Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKLMNOPQRS[T]UVWXYZ

This page was generated on 2024-11-20 12:08 -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 2170/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TPP 3.34.0  (landing page)
Dorothee Childs
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/TPP
git_branch: RELEASE_3_20
git_last_commit: 55ca4d4
git_last_commit_date: 2024-10-29 10:00:25 -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 TPP on kunpeng2

To the developers/maintainers of the TPP package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TPP.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: TPP
Version: 3.34.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:TPP.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings TPP_3.34.0.tar.gz
StartedAt: 2024-11-20 13:22:04 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 13:32:15 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 611.0 seconds
RetCode: 0
Status:   OK  
CheckDir: TPP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:TPP.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings TPP_3.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/TPP.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TPP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TPP’ version ‘3.34.0’
* 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 ‘TPP’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data           1.9Mb
    example_data   8.0Mb
    test_data      1.9Mb
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    Updated package vignette.
  Cannot process chunk/lines:
    Removed unit test that causes R CMD check to crash  since the latest update of package 'testthat'.
  Cannot process chunk/lines:
    Fixed bug in plotColors for the case when no comparisons are specified
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘broom’
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  ‘doParallel:::.options’ ‘mefa:::rep.data.frame’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘TPP/R/TPP.R’:
  .onLoad calls:
    packageStartupMessage(msgText, "\n")

See section ‘Good practice’ in '?.onAttach'.

fitSigmoidCCR: no visible global function definition for
  ‘capture.output’
modelSelector: no visible binding for global variable ‘testHypothesis’
modelSelector: no visible binding for global variable ‘fitMetric’
modelSelector: no visible binding for global variable ‘minMetric’
plot_fSta_distribution: no visible binding for global variable
  ‘density’
plot_pVal_distribution: no visible binding for global variable
  ‘..density..’
tpp2dCreateTPPTRreference: no visible binding for global variable
  ‘meltcurve_plot’
tpp2dCreateTPPTRreference: no visible binding for global variable
  ‘Protein_ID’
tpp2dExport: no visible binding for global variable ‘temperature’
tpp2dImport: no visible binding for global variable ‘temperature’
tpp2dNormalize: no visible binding for global variable ‘temperature’
Undefined global functions or variables:
  ..density.. Protein_ID capture.output density fitMetric
  meltcurve_plot minMetric temperature testHypothesis
Consider adding
  importFrom("stats", "density")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) analyzeTPPTR.Rd:146-147: Lost braces in \itemize; meant \describe ?
checkRd: (-1) analyzeTPPTR.Rd:148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) analyzeTPPTR.Rd:149: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hdacCCR_data.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hdacCCR_data.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hdacTR_data.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hdacTR_data.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hdacTR_data.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hdacTR_data.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tppccrCurveFit.Rd:42: Lost braces
    42 |   code{featureData(S)}.
       |       ^
checkRd: (-1) tppccrImport.Rd:71-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tppccrImport.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tppccrPlotCurves.Rd:45: Lost braces
    45 |   produced plots are stored in code{featureData(S)$plot}.
       |                                    ^
checkRd: (-1) tpptrImport.Rd:76-77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tpptrImport.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tpptrImport.Rd:79: Lost braces in \itemize; meant \describe ?
* 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
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
analyzeTPPTR                   44.542  0.156  44.791
tpptrSplineFitAndTest          25.845  0.385  31.758
tpp2dSplineFitAndTest          16.107  0.285  16.428
tppQCPlotsCorrelateExperiments 15.613  0.268  15.913
tpptrPlotSplines               14.610  0.280  14.917
tpptrFTest                     14.697  0.166  14.887
tpp2dCreateDRplots             13.773  0.120  13.921
tpp2dMerge2dRef                 7.882  0.182   8.080
tppccrPlotCurves                7.543  0.113   7.670
analyze2DTPP                    7.220  0.281   7.515
tpp2dCurveFit                   7.210  0.201   7.427
* 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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/TPP.Rcheck/00check.log’
for details.


Installation output

TPP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL TPP
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘TPP’ ...
** 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 (TPP)

Tests output

TPP.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: aarch64-unknown-linux-gnu

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(TPP)
Loading required package: Biobase
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, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

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

Loading required package: dplyr

Attaching package: 'dplyr'

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

    combine

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

    combine, intersect, setdiff, union

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: magrittr

Attaching package: 'magrittr'

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

    equals, is_less_than, not

Loading required package: tidyr

Attaching package: 'tidyr'

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

    extract

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

    matches

> 
> test_check("TPP")
[[1]]

[[2]]

[[3]]

[[1]]

[[2]]

[[3]]

[[1]]

[[2]]

[[3]]

[[1]]

[[2]]

[[3]]

[[1]]

[[2]]

[[3]]

[[1]]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 303 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 303 ]
> 
> proc.time()
   user  system elapsed 
284.176   5.369 298.398 

Example timings

TPP.Rcheck/TPP-Ex.timings

nameusersystemelapsed
analyze2DTPP7.2200.2817.515
analyzeTPPCCR4.9300.0414.981
analyzeTPPTR44.542 0.15644.791
tpp2dAddAdditionalInfo0.0230.0000.024
tpp2dCalcFractAbundance3.4220.0043.433
tpp2dComputeFoldChanges0.5040.0000.505
tpp2dCreateDRplots13.773 0.12013.921
tpp2dCurveFit7.2100.2017.427
tpp2dExport0.0410.0000.043
tpp2dImport0.4110.0040.417
tpp2dMerge2dRef7.8820.1828.080
tpp2dNormalize0.6750.0200.696
tpp2dSplineFitAndTest16.107 0.28516.428
tpp2dSplinePlot0.0070.0000.008
tpp2dTRReferenceObject0.0190.0000.021
tppDefaultTheme0.4940.0040.500
tppExport0.3490.0120.362
tppQCPlotsCorrelateExperiments15.613 0.26815.913
tppccrCurveFit4.8500.0794.937
tppccrImport0.1460.0000.146
tppccrNormalize0.1770.0000.177
tppccrNormalizeToReference0.2270.0000.228
tppccrPlotCurves7.5430.1137.670
tppccrResultTable4.5430.1524.704
tppccrTransform0.2080.0000.209
tpptrAnalyzeMeltingCurves0.4560.0000.457
tpptrCurveFit1.0710.0041.074
tpptrDefaultNormReqs0.4600.0000.461
tpptrFTest14.697 0.16614.887
tpptrFitSplines1.7240.0021.728
tpptrImport0.2200.0040.224
tpptrNormalize0.8060.0390.847
tpptrPlotSplines14.610 0.28014.917
tpptrSplineFitAndTest25.845 0.38531.758
tpptrTidyUpESets0.5050.0080.569