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This page was generated on 2022-10-19 13:21:00 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for TrajectoryGeometry on nebbiolo1


To the developers/maintainers of the TrajectoryGeometry package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TrajectoryGeometry.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2034/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TrajectoryGeometry 1.4.0  (landing page)
Michael Shapiro
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/TrajectoryGeometry
git_branch: RELEASE_3_15
git_last_commit: 1ec0987
git_last_commit_date: 2022-04-26 12:12:50 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TrajectoryGeometry
Version: 1.4.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:TrajectoryGeometry.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings TrajectoryGeometry_1.4.0.tar.gz
StartedAt: 2022-10-18 22:11:54 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 22:12:56 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 62.0 seconds
RetCode: 0
Status:   OK  
CheckDir: TrajectoryGeometry.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:TrajectoryGeometry.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings TrajectoryGeometry_1.4.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/TrajectoryGeometry.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TrajectoryGeometry/DESCRIPTION’ ... OK
* this is package ‘TrajectoryGeometry’ version ‘1.4.0’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
testPathForDirectionality 10.998  0.024  11.024
analyseBranchPoint        10.628  0.052  10.680
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/TrajectoryGeometry.Rcheck/00check.log’
for details.



Installation output

TrajectoryGeometry.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL TrajectoryGeometry
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* 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
** 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 (TrajectoryGeometry)

Tests output


Example timings

TrajectoryGeometry.Rcheck/TrajectoryGeometry-Ex.timings

nameusersystemelapsed
analyseBranchPoint10.628 0.05210.680
analyseSingleCellTrajectory2.1000.0162.115
circleOnTheUnitSphere0.0010.0000.001
distanceBetweenTrajectories1.1030.0081.111
findSphereClusterCenter0.0560.0000.055
findSphericalDistance0.0000.0000.001
generateRandomPaths0.0010.0000.001
generateRandomUnitVector0.0010.0000.000
getDistanceDataForPaths0.3290.0000.329
getSphericalData0.0480.0000.048
getStepLengths0.0010.0000.000
orthonormalBasis0.0000.0000.001
pathProgression0.0010.0000.001
pathToSphericalData0.0490.0030.053
plotPathProjectionCenterAndCircle0.0410.0350.061
projectPathToSphere0.0010.0000.001
samplePath0.0030.0000.004
testPathForDirectionality10.998 0.02411.024
visualiseBranchPointStats0.9730.0000.974
visualiseTrajectoryStats2.2460.0442.290