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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TrajectoryGeometry.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings TrajectoryGeometry_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/TrajectoryGeometry.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TrajectoryGeometry/DESCRIPTION' ... OK
* this is package 'TrajectoryGeometry' version '1.0.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'TrajectoryGeometry' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
visualiseBranchPointStats: no visible binding for global variable
  'value'
visualiseBranchPointStats: no visible binding for global variable
  'logPValue'
visualiseTrajectoryStats: no visible binding for global variable 'type'
visualiseTrajectoryStats: no visible binding for global variable
  'value'
Undefined global functions or variables:
  logPValue type value
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
testPathForDirectionality 12.01      0   12.01
analyseBranchPoint        11.45      0   11.45
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
testPathForDirectionality 14.53      0   14.53
analyseBranchPoint        13.48      0   13.48
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/TrajectoryGeometry.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/TrajectoryGeometry_1.0.0.tar.gz && rm -rf TrajectoryGeometry.buildbin-libdir && mkdir TrajectoryGeometry.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TrajectoryGeometry.buildbin-libdir TrajectoryGeometry_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL TrajectoryGeometry_1.0.0.zip && rm TrajectoryGeometry_1.0.0.tar.gz TrajectoryGeometry_1.0.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  7 1422k    7  113k    0     0   572k      0  0:00:02 --:--:--  0:00:02  572k
100 1422k  100 1422k    0     0  1394k      0  0:00:01  0:00:01 --:--:-- 1395k

install for i386

* installing *source* package 'TrajectoryGeometry' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TrajectoryGeometry'
    finding HTML links ... done
    analyseBranchPoint                      html  
    analyseSingleCellTrajectory             html  
    chol_answers                            html  
    chol_attributes                         html  
    chol_branch_point_results               html  
    chol_pseudo_time                        html  
    chol_pseudo_time_normalised             html  
    circleOnTheUnitSphere                   html  
    crooked_path                            html  
    crooked_path_center                     html  
    crooked_path_projection                 html  
    crooked_path_radius                     html  
    distanceBetweenTrajectories             html  
    findSphereClusterCenter                 html  
    findSphericalDistance                   html  
    generateRandomPaths                     html  
    generateRandomUnitVector                html  
    getDistanceDataForPaths                 html  
    getSphericalData                        html  
    getStepLengths                          html  
    hep_answers                             html  
    hep_attributes                          html  
    hep_pseudo_time                         html  
    hep_pseudo_time_normalised              html  
    orthonormalBasis                        html  
    oscillation                             html  
    pathProgression                         html  
    pathToSphericalData                     html  
    plotPathProjectionCenterAndCircle       html  
    projectPathToSphere                     html  
    samplePath                              html  
    single_cell_matrix                      html  
    straight_path                           html  
    straight_path_center                    html  
    straight_path_projection                html  
    straight_path_radius                    html  
    testPathForDirectionality               html  
    visualiseBranchPointStats               html  
    visualiseTrajectoryStats                html  
** 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

install for x64

* installing *source* package 'TrajectoryGeometry' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TrajectoryGeometry' as TrajectoryGeometry_1.0.0.zip
* DONE (TrajectoryGeometry)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'TrajectoryGeometry' successfully unpacked and MD5 sums checked