Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:14 -0400 (Fri, 15 Oct 2021).

CHECK results for NOISeq on tokay2

To the developers/maintainers of the NOISeq package:
- Please 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 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 1274/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NOISeq 2.36.0  (landing page)
Sonia Tarazona
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/NOISeq
git_branch: RELEASE_3_13
git_last_commit: c6b5b95
git_last_commit_date: 2021-05-19 11:54:29 -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: NOISeq
Version: 2.36.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NOISeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings NOISeq_2.36.0.tar.gz
StartedAt: 2021-10-15 02:46:06 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 02:48:45 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 159.4 seconds
RetCode: 0
Status:   OK  
CheckDir: NOISeq.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NOISeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings NOISeq_2.36.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/NOISeq.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'NOISeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'NOISeq' version '2.36.0'
* 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 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
.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 ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
noiseq    16.67   0.38   17.14
noiseqbio  8.02   0.05    8.09
QCreport   6.58   0.14    6.78
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
noiseq    15.20   0.49   15.69
noiseqbio  8.24   0.05    8.28
QCreport   6.75   0.11    6.86
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/NOISeq.Rcheck/00check.log'
for details.



Installation output

NOISeq.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/NOISeq_2.36.0.tar.gz && rm -rf NOISeq.buildbin-libdir && mkdir NOISeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NOISeq.buildbin-libdir NOISeq_2.36.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL NOISeq_2.36.0.zip && rm NOISeq_2.36.0.tar.gz NOISeq_2.36.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  757k  100  757k    0     0  2010k      0 --:--:-- --:--:-- --:--:-- 2015k

install for i386

* installing *source* package 'NOISeq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'NOISeq'
    finding HTML links ... done
    ARSyNSeq                                html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/NOISeq.buildbin-libdir/00LOCK-NOISeq/00new/NOISeq/help/arsynseq.html
    Biodetection                            html  
    CD                                      html  
    CountsBio                               html  
    DE.plot                                 html  
    GCcontentBias                           html  
    LengthBias                              html  
    Marioni                                 html  
    Output                                  html  
    PCA.GENES                               html  
    PCA                                     html  
    QCreport                                html  
    Saturation                              html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/NOISeq.buildbin-libdir/00LOCK-NOISeq/00new/NOISeq/help/saturation.html
    dat                                     html  
    dat2save                                html  
    degenes                                 html  
    example                                 html  
    explo.plot                              html  
    filter.low.counts                       html  
    myCounts                                html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/NOISeq.buildbin-libdir/00LOCK-NOISeq/00new/NOISeq/help/myCounts.html
    noiseq                                  html  
    noiseqbio                               html  
    normalization                           html  
    readData                                html  
** building package indices
** installing vignettes
   'NOISeq.Rnw' using 'UTF-8' 
** 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

install for x64

* installing *source* package 'NOISeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'NOISeq' as NOISeq_2.36.0.zip
* DONE (NOISeq)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'NOISeq' successfully unpacked and MD5 sums checked

Tests output


Example timings

NOISeq.Rcheck/examples_i386/NOISeq-Ex.timings

nameusersystemelapsed
ARSyNSeq1.870.051.93
DE.plot0.690.010.70
PCA.GENES0.010.000.02
QCreport6.580.146.78
dat0.190.030.22
dat2save0.140.040.17
degenes0.060.030.10
explo.plot0.170.040.21
filter.low.counts0.490.000.49
noiseq16.67 0.3817.14
noiseqbio8.020.058.09
normalization000
readData0.200.000.21

NOISeq.Rcheck/examples_x64/NOISeq-Ex.timings

nameusersystemelapsed
ARSyNSeq2.230.042.27
DE.plot0.640.030.67
PCA.GENES000
QCreport6.750.116.86
dat0.200.010.22
dat2save0.160.030.19
degenes0.070.000.08
explo.plot0.190.030.22
filter.low.counts0.550.000.54
noiseq15.20 0.4915.69
noiseqbio8.240.058.28
normalization000
readData0.140.010.16