Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-08-07 12:05 -0400 (Thu, 07 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4815
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4550
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4592
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4534
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 2000/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sitePath 1.25.0  (landing page)
Chengyang Ji
Snapshot Date: 2025-08-06 14:04 -0400 (Wed, 06 Aug 2025)
git_url: https://git.bioconductor.org/packages/sitePath
git_branch: devel
git_last_commit: dc3e9e7
git_last_commit_date: 2025-04-15 11:43:03 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
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
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for sitePath on nebbiolo2

To the developers/maintainers of the sitePath package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sitePath.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: sitePath
Version: 1.25.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:sitePath.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings sitePath_1.25.0.tar.gz
StartedAt: 2025-08-07 02:58:41 -0400 (Thu, 07 Aug 2025)
EndedAt: 2025-08-07 03:06:45 -0400 (Thu, 07 Aug 2025)
EllapsedTime: 483.5 seconds
RetCode: 0
Status:   OK  
CheckDir: sitePath.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:sitePath.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings sitePath_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/sitePath.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘sitePath/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sitePath’ version ‘1.25.0’
* 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 ‘sitePath’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    extdata   1.3Mb
    libs      5.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 loading without being on the library search path ... 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
.createSNPplot: no visible binding for global variable ‘Pos’
.createSNPplot: no visible binding for global variable ‘Accession’
.createSNPplot: no visible binding for global variable ‘SNP’
plot.fixationPath: no visible binding for global variable ‘branch’
plot.fixationPath: no visible binding for global variable ‘SNPs’
plot.fixationSites: no visible binding for global variable ‘group’
plot.fixationSites: no visible binding for global variable ‘branch’
plot.fixationSites: no visible binding for global variable ‘SNPs’
plot.parallelSites: no visible binding for global variable ‘branch’
plot.parallelSites: no visible binding for global variable ‘SNPs’
plot.sitePath: no visible binding for global variable ‘branch’
plot.sitePath: no visible binding for global variable ‘SNPs’
plotMutSites.lineagePath: no visible binding for global variable ‘node’
plotMutSites.paraFixSites: no visible binding for global variable
  ‘group’
plotMutSites.paraFixSites: no visible binding for global variable
  ‘branch’
plotMutSites.paraFixSites: no visible binding for global variable
  ‘SNPs’
plotSingleSite.parallelSites: no visible binding for global variable
  ‘branch’
plotSingleSite.parallelSites: no visible binding for global variable
  ‘SNPs’
Undefined global functions or variables:
  Accession Pos SNP SNPs branch group node
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  addMSA.Rd: seqinr, phylo, ape, ggtree, multi2di, is.binary
  lineagePath.Rd: seqinr
  paraFixSites.Rd: seqinr
  plotFunctions.Rd: ggplot2, ggtree
  plotSingleSite.Rd: ggtree
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
plotFunctions     15.203  0.065  15.270
plotParallelSites  8.320  0.037   8.359
plotSingleSite     8.052  0.004   8.057
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/sitePath.Rcheck/00check.log’
for details.


Installation output

sitePath.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL sitePath
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘sitePath’ ...
** this is package ‘sitePath’ version ‘1.25.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c lumpyCluster.cpp -o lumpyCluster.o
lumpyCluster.cpp: In member function ‘void LumpyCluster::Base::mergeClusters(const Treemer::clusters&, int)’:
lumpyCluster.cpp:96:24: warning: comparison of integer expressions of different signedness: ‘std::vector<Treemer::TipSeqLinker*>::size_type’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
   96 |     if (allTips.size() >= m_maxSNPnum) {
      |         ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c minEntropy.cpp -o minEntropy.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c searchNode.cpp -o searchNode.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c searchTree.cpp -o searchTree.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c treemer.cpp -o treemer.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c util.cpp -o util.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o sitePath.so RcppExports.o lumpyCluster.o minEntropy.o searchNode.o searchTree.o treemer.o util.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-sitePath/00new/sitePath/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sitePath)

Tests output

sitePath.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(sitePath)
> 
> test_check("sitePath")
Using 2 cores..
Multiprocessing ended.
Using 2 cores..
Multiprocessing ended.
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 2312 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 2312 ]
> 
> proc.time()
   user  system elapsed 
269.713   2.704 353.721 

Example timings

sitePath.Rcheck/sitePath-Ex.timings

nameusersystemelapsed
SNPsites0.6130.0250.639
addMSA1.7040.0031.709
allSitesName2.0990.0062.106
as.data.frame1.4570.0161.473
extractSite1.5260.0201.547
extractTips1.6580.0141.672
fixationIndels1.3300.0061.336
fixationPath1.4450.0011.446
fixationSites1.4230.0261.450
groupTips1.7280.0021.731
lineagePath3.2380.0053.244
paraFixSites1.5730.0271.601
parallelSites1.5230.0011.524
plotFixationSites2.0050.0022.007
plotFunctions15.203 0.06515.270
plotMutSites1.1290.0081.190
plotParallelSites8.3200.0378.359
plotSingleSite8.0520.0048.057
setSiteNumbering1.9310.0011.931
similarityMatrix1.8140.0001.813
sitesMinEntropy1.5030.0341.537