installation error?

[13479776]

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'

[xiaodfeng]

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.
  Run rlang::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, xtabs

The 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.min

Loading 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, unname

Loading required package: ProtGenerics

Attaching package: ‘ProtGenerics’

The following object is masked from ‘package:stats’:

smooth

This 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, ProcessingStep

The following object is masked from ‘package:base’:

trimws

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’

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’:

sigma

sessionInfo()
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
`