This page was generated on 2024-05-07 11:32:31 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup"
| 4461 |
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 |
| CNAnorm 1.50.0 (landing page) Stefano Berri
Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 May 2024) |
git_url: https://git.bioconductor.org/packages/CNAnorm |
git_branch: RELEASE_3_19 |
git_last_commit: a0fa3b7 |
git_last_commit_date: 2024-04-30 10:25:46 -0400 (Tue, 30 Apr 2024) |
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | |
CHECK results for CNAnorm on kjohnson3
To the developers/maintainers of the CNAnorm package:
- 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
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNAnorm.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNAnorm_1.50.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/CNAnorm.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-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 Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNAnorm/DESCRIPTION’ ... OK
* this is package ‘CNAnorm’ version ‘1.50.0’
* 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 ‘CNAnorm’ can be installed ... OK
* used Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’
* used SDK: ‘MacOSX11.3.sdk’
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.exportTable: no visible global function definition for ‘write.table’
.gaussianWeights: no visible global function definition for ‘median’
.gaussianWeights: no visible global function definition for ‘sd’
.guessPeaksAndPloidy: no visible global function definition for
‘density’
.guessPeaksAndPloidy: no visible global function definition for
‘median’
.OTquantileWeights: no visible global function definition for ‘median’
.OTquantileWeights: no visible global function definition for
‘quantile’
.peakPloidy: no visible global function definition for ‘median’
.plotGenome: no visible global function definition for ‘text’
.plotGenome: no visible global function definition for ‘par’
.plotGenome: no visible global function definition for ‘points’
.plotGenome: no visible global function definition for ‘axis’
.plotGenome: no visible global function definition for ‘axTicks’
.plotGenome: no visible global function definition for ‘title’
.plotGenome: no visible global function definition for ‘mtext’
.plotGenome: no visible global function definition for ‘abline’
.plotGenome: no visible global function definition for ‘data’
.plotGenome: no visible global function definition for ‘lines’
.plotPeaks: no visible global function definition for ‘density’
.plotPeaks: no visible global function definition for ‘median’
.plotPeaks: no visible global function definition for ‘lines’
.plotPeaks: no visible global function definition for ‘abline’
.plotPeaks: no visible global function definition for ‘text’
.plotPeaks: no visible global function definition for ‘legend’
.plotPeaks_old: no visible global function definition for ‘median’
.plotPeaks_old: no visible global function definition for ‘lines’
.plotPeaks_old: no visible global function definition for ‘abline’
.plotPeaks_old: no visible global function definition for ‘text’
.plotPeaks_old: no visible global function definition for ‘legend’
.TTquantileWeights: no visible global function definition for ‘median’
.TTquantileWeights: no visible global function definition for
‘quantile’
bandseg: no visible global function definition for ‘filter’
brute.seg: no visible global function definition for ‘median’
findOutliers: no visible global function definition for ‘median’
findOutliers: no visible global function definition for ‘density’
gcNormalize: no visible global function definition for ‘loess’
gcNormalize: no visible global function definition for ‘predict’
gcNormalize: no visible global function definition for ‘median’
get.initial.values: no visible global function definition for ‘var’
get.initial.values: no visible global function definition for
‘quantile’
getMQR: no visible global function definition for ‘lm’
global.norm: no visible global function definition for ‘lm’
global.norm: no visible global function definition for ‘predict’
medianWinSize: no visible global function definition for ‘median’
myDensity: no visible global function definition for ‘median’
myDensity: no visible global function definition for ‘sd’
myDensity: no visible global function definition for ‘density’
myPeaks: no visible global function definition for ‘embed’
pdetect: no visible global function definition for ‘rnorm’
pdetect: no visible global function definition for ‘density’
pdetect: no visible global function definition for ‘var’
pdetect: no visible global function definition for ‘quantile’
pdetect: no visible global function definition for ‘dnorm’
pdetect: no visible global function definition for ‘median’
pdetect.iter: no visible global function definition for ‘var’
pdetect.iter: no visible global function definition for ‘dnorm’
pdetect.iter: no visible global function definition for ‘median’
plotPeaksMixture: no visible global function definition for ‘median’
plotPeaksMixture: no visible global function definition for ‘hist’
plotPeaksMixture: no visible global function definition for ‘abline’
Rcheck: no visible global function definition for ‘lm’
rseg: no visible global function definition for ‘median’
smoothseg: no visible global function definition for ‘lines’
exportTable,CNAnorm: no visible global function definition for
‘write.table’
peakPloidy,CNAnorm: no visible global function definition for ‘median’
plotGenome,CNAnorm: no visible global function definition for ‘text’
plotGenome,CNAnorm: no visible global function definition for ‘par’
plotGenome,CNAnorm: no visible global function definition for ‘points’
plotGenome,CNAnorm: no visible global function definition for ‘axis’
plotGenome,CNAnorm: no visible global function definition for ‘axTicks’
plotGenome,CNAnorm: no visible global function definition for ‘title’
plotGenome,CNAnorm: no visible global function definition for ‘mtext’
plotGenome,CNAnorm: no visible global function definition for ‘abline’
plotGenome,CNAnorm: no visible global function definition for ‘data’
plotGenome,CNAnorm: no visible global function definition for ‘lines’
plotPeaks,CNAnorm: no visible global function definition for ‘density’
plotPeaks,CNAnorm: no visible global function definition for ‘median’
plotPeaks,CNAnorm: no visible global function definition for ‘lines’
plotPeaks,CNAnorm: no visible global function definition for ‘abline’
plotPeaks,CNAnorm: no visible global function definition for ‘text’
plotPeaks,CNAnorm: no visible global function definition for ‘legend’
Undefined global functions or variables:
abline axis axTicks data density dnorm embed filter hist legend lines
lm loess median mtext par points predict quantile rnorm sd text title
var write.table
Consider adding
importFrom("graphics", "abline", "axis", "axTicks", "hist", "legend",
"lines", "mtext", "par", "points", "text", "title")
importFrom("stats", "density", "dnorm", "embed", "filter", "lm",
"loess", "median", "predict", "quantile", "rnorm", "sd",
"var")
importFrom("utils", "data", "write.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) peakPloidy.Rd:67-68: Lost braces
67 | \bold{peakRatio}{Threshold used to call a peak. Peaks smaller than
| ^
checkRd: (-1) peakPloidy.Rd:70-73: Lost braces
70 | \bold{spacingTolerance}{A parameter smaller than 1 which describes how
| ^
checkRd: (-1) peakPloidy.Rd:75-76: Lost braces
75 | \bold{interceptRatio}{Minimum value for the intercept of the linear model.
| ^
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking usage of KIND in Fortran files ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/CNAnorm.Rcheck/00check.log’
for details.
Installation output
CNAnorm.Rcheck/00install.out
Tests output
Example timings
CNAnorm.Rcheck/CNAnorm-Ex.timings