R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
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Platform: x86_64-w64-mingw32/x64

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> library(testthat)
> library(xcms)
Loading required package: BiocParallel

This is xcms version 4.3.1 


Attaching package: 'xcms'

The following object is masked from 'package:stats':

    sigma

> library(faahKO)
> library(msdata)
> 
> attr(faahko, "filepaths") <- sapply(
+     as.list(basename(attr(faahko, "filepaths"))),
+     function(x) system.file("cdf", if (length(grep("ko",x)) > 0) "KO" else "WT",
+                             x, package = "faahKO"))
> register(SerialParam())
> 
> ## Create some objects we can re-use in different tests:
> faahko_3_files <- c(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
+                     system.file('cdf/KO/ko16.CDF', package = "faahKO"),
+                     system.file('cdf/KO/ko18.CDF', package = "faahKO"))
> 
> ## An xcmsRaw for the first file:
> faahko_xr_1 <- xcmsRaw(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
+                        profstep = 0)
> faahko_od <- readMSData(faahko_3_files, mode = "onDisk")
Error in readMSData(faahko_3_files, mode = "onDisk") : 
  could not find function "readMSData"
Execution halted

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no xcms_4.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc-longtests/meat/xcms.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using options '--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error'
* checking for file 'xcms/DESCRIPTION' ... OK
* this is package 'xcms' version '4.3.1'
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'xcms' can be installed ... WARNING
Found the following significant warnings:
  fastMatch.c:32:69: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  mzROI.c:79:77: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  mzROI.c:102:75: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  mzROI.c:331:75: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  mzROI.c:629:74: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  mzROI.c:633:74: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
See 'F:/biocbuild/bbs-3.20-bioc-longtests/meat/xcms.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking installed package size ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    help   1.0Mb
    libs   1.1Mb
* checking package 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 code 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'MALDIquant:::.localMaxima' 'MSnbase:::.MSnExpReqFvarLabels'
  'MSnbase:::.plotXIC' 'MSnbase:::.vertical_sub_layout'
  'MSnbase:::formatFileSpectrumNames' 'Spectra:::.concatenate_spectra'
  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:
  '.copy_env' 'MSW.cwt' 'MSW.getLocalMaximumCWT' 'MSW.getRidge'
  'descendMin' 'descendMinTol' 'estimateChromNoise'
  'getLocalNoiseEstimate' 'na.flatfill' 'patternVsRowScore'
* 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'
plotPrecursorIons: no visible global function definition for
  'filterEmptySpectra'
plotQC: no visible global function definition for 'sampleNames'
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'
xcmsSet: no visible global function definition for 'bpstopOnError'
xcmsSet: no visible global function definition for 'bptry'
xcmsSet: no visible global function definition for 'bpok'
plotSurf,xcmsRaw: no visible global function definition for 'clear3d'
plotSurf,xcmsRaw: no visible global function definition for 'surface3d'
plotSurf,xcmsRaw: no visible global function definition for 'points3d'
plotSurf,xcmsRaw: no visible global function definition for 'bbox3d'
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:
  addChildren addEdge base64encode bbox3d bpok bpstopOnError bptry
  checkCluster checkForRemoteErrors clear3d edgemode<-
  filterEmptySpectra 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
  points3d recvOneResult sampleNames saveXML sendCall surface3d
  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 ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking files in 'vignettes' ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in 'longtests' ... OK
* checking tests in 'longtests' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'longtests/testthat.R' failed.
Last 13 lines of output:
  +                             x, package = "faahKO"))
  > register(SerialParam())
  > 
  > ## Create some objects we can re-use in different tests:
  > faahko_3_files <- c(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
  +                     system.file('cdf/KO/ko16.CDF', package = "faahKO"),
  +                     system.file('cdf/KO/ko18.CDF', package = "faahKO"))
  > 
  > ## An xcmsRaw for the first file:
  > faahko_xr_1 <- xcmsRaw(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
  +                        profstep = 0)
  > faahko_od <- readMSData(faahko_3_files, mode = "onDisk")
  Error in readMSData(faahko_3_files, mode = "onDisk") : 
    could not find function "readMSData"
  Execution halted
* DONE

Status: 1 ERROR, 1 WARNING, 5 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc-longtests/meat/xcms.Rcheck/00check.log'
for details.

* installing *source* package 'xcms' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c massifquant/Tracker.cpp -o massifquant/Tracker.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c massifquant/SegProc.cpp -o massifquant/SegProc.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c obiwarp/mat.cpp -o obiwarp/mat.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c obiwarp/vec.cpp -o obiwarp/vec.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -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]
 1113 |   float bestscore;
      |         ^~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c xcms_obiwarp.cpp -o xcms_obiwarp.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -fno-inline -c fastMatch.c -o fastMatch.o
fastMatch.c: In function 'fastMatch':
fastMatch.c:32:69: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
   32 |         error("fastMatch/calloc: memory could not be allocated ! (%lu bytes)\n", nx  * sizeof(struct idxStruct) );
      |                                                                   ~~^            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                     |                |
      |                                                                     |                long long unsigned int
      |                                                                     long unsigned int
      |                                                                   %llu
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -fno-inline -c mzClust_hclust.c -o mzClust_hclust.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -fno-inline -c mzROI.c -o mzROI.o
mzROI.c: In function 'checkmzROIBufSize':
mzROI.c:79:77: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
   79 |         error("findmzROI/realloc: buffer memory could not be allocated ! (%lu bytes)\n", newLength * sizeof(struct mzROIStruct) );
      |                                                                           ~~^            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                             |                      |
      |                                                                             long unsigned int      long long unsigned int
      |                                                                           %llu
mzROI.c: In function 'checkmzvalBufSize':
mzROI.c:102:75: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  102 |       error("findmzROI/realloc: buffer memory could not be allocated ! (%lu bytes)\n", newLength * sizeof(struct mzROIStruct));
      |                                                                         ~~^            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                           |                      |
      |                                                                           long unsigned int      long long unsigned int
      |                                                                         %llu
mzROI.c: In function 'cleanup':
mzROI.c:331:75: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  331 |       error("findmzROI/cleanup: buffer memory could not be allocated ! (%lu bytes)\n", (mzLength->mzval - del) * sizeof(struct mzROIStruct));
      |                                                                         ~~^            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                           |                                    |
      |                                                                           long unsigned int                    long long unsigned int
      |                                                                         %llu
mzROI.c: In function 'findmzROI':
mzROI.c:629:74: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  629 |       error("findmzROI/calloc: buffer memory could not be allocated ! (%lu bytes)\n",ROI_INIT_LENGTH  * sizeof(struct mzROIStruct) );
      |                                                                        ~~^
      |                                                                          |
      |                                                                          long unsigned int
      |                                                                        %llu
mzROI.c:633:74: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  633 |       error("findmzROI/calloc: buffer memory could not be allocated ! (%lu bytes)\n",MZVAL_INIT_LENGTH  * sizeof(struct mzROIStruct) );
      |                                                                        ~~^
      |                                                                          |
      |                                                                          long unsigned int
      |                                                                        %llu
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -fno-inline -c util.c -o util.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -fno-inline -c xcms.c -o xcms.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -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]
  357 |   int idx = 0;
      |       ^~~
g++ -std=gnu++17 -shared -s -static-libgcc -o xcms.dll tmp.def massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o binners.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc-longtests/meat/xcms.Rcheck/00LOCK-xcms/00new/xcms/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'group' in package 'xcms'
Creating a new generic function for 'sigma' in package 'xcms'
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (xcms)