Back to Multiple platform build/check report for BioC 3.13
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2021-10-15 15:05:46 -0400 (Fri, 15 Oct 2021).

CHECK results for msmsEDA on nebbiolo1

To the developers/maintainers of the msmsEDA package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/msmsEDA.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1201/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
msmsEDA 1.30.0  (landing page)
Josep Gregori
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/msmsEDA
git_branch: RELEASE_3_13
git_last_commit: e9ca537
git_last_commit_date: 2021-05-19 11:59:48 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: msmsEDA
Version: 1.30.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:msmsEDA.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings msmsEDA_1.30.0.tar.gz
StartedAt: 2021-10-14 10:43:23 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 10:44:49 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 86.1 seconds
RetCode: 0
Status:   OK  
CheckDir: msmsEDA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:msmsEDA.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings msmsEDA_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/msmsEDA.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘msmsEDA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘msmsEDA’ version ‘1.30.0’
* package encoding: latin1
* 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 ‘msmsEDA’ 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 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 ... NOTE
Package in Depends field not imported from: ‘MSnbase’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘MSnbase:::logging’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
batch.neutralize: no visible global function definition for
  ‘model.matrix’
count.stats: no visible global function definition for ‘exprs’
count.stats: no visible binding for global variable ‘fivenum’
counts.hc: no visible global function definition for ‘exprs’
counts.hc: no visible global function definition for ‘hclust’
counts.hc: no visible global function definition for ‘dist’
counts.hc: no visible global function definition for ‘par’
counts.hc: no visible global function definition for ‘pData’
counts.hc: no visible global function definition for ‘as.dendrogram’
counts.hc: no visible global function definition for ‘dendrapply’
counts.hc: no visible global function definition for ‘title’
counts.heatmap: no visible global function definition for ‘exprs’
counts.heatmap: no visible global function definition for ‘pdf’
counts.heatmap: no visible global function definition for ‘heatmap’
counts.heatmap: no visible global function definition for ‘dev.off’
counts.pca: no visible global function definition for ‘exprs’
counts.pca: no visible global function definition for ‘prcomp’
counts.pca: no visible global function definition for ‘pData’
counts.pca: no visible global function definition for ‘text’
counts.pca: no visible global function definition for ‘abline’
counts.pca: no visible global function definition for ‘title’
disp.estimates: no visible global function definition for ‘exprs’
disp.estimates: no visible global function definition for ‘pData’
disp.estimates: no visible global function definition for ‘pdf’
disp.estimates: no visible global function definition for ‘par’
disp.estimates: no visible global function definition for ‘quantile’
disp.estimates: no visible global function definition for ‘density’
disp.estimates: no visible global function definition for ‘abline’
disp.estimates: no visible global function definition for ‘title’
disp.estimates: no visible global function definition for ‘dev.off’
edgeCol: no visible global function definition for ‘is.leaf’
filter.flags: no visible binding for global variable ‘var’
filter.flags: no visible global function definition for ‘quantile’
norm.counts: no visible global function definition for ‘exprs’
norm.counts: no visible global function definition for ‘exprs<-’
pp.msms.data: no visible global function definition for ‘exprs’
pp.msms.data: no visible global function definition for ‘exprs<-’
residual.var : ss: no visible global function definition for ‘var’
spc.barplots: no visible global function definition for ‘median’
spc.barplots: no visible global function definition for ‘par’
spc.barplots: no visible global function definition for ‘barplot’
spc.barplots: no visible global function definition for ‘abline’
spc.boxplots: no visible global function definition for ‘par’
spc.boxplots: no visible global function definition for ‘boxplot’
spc.boxplots: no visible global function definition for ‘axis’
spc.boxplots: no visible global function definition for ‘legend’
spc.densityplots: no visible global function definition for ‘density’
spc.densityplots: no visible global function definition for ‘par’
spc.densityplots: no visible global function definition for ‘abline’
spc.densityplots: no visible global function definition for ‘lines’
spc.densityplots: no visible global function definition for ‘legend’
spc.scatterplot: no visible global function definition for ‘par’
spc.scatterplot: no visible global function definition for ‘points’
spc.scatterplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline as.dendrogram axis barplot boxplot dendrapply density dev.off
  dist exprs exprs<- fivenum hclust heatmap is.leaf legend lines median
  model.matrix pData par pdf points prcomp quantile text title var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "axis", "barplot", "boxplot",
             "legend", "lines", "par", "points", "text", "title")
  importFrom("stats", "as.dendrogram", "dendrapply", "density", "dist",
             "fivenum", "hclust", "heatmap", "is.leaf", "median",
             "model.matrix", "prcomp", "quantile", "var")
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 ... 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 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/msmsEDA.Rcheck/00check.log’
for details.



Installation output

msmsEDA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL msmsEDA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘msmsEDA’ ...
** using staged installation
** R
** data
** 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 (msmsEDA)

Tests output


Example timings

msmsEDA.Rcheck/msmsEDA-Ex.timings

nameusersystemelapsed
batch.neutralize0.1090.0050.113
count.stats0.0280.0040.031
counts.hc0.0540.0110.066
counts.heatmap0.5300.0080.539
counts.pca0.0520.0040.057
disp.estimates0.2490.0010.250
filter.flags0.0280.0030.030
gene.table0.0080.0000.009
msms.dataset0.0110.0000.011
norm.counts0.0350.0000.034
pnms0.0090.0000.010
pp.msms.data0.0240.0000.025
spc.barplots0.0020.0030.006
spc.boxplots0.0170.0000.016
spc.densityplots0.0340.0000.033
spc.scatterplot0.0530.0040.058