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This page was generated on 2023-01-02 09:00:52 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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 spicyR on palomino5


To the developers/maintainers of the spicyR package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1920/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
spicyR 1.11.3  (landing page)
Ellis Patrick
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/spicyR
git_branch: master
git_last_commit: db6785f
git_last_commit_date: 2022-11-16 19:47:43 -0500 (Wed, 16 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  

Summary

Package: spicyR
Version: 1.11.3
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:spicyR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings spicyR_1.11.3.tar.gz
StartedAt: 2022-12-29 03:50:31 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 03:53:50 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 199.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: spicyR.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:spicyR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings spicyR_1.11.3.tar.gz
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/spicyR.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'spicyR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'spicyR' version '1.11.3'
* 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 'spicyR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
* 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
bubblePlot: no visible binding for global variable 'condition'
calcWeights: no visible binding for global variable 'pairwiseAssoc'
inhomL: no visible binding for global variable 'j'
inhomL: no visible binding for global variable 'value'
inhomL: no visible binding for global variable 'i'
inhomL: no visible binding for global variable 'd'
inhomL: no visible binding for global variable 'cellTypeI'
inhomL: no visible binding for global variable 'cellTypeJ'
inhomL: no visible global function definition for '.'
inhomL: no visible binding for global variable 'wt'
inhomLPair: no visible binding for global variable 'i'
Undefined global functions or variables:
  . cellTypeI cellTypeJ condition d i j pairwiseAssoc value wt
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'diabetesData_SCE'
Undocumented data sets:
  'diabetesData_SCE'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'colTest':
colTest
  Code: function(df, condition, type = "ttest", feature = NULL, imageID
                 = "imageID")
  Docs: function(df, condition, type = "wilcox", feature = NULL,
                 imageID = "imageID")
  Mismatches in argument default values:
    Name: 'type' Code: "ttest" Docs: "wilcox"

* 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
spicy 12.19   0.21   12.41
* 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: 2 WARNINGs, 2 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/spicyR.Rcheck/00check.log'
for details.



Installation output

spicyR.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL spicyR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'spicyR' ...
** 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 (spicyR)

Tests output


Example timings

spicyR.Rcheck/spicyR-Ex.timings

nameusersystemelapsed
Accessors0.850.000.84
SegmentedCells0.200.020.22
colTest2.890.022.91
getPairwise3.240.073.30
getProp0.820.000.82
plot-SegmentedCells0.180.000.18
show-SegmentedCells0.230.000.23
signifPlot0.830.040.86
spicy12.19 0.2112.41
topPairs0.010.000.01