Multiple platform build/check report for BioC 3.21 - CHECK results for CNAnorm on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4704
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4467
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"	4478
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*

CHECK results for CNAnorm on nebbiolo1

To the developers/maintainers of the CNAnorm package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CNAnorm.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: CNAnorm

Version: 1.53.0

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:CNAnorm.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings CNAnorm_1.53.0.tar.gz

StartedAt: 2025-02-02 20:57:46 -0500 (Sun, 02 Feb 2025)

EndedAt: 2025-02-02 20:58:36 -0500 (Sun, 02 Feb 2025)

EllapsedTime: 50.1 seconds

RetCode: 0

Status: OK

CheckDir: CNAnorm.Rcheck

Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:CNAnorm.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings CNAnorm_1.53.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CNAnorm.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* 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 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘CNAnorm/DESCRIPTION’ ... OK
* this is package ‘CNAnorm’ version ‘1.53.0’
* 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 (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 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
.OTquantileWeights: no visible global function definition for ‘median’
.OTquantileWeights: no visible global function definition for
  ‘quantile’
.TTquantileWeights: no visible global function definition for ‘median’
.TTquantileWeights: no visible global function definition for
  ‘quantile’
.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’
.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’
Rcheck: no visible global function definition for ‘lm’
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’
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 axTicks axis 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", "axTicks", "axis", "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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
peakPloidy 10.039  0.041  10.081
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/CNAnorm.Rcheck/00check.log’
for details.

Installation output

CNAnorm.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL CNAnorm
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘CNAnorm’ ...
** this is package ‘CNAnorm’ version ‘1.53.0’
** using staged installation
** libs
using Fortran compiler: ‘GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gfortran  -fpic  -g -O2  -c daxpy.f -o daxpy.o
gfortran  -fpic  -g -O2  -c ddot.f -o ddot.o
gfortran  -fpic  -g -O2  -c dgbfa.f -o dgbfa.o
gfortran  -fpic  -g -O2  -c dgbsl.f -o dgbsl.o
gfortran  -fpic  -g -O2  -c dscal.f -o dscal.o
gfortran  -fpic  -g -O2  -c dsmooth.f -o dsmooth.o
gfortran  -fpic  -g -O2  -c idamax.f -o idamax.o
gcc -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o CNAnorm.so daxpy.o ddot.o dgbfa.o dgbsl.o dscal.o dsmooth.o idamax.o -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-CNAnorm/00new/CNAnorm/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 (CNAnorm)

Tests output

Example timings

CNAnorm.Rcheck/CNAnorm-Ex.timings

name	user	system	elapsed
CNAnorm-class	0.014	0.002	0.016
DerivData-class	0.002	0.001	0.003
InData-class	0.002	0.001	0.003
Params-class	0.002	0.001	0.003
addDNACopy-methods	0.513	0.006	0.519
addSmooth-methods	0.459	0.005	0.465
chrsAndpos-methods	0.019	0.000	0.018
dataFrame2object	0.002	0.001	0.003
discreteNorm-methods	0.009	0.001	0.011
exportTable-method	0.07	0.00	0.07
gcNorm-methods	0.409	0.000	0.408
peakPloidy	10.039	0.041	10.081
plotGenome-methods	0.673	0.003	0.676
plotPeaks-methods	0.162	0.002	0.164
ratio-methods	0.411	0.000	0.411
suggValid-methods	0.011	0.000	0.010
validation-methods	0.007	0.000	0.007
workflowWrapper	0.607	0.003	0.610