Back to Multiple platform build/check report for BioC 3.18:   simplified   long
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-03-27 11:36:33 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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 429/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
contiBAIT 1.30.0  (landing page)
Kieran O'Neill
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/contiBAIT
git_branch: RELEASE_3_18
git_last_commit: 4d4e432
git_last_commit_date: 2023-10-24 10:47:36 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 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
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for contiBAIT on palomino4


To the developers/maintainers of the contiBAIT package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/contiBAIT.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: contiBAIT
Version: 1.30.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:contiBAIT.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings contiBAIT_1.30.0.tar.gz
StartedAt: 2024-03-25 23:44:09 -0400 (Mon, 25 Mar 2024)
EndedAt: 2024-03-25 23:50:37 -0400 (Mon, 25 Mar 2024)
EllapsedTime: 387.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: contiBAIT.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:contiBAIT.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings contiBAIT_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/contiBAIT.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'contiBAIT/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'contiBAIT' version '1.30.0'
* 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 whether package 'contiBAIT' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT'
See 'F:/biocbuild/bbs-3.18-bioc/meat/contiBAIT.Rcheck/00install.out' for details.
* used C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   3.4Mb
    libs      1.0Mb
* 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
ideogramPlot.func: no visible binding for global variable 'w'
ideogramPlot.func: no visible binding for global variable 'w2'
makeChrTable: no visible global function definition for 'queryHits'
makeChrTable: no visible global function definition for 'subjectHits'
orderContigsGreedy: no visible global function definition for
  'makeCluster'
orderContigsGreedy: no visible global function definition for
  'clusterCall'
orderContigsGreedy: no visible global function definition for
  'stopCluster'
strandSeqFreqTable: no visible global function definition for
  'queryHits'
strandSeqFreqTable: no visible global function definition for
  'subjectHits'
ideogramPlot,StrandReadMatrix-StrandReadMatrix-ChrTable: no visible
  binding for global variable 'w'
ideogramPlot,StrandReadMatrix-StrandReadMatrix-ChrTable: no visible
  binding for global variable 'w2'
Undefined global functions or variables:
  clusterCall makeCluster queryHits stopCluster subjectHits w w2
* 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
Documented arguments not in \usage in documentation object 'plotLGDistances,LinkageGroupList,StrandStateMatrix-method':
  '...'

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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.18-bioc/R/library/contiBAIT/libs/x64/contiBAIT.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
contiBAIT 5.99   0.25    6.24
* 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, 3 NOTEs
See
  'F:/biocbuild/bbs-3.18-bioc/meat/contiBAIT.Rcheck/00check.log'
for details.



Installation output

contiBAIT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL contiBAIT
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'contiBAIT' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/BH/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c buildLinkageGroups.cpp -o buildLinkageGroups.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/BH/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c computeSim.cpp -o computeSim.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/BH/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c orderContigsGreedy.cpp -o orderContigsGreedy.o
g++ -std=gnu++17 -shared -s -static-libgcc -o contiBAIT.dll tmp.def buildLinkageGroups.o computeSim.o orderContigsGreedy.o -lm -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-bioc/R/library/00LOCK-contiBAIT/00new/contiBAIT/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT'
** testing if installed package keeps a record of temporary installation path
* DONE (contiBAIT)

Tests output


Example timings

contiBAIT.Rcheck/contiBAIT-Ex.timings

nameusersystemelapsed
BAIT000
ContigOrdering000
LibraryGroupList000
LinkageGroupList000
StrandFreqMatrix0.010.020.03
StrandReadMatrix0.020.000.02
StrandStateMatrix000
barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method0.340.040.39
clusterContigs-StrandStateMatrix-method0.030.000.03
contiBAIT5.990.256.24
findSimilarLibraries4.440.024.45
ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method2.170.052.22
makeBoxPlot0.030.010.04
makeChrTable0.860.020.88
orderAllLinkageGroups0.370.030.41
plotContigOrder0.440.010.45
plotLGDistances-LinkageGroupList-StrandStateMatrix-method0.080.040.11
plotWCdistribution-StrandFreqMatrix-method0.110.000.11
preprocessStrandTable-StrandFreqMatrix-method0.220.000.22
reorientAndMergeLGs0.110.010.12
strandSeqFreqTable3.440.083.51
thoroughBed0.060.000.06
writeBed000