Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-03-29 11:05:27 -0400 (Wed, 29 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4482
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4278
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4306
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 Cepo on palomino4


To the developers/maintainers of the Cepo package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Cepo.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 290/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Cepo 1.4.0  (landing page)
Hani Jieun Kim
Snapshot Date: 2023-03-27 14:00:04 -0400 (Mon, 27 Mar 2023)
git_url: https://git.bioconductor.org/packages/Cepo
git_branch: RELEASE_3_16
git_last_commit: 7410238
git_last_commit_date: 2022-11-01 11:26:00 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: Cepo
Version: 1.4.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Cepo.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings Cepo_1.4.0.tar.gz
StartedAt: 2023-03-27 23:47:32 -0400 (Mon, 27 Mar 2023)
EndedAt: 2023-03-27 23:52:50 -0400 (Mon, 27 Mar 2023)
EllapsedTime: 317.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Cepo.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Cepo.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings Cepo_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/Cepo.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Cepo/DESCRIPTION' ... OK
* this is package 'Cepo' 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 whether package 'Cepo' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... WARNING
Invalid license file pointers: LICENSE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'patchwork'
A package should be listed in only one of these fields.
* 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 ... WARNING
'::' or ':::' import not declared from: 'purrr'
Package in Depends field not imported from: 'GSEABase'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'rowMeans_withnames' 'rowSds_withnames'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bootFastCepo : <anonymous>: no visible binding for global variable '.'
bootFastCepo: no visible binding for global variable '.'
Undefined global functions or variables:
  .
* 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 ... WARNING
Undocumented arguments in documentation object 'Cepo'
  'prefilter_pzero'
Documented arguments not in \usage in documentation object 'Cepo':
  'prefilter_pzeros'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
plotDensities 5.72   0.16    5.88
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.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: 3 WARNINGs, 1 NOTE
See
  'F:/biocbuild/bbs-3.16-bioc/meat/Cepo.Rcheck/00check.log'
for details.



Installation output

Cepo.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL Cepo
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'Cepo' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** 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 (Cepo)

Tests output

Cepo.Rcheck/tests/testthat.Rout


R version 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(Cepo)
Loading required package: GSEABase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'IRanges'

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

    windows

Loading required package: XML
Loading required package: graph

Attaching package: 'graph'

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

    addNode

> 
> test_check("Cepo")
Computed statistics: 
 
DataFrame with 50 rows and 3 columns
               a          b           c
       <numeric>  <numeric>   <numeric>
gene38  0.551471  -0.441176 -0.11029412
gene41  0.404412  -0.411765  0.00735294
gene29  0.330882   0.117647 -0.44852941
gene21  0.325980  -0.181373 -0.14460784
gene32  0.321078  -0.289216 -0.03186275
...          ...        ...         ...
gene1  -0.370098 0.05637255   0.3137255
gene24 -0.375000 0.12500000   0.2500000
gene45 -0.379902 0.00245098   0.3774510
gene2  -0.448529 0.33088235   0.1176471
gene4  -0.531863 0.57107843  -0.0392157
Computed p-values: 
DataFrame with 50 rows and 3 columns
                a          b         c
        <numeric>  <numeric> <numeric>
gene38 0.02235891   0.934256  0.721275
gene41 0.11378279   0.873406  0.539946
gene29 0.11634117   0.238066  0.987330
gene21 0.00212245   0.988726  0.759055
gene32 0.06175835   0.863106  0.563826
...           ...        ...       ...
gene1    0.824329 0.61332493 0.0937726
gene24   0.988888 0.38794339 0.0753923
gene45   0.850877 0.57434720 0.0642338
gene2    0.885892 0.14074781 0.4028927
gene4    0.923960 0.00202297 0.8289986
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
  20.09    1.14   98.65 

Example timings

Cepo.Rcheck/Cepo-Ex.timings

nameusersystemelapsed
Cepo1.380.001.37
plotDensities5.720.165.88
setCepoBPPARAM000
topGenes0.030.000.03