Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1421/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NOISeq 2.50.0  (landing page)
Sonia Tarazona
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/NOISeq
git_branch: RELEASE_3_20
git_last_commit: d0c8920
git_last_commit_date: 2024-10-29 09:43:13 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 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
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for NOISeq on nebbiolo2

To the developers/maintainers of the NOISeq package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NOISeq.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: NOISeq
Version: 2.50.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:NOISeq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings NOISeq_2.50.0.tar.gz
StartedAt: 2024-12-20 03:39:36 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 03:45:17 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 341.2 seconds
RetCode: 0
Status:   OK  
CheckDir: NOISeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:NOISeq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings NOISeq_2.50.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/NOISeq.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘NOISeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NOISeq’ version ‘2.50.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘NOISeq’ can be installed ... OK
* 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
.calcFactorQuantile : <anonymous>: no visible global function
  definition for ‘quantile’
CV: no visible global function definition for ‘sd’
DE.plot: no visible global function definition for ‘par’
DE.plot: no visible global function definition for ‘points’
DE.plot: no visible global function definition for ‘axis’
DE.plot: no visible global function definition for ‘na.omit’
DE.plot: no visible global function definition for ‘aggregate’
DE.plot: no visible global function definition for ‘abline’
DE.plot: no visible global function definition for ‘rect’
DE.plot: no visible global function definition for ‘segments’
DE.plot: no visible global function definition for ‘text’
DE.plot: no visible global function definition for ‘layout’
DE.plot: no visible global function definition for ‘barplot’
DE.plot: no visible global function definition for ‘legend’
GC.dat: no visible global function definition for ‘quantile’
GC.dat: no visible global function definition for ‘aggregate’
GC.dat: no visible global function definition for ‘lm’
GC.plot: no visible global function definition for ‘par’
GC.plot: no visible global function definition for ‘matplot’
GC.plot: no visible global function definition for ‘text’
GC.plot: no visible global function definition for ‘pf’
GC.plot: no visible global function definition for ‘legend’
GC.plot: no visible global function definition for ‘layout’
MD: no visible global function definition for ‘combn’
MD.plot: no visible global function definition for ‘quantile’
MD.plot: no visible global function definition for ‘points’
MD.plot: no visible global function definition for ‘legend’
MDbio: no visible global function definition for ‘combn’
MDbio: no visible global function definition for ‘quantile’
PCA.plot: no visible global function definition for ‘colors’
PCA.plot: no visible global function definition for ‘points’
PCA.plot: no visible global function definition for ‘legend’
QCreport: no visible global function definition for ‘pdf’
QCreport: no visible global function definition for ‘layout’
QCreport: no visible global function definition for ‘par’
QCreport: no visible global function definition for ‘text’
QCreport: no visible global function definition for ‘abline’
QCreport : <anonymous>: no visible global function definition for ‘pf’
QCreport: no visible global function definition for ‘dev.off’
allMDbio: no visible binding for global variable ‘sd’
biodetection.plot: no visible global function definition for ‘par’
biodetection.plot: no visible global function definition for ‘barplot’
biodetection.plot: no visible global function definition for ‘axis’
biodetection.plot: no visible global function definition for ‘abline’
biodetection.plot: no visible global function definition for ‘legend’
biodetection.plot: no visible global function definition for
  ‘prop.test’
biodetection.plot: no visible global function definition for ‘lines’
cd.dat : <anonymous>: no visible binding for global variable ‘median’
cd.dat: no visible binding for global variable ‘quantile’
cd.plot: no visible binding for global variable ‘density’
cd.plot: no visible global function definition for ‘abline’
cd.plot: no visible global function definition for ‘median’
cd.plot: no visible global function definition for ‘lines’
cd.plot: no visible global function definition for ‘legend’
countsbio.plot: no visible global function definition for ‘par’
countsbio.plot: no visible global function definition for ‘barplot’
countsbio.plot: no visible global function definition for ‘abline’
countsbio.plot: no visible global function definition for ‘mtext’
countsbio.plot: no visible global function definition for ‘legend’
countsbio.plot: no visible global function definition for ‘boxplot’
countsbio.plot: no visible global function definition for ‘axis’
degenes: no visible global function definition for ‘na.omit’
