xcms 1.50.1
Steffen Neumann
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/xcms | | Last Changed Rev: 125337 / Revision: 128728 | | Last Changed Date: 2016-12-20 09:03:43 -0500 (Tue, 20 Dec 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings xcms_1.50.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/xcms.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘xcms/DESCRIPTION’ ... OK
* this is package ‘xcms’ version ‘1.50.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘xcms’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
GPL (>= 2) + file LICENSE
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘mzR:::rampCloseAll’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘findEqualGreaterUnsorted’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.xcmsFragments.plotTree: no visible global function definition for
‘edgemode<-’
.xcmsFragments.plotTree: no visible global function definition for
‘addEdge’
buildAnalysisSummary: no visible global function definition for
‘newXMLNode’
buildAssayList : <anonymous>: no visible global function definition for
‘newXMLNode’
buildAssayList: no visible global function definition for ‘newXMLNode’
buildAuditCollection: no visible global function definition for
‘newXMLNode’
buildCVlist: no visible global function definition for ‘newXMLNode’
buildCVlist: no visible global function definition for ‘addChildren’
buildCvParams : <anonymous>: no visible global function definition for
‘newXMLNode’
buildDataProcessingList: no visible global function definition for
‘newXMLNode’
buildFeatureList : <anonymous>: no visible global function definition
for ‘newXMLNode’
buildInputFiles : <anonymous>: no visible global function definition
for ‘newXMLNode’
buildInputFiles: no visible global function definition for ‘newXMLNode’
buildMzq: no visible global function definition for ‘xmlTree’
buildSmallMoleculeList : <anonymous>: no visible global function
definition for ‘newXMLNode’
buildSmallMoleculeList: no visible global function definition for
‘newXMLNode’
buildSoftwareList: no visible global function definition for
‘newXMLNode’
buildStudyVariableList : <anonymous>: no visible global function
definition for ‘newXMLNode’
buildStudyVariableList : <anonymous> : <anonymous>: no visible global
function definition for ‘newXMLNode’
buildStudyVariableList: no visible global function definition for
‘newXMLNode’
do_detectFeatures_centWave : <anonymous>: no visible global function
definition for ‘Rle’
do_detectFeatures_matchedFilter_newer: no visible binding for global
variable ‘profparam’
do_detectFeatures_matchedFilter_newer: possible error in binYonX(mz,
int, fromIdx = fromX, toIdx = toX, binFromX = mass[1], binToX =
mass[length(mass)], shiftByHalfBinSize = shiftBy, impute =
imputeMethod, sortedY = TRUE, binSize = step, returnIndex = TRUE):
unused arguments (impute = imputeMethod, sortedY = TRUE)
rampRawData: no visible global function definition for
‘rampScanHeaders’
rampRawData: no visible global function definition for ‘rampSIPeaks’
rampRawDataMSn: no visible global function definition for
‘rampScanHeaders’
rampRawDataMSn: no visible global function definition for ‘rampSIPeaks’
running: multiple local function definitions for ‘funct’ with different
formal arguments
verify.mzQuantML: no visible global function definition for
‘xmlTreeParse’
verify.mzQuantML: no visible global function definition for
‘xmlInternalTreeParse’
verify.mzQuantML: no visible global function definition for
‘xmlSchemaValidate’
xcmsClusterApply: no visible global function definition for
‘checkCluster’
xcmsClusterApply : submit: no visible global function definition for
‘sendCall’
xcmsClusterApply: no visible global function definition for
‘recvOneResult’
xcmsClusterApply: no visible global function definition for
‘checkForRemoteErrors’
xcmsPapply: no visible global function definition for ‘mpi.comm.size’
xcmsPapply: no visible global function definition for
‘mpi.spawn.Rslaves’
xcmsPapply: no visible global function definition for ‘mpi.comm.rank’
xcmsPapply : papply_int_slavefunction: no visible global function
definition for ‘mpi.send.Robj’
xcmsPapply : papply_int_slavefunction: no visible global function
definition for ‘mpi.recv.Robj’
xcmsPapply : papply_int_slavefunction: no visible global function
definition for ‘mpi.any.source’
xcmsPapply : papply_int_slavefunction: no visible global function
definition for ‘mpi.any.tag’
xcmsPapply : papply_int_slavefunction: no visible global function
