 4.1.3 Warning: multiple methods tables found for 'bin' Warning: multiple methods tables found for 'compareSpectra' testing if installed package can be loaded from final location ** arch - i386 Warning in fun(libname, pkgname) : mzR has been built against a different Rcpp version (1.0.7) than is installed on your system (1.0.9). 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. Warning: package 'S4Vectors' was built under R version 4.1.3 Warning: multiple methods tables found for 'bin' Warning: multiple methods tables found for 'compareSpectra' arch - x64 Warning in fun(libname, pkgname) : mzR has been built against a different Rcpp version (1.0.7) than is installed on your system (1.0.9). 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. Warning: package 'S4Vectors' was built under R version 4.1.3 Warning: multiple methods tables found for 'bin' Warning: multiple methods tables found for 'compareSpectra' ** testing if installed package keeps a record of temporary installation path
- DONE (xcms)
Making 'packages.html' ... done
Warning message:
In devtools::install("d:/OneDrive/github/DynamicXCMS", update = FALSE) :
Arguments in
...must be used. x Problematic argument: - update = FALSE i Did you misspell an argument name? library(MSnbase) Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabsThe following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl,
intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce,
rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.minLoading required package: Biobase Welcome to Bioconductor
Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages
'citation("pkgname")'.Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
expand.grid, I, unnameLoading required package: ProtGenerics
Attaching package: ‘ProtGenerics’
The following object is masked from ‘package:stats’:
smoothThis is MSnbase version 2.14.2 Visit https://lgatto.github.io/MSnbase/ to get started.
Attaching package: ‘MSnbase’
The following objects are masked from ‘package:ProtGenerics’:
bin, compareSpectra, executeProcessingStep, ProcessingStepThe following object is masked from ‘package:base’:
trimwsWarning messages: 1: In fun(libname, pkgname) : mzR has been built against a different Rcpp version (1.0.7) than is installed on your system (1.0.9). 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. 2: package ‘S4Vectors’ was built under R version 4.1.3 3: multiple methods tables found for ‘bin’ 4: multiple methods tables found for ‘compareSpectra’
library(xcms) Loading required package: BiocParallel
This is xcms version 3.8.2.1
Attaching package: ‘xcms’
The following object is masked from ‘package:stats’:
sigmasessionInfo() R version 4.1.2 (2021-11-01) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17134)
Matrix products: default
locale:
[1] LC_COLLATE=Dutch_Netherlands.1252 LC_CTYPE=Dutch_Netherlands.1252 LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C
[5] LC_TIME=Dutch_Netherlands.1252
attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] xcms_3.8.2.1 BiocParallel_1.28.3 MSnbase_2.14.2 ProtGenerics_1.26.0 S4Vectors_0.32.4 mzR_2.28.0 Rcpp_1.0.9
[8] Biobase_2.54.0 BiocGenerics_0.40.0
loaded via a namespace (and not attached):
[1] fs_1.5.2 usethis_2.2.2 devtools_2.4.5 doParallel_1.0.17 RColorBrewer_1.1-3 rprojroot_2.0.3
[7] tools_4.1.2 profvis_0.3.8 utf8_1.2.3 R6_2.5.1 affyio_1.64.0 DBI_1.1.3
[13] colorspace_2.1-0 urlchecker_1.0.1 withr_2.5.0 tidyselect_1.2.0 prettyunits_1.1.1 processx_3.8.1
[19] MassSpecWavelet_1.60.1 compiler_4.1.2 preprocessCore_1.56.0 cli_3.6.1 desc_1.4.2 scales_1.2.1
[25] DEoptimR_1.0-12 robustbase_0.95-1 affy_1.72.0 callr_3.7.3 stringr_1.5.0 digest_0.6.31
[31] pkgconfig_2.0.3 htmltools_0.5.5 sessioninfo_1.2.2 fastmap_1.1.1 limma_3.50.3 htmlwidgets_1.6.2
[37] rlang_1.1.0 rstudioapi_0.15.0 impute_1.68.0 shiny_1.7.4.1 generics_0.1.3 mzID_1.32.0
[43] dplyr_1.1.2 magrittr_2.0.3 Matrix_1.3-4 MALDIquant_1.22.1 munsell_0.5.0 fansi_1.0.4
[49] lifecycle_1.0.3 vsn_3.62.0 stringi_1.7.12 MASS_7.3-54 zlibbioc_1.40.0 pkgbuild_1.4.0
[55] plyr_1.8.8 grid_4.1.2 parallel_4.1.2 promises_1.2.0.1 crayon_1.5.2 miniUI_0.1.1.1
[61] lattice_0.20-45 splines_4.1.2 multtest_2.50.0 ps_1.7.5 pillar_1.9.0 codetools_0.2-18
[67] pkgload_1.3.2 XML_3.99-0.14 glue_1.6.2 pcaMethods_1.86.0 remotes_2.4.2 BiocManager_1.30.20
[73] vctrs_0.6.1 httpuv_1.6.11 foreach_1.5.2 RANN_2.6.1 gtable_0.3.3 purrr_1.0.1
[79] cachem_1.0.7 ggplot2_3.4.2 mime_0.12 xtable_1.8-4 later_1.3.0 ncdf4_1.21
[85] survival_3.2-13 tibble_3.2.1 iterators_1.0.14 memoise_2.0.1 IRanges_2.28.0 ellipsis_0.3.2
`
Loading xcms Creating a new generic function for ‘sigma’ in package ‘xcms’ Error in reconcilePropertiesAndPrototype(name, slots, prototype, superClasses, : no definition was found for superclass “Chromatograms” in the specification of class “XChromatograms” In addition: Warning messages: 1: objects ‘Chromatograms’, ‘Spectra’ are not exported by 'namespace:MSnbase' 2: classes "Chromatograms", "Spectra" are not exported by 'namespace:MSnbase'