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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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

Package 1819/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rtpca 1.16.0  (landing page)
Nils Kurzawa
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/Rtpca
git_branch: RELEASE_3_20
git_last_commit: 40d3ded
git_last_commit_date: 2024-10-29 10:48:09 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for Rtpca on lconway

To the developers/maintainers of the Rtpca package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rtpca.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: Rtpca
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rtpca.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rtpca_1.16.0.tar.gz
StartedAt: 2024-11-20 02:09:39 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 02:14:21 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 281.8 seconds
RetCode: 0
Status:   OK  
CheckDir: Rtpca.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rtpca.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rtpca_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Rtpca.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rtpca/DESCRIPTION’ ... OK
* this is package ‘Rtpca’ version ‘1.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘Rtpca’ 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 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getRandomProteinPairs: no visible binding for global variable ‘pair’
Undefined global functions or variables:
  pair
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/Rtpca.Rcheck/00check.log’
for details.


Installation output

Rtpca.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rtpca
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘Rtpca’ ...
** using staged installation
** R
** data
** 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 (Rtpca)

Tests output

Rtpca.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(Rtpca)
Loading required package: dplyr

Attaching package: 'dplyr'

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: tidyr

Attaching package: 'tidyr'

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

    matches

> 
> test_check("Rtpca")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 38 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
  3.667   0.193   3.907 

Example timings

Rtpca.Rcheck/Rtpca-Ex.timings

nameusersystemelapsed
CommonFeatures-tpcaResult-method0.2670.0050.272
ComplexAnnotation-tpcaResult-method0.0020.0010.002
ComplexBackgroundDistributionList-tpcaResult-method0.0010.0000.000
ComplexRocTable-tpcaResult-method0.0000.0000.001
ContrastCondName-tpcaResult-method000
ContrastDistMat-tpcaResult-method0.0010.0000.001
ContrastList-tpcaResult-method0.0010.0000.001
CtrlCondName-tpcaResult-method000
DistMat-tpcaResult-method0.0010.0000.001
DistMethod-tpcaResult-method000
ObjList-tpcaResult-method0.0010.0010.002
PPiAnnotation-tpcaResult-method0.0010.0000.001
PPiRocTable-tpcaResult-method0.0010.0000.001
PPiRocTableAnno-tpcaResult-method0.0010.0000.001
SetCommonFeatures-tpcaResult-method0.0010.0000.002
SetComplexAnnotation-tpcaResult-method0.0020.0000.002
SetComplexBackgroundDistributionList-tpcaResult-method0.0010.0000.002
SetComplexRocTable-tpcaResult-method0.0010.0010.002
SetContrastCondName-tpcaResult-method0.0000.0010.001
SetContrastDistMat-tpcaResult-method0.0010.0010.001
SetCtrlCondName-tpcaResult-method0.0000.0010.001
SetDiffTpcaResultTable-tpcaResult-method0.0010.0010.002
SetDistMat-tpcaResult-method0.0010.0010.002
SetDistMethod-tpcaResult-method0.0010.0010.002
SetPPiRocTable-tpcaResult-method0.0020.0000.002
SetPPiRocTableAnno-tpcaResult-method0.0020.0010.003
SetSummaryMethod-tpcaResult-method0.0000.0010.001
SetTpcaResultTable-tpcaResult-method0.0010.0000.002
SummaryMethod-tpcaResult-method000
createDistMat0.1250.0030.129
diffTpcaResultTable-tpcaResult-method0.0010.0000.001
ori_et_al_complex_ppis0.0400.0040.053
ori_et_al_complexes_df0.0090.0010.011
plotComplexRoc0.2940.0060.302
plotDiffTpcaVolcano0.1690.0150.185
plotPPiProfiles1.1370.0581.199
plotPPiRoc0.0880.0110.100
plotTpcaVolcano0.6230.0200.643
runDiffTPCA0.0770.0030.080
runTPCA0.2130.0020.215
string_ppi_df1.0110.0121.024
tpcaResult-class0.0010.0000.000
tpcaResultTable-tpcaResult-method0.0010.0000.001