definition for ‘mpi.get.sourcetag’
xcmsPapply: no visible global function definition for
‘mpi.bcast.Robj2slave’
xcmsPapply: no visible global function definition for ‘mpi.bcast.cmd’
xcmsPapply: no visible global function definition for ‘mpi.recv.Robj’
xcmsPapply: no visible global function definition for ‘mpi.any.source’
xcmsPapply: no visible global function definition for ‘mpi.any.tag’
xcmsPapply: no visible global function definition for
‘mpi.get.sourcetag’
xcmsPapply: no visible global function definition for ‘mpi.send.Robj’
xcmsParallelSetup: no visible global function definition for
‘mpi.spawn.Rslaves’
xcmsParallelSetup: no visible global function definition for
‘mpi.comm.size’
xcmsParallelSetup: no visible global function definition for
‘mpi.comm.rank’
xcmsParallelSetup: no visible global function definition for
‘makeCluster’
findPeaks.addPredictedIsotopeFeatures,xcmsRaw : <anonymous>: no visible
binding for global variable ‘isOverlap’
plotSurf,xcmsRaw: no visible global function definition for ‘rgl.clear’
plotSurf,xcmsRaw: no visible global function definition for
‘rgl.surface’
plotSurf,xcmsRaw: no visible global function definition for
‘rgl.points’
plotSurf,xcmsRaw: no visible global function definition for ‘rgl.bbox’
plotTree,xcmsFragments: no visible global function definition for
‘edgemode<-’
plotTree,xcmsFragments: no visible global function definition for
‘addEdge’
write.cdf,xcmsRaw: no visible global function definition for
‘ncdim_def’
write.cdf,xcmsRaw: no visible global function definition for
‘ncvar_def’
write.cdf,xcmsRaw: no visible global function definition for
‘nc_create’
write.cdf,xcmsRaw: no visible global function definition for
‘ncvar_put’
write.cdf,xcmsRaw: no visible global function definition for
‘ncatt_put’
write.cdf,xcmsRaw: no visible global function definition for ‘nc_close’
write.mzQuantML,xcmsSet: no visible global function definition for
‘saveXML’
write.mzdata,xcmsRaw: no visible global function definition for
‘base64encode’
Undefined global functions or variables:
Rle addChildren addEdge base64encode checkCluster
checkForRemoteErrors edgemode<- isOverlap makeCluster mpi.any.source
mpi.any.tag mpi.bcast.Robj2slave mpi.bcast.cmd mpi.comm.rank
mpi.comm.size mpi.get.sourcetag mpi.recv.Robj mpi.send.Robj
mpi.spawn.Rslaves nc_close nc_create ncatt_put ncdim_def ncvar_def
ncvar_put newXMLNode profparam rampSIPeaks rampScanHeaders
recvOneResult rgl.bbox rgl.clear rgl.points rgl.surface saveXML
sendCall xmlInternalTreeParse xmlSchemaValidate xmlTree xmlTreeParse
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘xcms/libs/xcms.so’:
Found ‘rand’, possibly from ‘rand’ (C)
Object: ‘massifquant/TrMgr.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
findPeaks.massifquant-methods 0.056 0.024 8.328
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘doRUnit.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/xcms.Rcheck/00check.log’
for details.
* installing *source* package ‘xcms’ ...
** libs
rm -f 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
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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);
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c massifquant/Tracker.cpp -o massifquant/Tracker.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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;
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c obiwarp/mat.cpp -o obiwarp/mat.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c obiwarp/vec.cpp -o obiwarp/vec.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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;
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c xcms_obiwarp.cpp -o xcms_obiwarp.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fastMatch.c -o fastMatch.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c mzClust_hclust.c -o mzClust_hclust.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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;
^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c util.c -o util.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c xcms.c -o xcms.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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);
^
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o xcms.so 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 -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/xcms.Rcheck/xcms/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (xcms)