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This page was generated on 2024-04-17 11:36:27 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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 2133/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tilingArray 1.80.0  (landing page)
Zhenyu Xu
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/tilingArray
git_branch: RELEASE_3_18
git_last_commit: 3382502
git_last_commit_date: 2023-10-24 09:34:45 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for tilingArray on nebbiolo2


To the developers/maintainers of the tilingArray package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tilingArray.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: tilingArray
Version: 1.80.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:tilingArray.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings tilingArray_1.80.0.tar.gz
StartedAt: 2024-04-16 04:46:05 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 04:49:07 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 181.6 seconds
RetCode: 0
Status:   OK  
CheckDir: tilingArray.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:tilingArray.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings tilingArray_1.80.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/tilingArray.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘tilingArray/DESCRIPTION’ ... OK
* this is package ‘tilingArray’ version ‘1.80.0’
* 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 ‘tilingArray’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘pixmap’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.onAttach: no visible global function definition for ‘addVigs2WinMenu’
comparisonPlot : myColors: no visible global function definition for
  ‘quantile’
grid.image: no visible global function definition for ‘colorRamp’
grid.image: no visible global function definition for ‘rgb’
interpolateZ: no visible global function definition for ‘approx’
matDensities : densXY: no visible global function definition for
  ‘density’
myPixmap: no visible global function definition for ‘pixmapGrey’
myWrite: no visible global function definition for ‘write.pnm’
normalizeByReference: no visible global function definition for ‘exprs’
normalizeByReference: no visible global function definition for
  ‘quantile’
normalizeByReference: no visible global function definition for
  ‘approxfun’
normalizeByReference: no visible global function definition for ‘pdf’
normalizeByReference: no visible global function definition for
  ‘smoothScatter’
normalizeByReference: no visible global function definition for ‘lines’
normalizeByReference: no visible global function definition for
  ‘dev.off’
normalizeByReference: no visible global function definition for
  ‘exprs<-’
plotAlongChrom: no visible global function definition for ‘colorRamp’
plotAlongChrom: no visible global function definition for ‘quantile’
plotFeatures: no visible global function definition for ‘listLen’
plotPenLL: no visible binding for global variable ‘quantile’
plotPenLL: no visible global function definition for ‘matplot’
plotPenLL: no visible global function definition for ‘segments’
plotPenLL: no visible global function definition for ‘legend’
plotSegmentationDots: no visible global function definition for
  ‘quantile’
plotSegmentationHeatmap: no visible global function definition for
  ‘colorRamp’
plotSegmentationHeatmap: no visible global function definition for
  ‘quantile’
qcPlots: no visible global function definition for ‘pData’
qcPlots: no visible global function definition for ‘exprs’
qcPlots: no visible global function definition for ‘png’
qcPlots: no visible global function definition for ‘boxplot’
qcPlots: no visible global function definition for ‘dev.off’
qcPlots: no visible global function definition for ‘matplot’
qcPlots: no visible global function definition for ‘jpeg’
raster.image: no visible global function definition for ‘colorRamp’
raster.image: no visible global function definition for ‘rgb’
readCel2eSet: no visible global function definition for ‘varLabels’
segChrom: no visible global function definition for ‘exprs’
plot,segmentation-ANY: no visible global function definition for ‘note’
plot,segmentation-ANY: no visible global function definition for
  ‘plot.default’
plot,segmentation-ANY: no visible global function definition for
  ‘abline’
plot,segmentation-ANY: no visible global function definition for
  ‘mtext’
Undefined global functions or variables:
  abline addVigs2WinMenu approx approxfun boxplot colorRamp density
  dev.off exprs exprs<- jpeg legend lines listLen matplot mtext note
  pData pdf pixmapGrey plot.default png quantile rgb segments
  smoothScatter varLabels write.pnm
Consider adding
  importFrom("grDevices", "colorRamp", "dev.off", "jpeg", "pdf", "png",
             "rgb")
  importFrom("graphics", "abline", "boxplot", "legend", "lines",
             "matplot", "mtext", "plot.default", "segments",
             "smoothScatter")
  importFrom("stats", "approx", "approxfun", "density", "quantile")
to your NAMESPACE file.
* 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 ... NOTE
S3 methods shown with full name in documentation object 'breakpointsPretend':
  ‘breakpoints.breakpointsPretend’

The \usage entries for S3 methods should use the \method markup and not
their full name.
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 for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘assessNorm.Rnw’... OK
  ‘costMatrix.Rnw’... OK
  ‘findsegments.Rnw’... OK
  ‘plotAlongChrom.Rnw’... OK
  ‘segmentation.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/tilingArray.Rcheck/00check.log’
for details.



Installation output

tilingArray.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL tilingArray
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘tilingArray’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c findsegments.c -o findsegments.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c sampleStep.c -o sampleStep.o
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o tilingArray.so findsegments.o sampleStep.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc/R/site-library/00LOCK-tilingArray/00new/tilingArray/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 (tilingArray)

Tests output


Example timings

tilingArray.Rcheck/tilingArray-Ex.timings

nameusersystemelapsed
PMindex0.0010.0000.000
class-segmentation0.0200.0040.024
comparisonPlot000
costMatrix0.0310.0040.035
findsegments0.0000.0000.001
gffSub0.0780.0000.078
normalizeByReference000
otherStrand0.0000.0000.001
plotAlongChrom0.1840.0080.192
plotAlongChromLegend000
plotSegmentationHeatmap0.0430.0000.043
plotpenLL0.1460.0000.147
posMin0.0010.0000.000
qcPlots000
readCel2eSet000
sampleStep0.0010.0000.001
segChrom000
segment0.0010.0000.001
segnf0.0470.0000.048