filtered.data : <anonymous>: no visible global function definition for
  ‘wilcox.test’
filtered.data: no visible global function definition for ‘p.adjust’
filtered.data : <anonymous>: no visible global function definition for
  ‘prop.test’
length.dat: no visible global function definition for ‘quantile’
length.dat: no visible global function definition for ‘aggregate’
length.dat: no visible global function definition for ‘lm’
length.plot: no visible global function definition for ‘par’
length.plot: no visible global function definition for ‘matplot’
length.plot: no visible global function definition for ‘text’
length.plot: no visible global function definition for ‘pf’
length.plot: no visible global function definition for ‘legend’
length.plot: no visible global function definition for ‘layout’
noiseqbio: no visible global function definition for ‘density’
noiseqbio: no visible global function definition for ‘approxfun’
noiseqbio: no visible global function definition for ‘lines’
noiseqbio: no visible global function definition for ‘legend’
plot.y2: no visible global function definition for ‘axis’
plot.y2: no visible global function definition for ‘points’
plot.y2: no visible global function definition for ‘lines’
plot.y2: no visible global function definition for ‘supsmu’
plot.y2: no visible global function definition for ‘mtext’
plot.y2: no visible global function definition for ‘par’
plot.y2: no visible global function definition for ‘box’
probdeg: no visible global function definition for ‘na.omit’
rpkm: no visible global function definition for ‘na.omit’
saturation.dat: no visible global function definition for ‘rmultinom’
saturation.plot: no visible global function definition for ‘par’
saturation.plot: no visible global function definition for ‘colors’
saturation.plot: no visible global function definition for ‘lines’
saturation.plot: no visible global function definition for ‘points’
saturation.plot: no visible global function definition for ‘na.omit’
saturation.plot: no visible global function definition for ‘layout’
saturation.plot: no visible global function definition for ‘rect’
saturation.plot: no visible global function definition for ‘text’
share.info: no visible global function definition for ‘kmeans’
share.info : <anonymous>: no visible global function definition for
  ‘sd’
share.info: no visible global function definition for ‘quantile’
sim.samples: no visible global function definition for ‘runif’
sim.samples: no visible global function definition for ‘rmultinom’
tmm: no visible global function definition for ‘na.omit’
uqua: no visible binding for global variable ‘quantile’
uqua: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  abline aggregate approxfun axis barplot box boxplot colors combn
  density dev.off kmeans layout legend lines lm matplot median mtext
  na.omit p.adjust par pdf pf points prop.test quantile rect rmultinom
  runif sd segments supsmu text wilcox.test
Consider adding
  importFrom("grDevices", "colors", "dev.off", "pdf")
  importFrom("graphics", "abline", "axis", "barplot", "box", "boxplot",
             "layout", "legend", "lines", "matplot", "mtext", "par",
             "points", "rect", "segments", "text")
  importFrom("stats", "aggregate", "approxfun", "density", "kmeans",
             "lm", "median", "na.omit", "p.adjust", "pf", "prop.test",
             "quantile", "rmultinom", "runif", "sd", "supsmu",
             "wilcox.test")
  importFrom("utils", "combn")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) myCounts.Rd:20: Lost braces; missing escapes or markup?
    20 | As \code{myCounts} derives from \code{eSet}, we have used the slot \code{assayData} to store all the expression data, \code{phenoData} to store the factors with the conditions, \code{featureData} which will contain the variables \code{Length}, \code{GCcontent}, \code{Biotype}, \code{Chromosome}, {Start Position}, \code{End Position} for each feature. It has been used the slot \code{experimentData} derived from \code{MIAME-class} which will contain the type of replicates (biological replicates, technical replicates or no replicates at all).
       |                                                                                                                                                                                                                                                                                                          ^
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
noiseq    13.426  0.152  13.579
noiseqbio  5.793  0.003   5.796
QCreport   5.251  0.014   5.266
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/NOISeq.Rcheck/00check.log’
for details.


Installation output

NOISeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL NOISeq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘NOISeq’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (NOISeq)

Tests output


Example timings

NOISeq.Rcheck/NOISeq-Ex.timings

nameusersystemelapsed
ARSyNSeq1.8360.0471.884
DE.plot0.5760.0060.583
PCA.GENES0.0050.0000.006
QCreport5.2510.0145.266
dat0.1220.0000.123
dat2save0.0850.0000.085
degenes0.0560.0000.055
explo.plot0.1170.0020.118
filter.low.counts0.3560.0000.356
noiseq13.426 0.15213.579
noiseqbio5.7930.0035.796
normalization0.0030.0000.004
readData0.1130.0030.116