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CHECK report for ABSSeq on tokay1

This page was generated on 2020-10-25 12:05:51 -0400 (Sun, 25 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ABSSeq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 10/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ABSSeq 1.43.0
Wentao Yang
Snapshot Date: 2020-10-24 14:40:19 -0400 (Sat, 24 Oct 2020)
URL: https://git.bioconductor.org/packages/ABSSeq
Branch: master
Last Commit: 2181a4f
Last Changed Date: 2020-04-27 14:39:30 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ABSSeq
Version: 1.43.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ABSSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ABSSeq_1.43.0.tar.gz
StartedAt: 2020-10-25 00:10:42 -0400 (Sun, 25 Oct 2020)
EndedAt: 2020-10-25 00:15:49 -0400 (Sun, 25 Oct 2020)
EllapsedTime: 307.8 seconds
RetCode: 0
Status:  OK  
CheckDir: ABSSeq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ABSSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ABSSeq_1.43.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ABSSeq.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ABSSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ABSSeq' version '1.43.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'ABSSeq' 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 ... NOTE
'library' or 'require' call to 'edgeR' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ABSDataSet: no visible global function definition for 'new'
ABSSeqlm: no visible global function definition for 'pnorm'
ABSSeqlm: no visible global function definition for 'p.adjust'
ReplaceOutliersByMAD: no visible global function definition for 'is'
ReplaceOutliersByMAD: no visible global function definition for
  'model.matrix'
ReplaceOutliersByMAD: no visible global function definition for
  'predict'
aFoldcomplexDesign: no visible binding for global variable 'sd'
aFoldcomplexDesign: no visible binding for global variable 'var'
aFoldcomplexDesign: no visible global function definition for 'sd'
callDEs: no visible global function definition for 'is'
callDEs: no visible binding for global variable 'p.adjust.methods'
callDEs: no visible global function definition for 'pnorm'
callDEs: no visible global function definition for 'pnbinom'
callDEs: no visible global function definition for 'p.adjust'
callParameter: no visible global function definition for 'is'
callParameter: no visible binding for global variable 'var'
callParameter: no visible global function definition for 'quantile'
callParameter: no visible global function definition for 'predict'
callParameter: no visible global function definition for 'model.matrix'
callParameterwithoutReplicates: no visible global function definition
  for 'is'
callParameterwithoutReplicates: no visible binding for global variable
  'sd'
callParameterwithoutReplicates: no visible global function definition
  for 'predict'
callParameterwithoutReplicates: no visible binding for global variable
  'var'
callParameterwithoutReplicates: no visible global function definition
  for 'quantile'
callParameterwithoutReplicates: no visible global function definition
  for 'model.matrix'
callPergroup: no visible binding for global variable 'var'
estimateSizeFactorsForMatrix: no visible binding for global variable
  'median'
genAFold: no visible binding for global variable 'var'
genAFold: no visible binding for global variable 'sd'
genAFold: no visible global function definition for 'sd'
normalFactors: no visible global function definition for 'is'
normalFactors: no visible global function definition for 'validObject'
normalFactors : rowQuar: no visible global function definition for
  'quantile'
normalFactors: no visible global function definition for
  'calcNormFactors'
plotDifftoBase: no visible global function definition for 'is'
preAFold: no visible global function definition for 'quantile'
preAFold: no visible global function definition for 'var'
preAFold: no visible global function definition for 'predict'
preAFoldComplex: no visible global function definition for 'quantile'
preAFoldComplex: no visible global function definition for 'var'
preAFoldComplex: no visible global function definition for 'predict'
qtotalNormalized : rowQuar: no visible global function definition for
  'quantile'
qtotalNormalized : rowQuar: no visible global function definition for
  'sd'
qtotalNormalized : rowQuar: no visible global function definition for
  'median'
qtotalNormalized : rowQuar : <anonymous>: no visible global function
  definition for 'median'
replaceByrow: no visible global function definition for 'median'
replaceByrow: no visible global function definition for 'mad'
LevelstoNormFC<-,ABSDataSet-numeric: no visible global function
  definition for 'validObject'
[[<-,SumInfo-character-missing: no visible global function definition
  for 'as'
counts<-,ABSDataSet-matrix: no visible global function definition for
  'validObject'
excounts<-,ABSDataSet-matrix: no visible global function definition for
  'validObject'
groups<-,ABSDataSet-factor: no visible global function definition for
  'validObject'
maxRates<-,ABSDataSet-numeric: no visible global function definition
  for 'validObject'
minRates<-,ABSDataSet-numeric: no visible global function definition
  for 'validObject'
minimalDispersion<-,ABSDataSet-numeric: no visible global function
  definition for 'validObject'
normMethod<-,ABSDataSet-character: no visible global function
  definition for 'validObject'
paired<-,ABSDataSet-logical: no visible global function definition for
  'validObject'
sFactors<-,ABSDataSet-numeric: no visible global function definition
  for 'validObject'
Undefined global functions or variables:
  as calcNormFactors is mad median model.matrix new p.adjust
  p.adjust.methods pnbinom pnorm predict quantile sd validObject var
Consider adding
  importFrom("methods", "as", "is", "new", "validObject")
  importFrom("stats", "mad", "median", "model.matrix", "p.adjust",
             "p.adjust.methods", "pnbinom", "pnorm", "predict",
             "quantile", "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
callDEs              13.30   0.00   13.30
ABSSeq               12.79   0.12   13.03
callParameter        11.74   0.00   11.73
results              10.86   0.02   10.88
plotDifftoBase       10.53   0.00   10.53
ReplaceOutliersByMAD 10.25   0.00   10.25
ABSSeqlm              8.69   0.00    8.69
excounts              7.52   0.00    7.52
aFoldcomplexDesign    5.09   0.00    5.09
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
results              13.36   0.03   13.39
ABSSeq               12.90   0.01   12.97
plotDifftoBase       11.56   0.00   11.56
ReplaceOutliersByMAD 11.04   0.02   11.07
excounts             10.90   0.00   10.91
callDEs              10.61   0.00   10.61
callParameter        10.03   0.01   10.05
ABSSeqlm              7.89   0.00    7.89
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/ABSSeq.Rcheck/00check.log'
for details.



Installation output

ABSSeq.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/ABSSeq_1.43.0.tar.gz && rm -rf ABSSeq.buildbin-libdir && mkdir ABSSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ABSSeq.buildbin-libdir ABSSeq_1.43.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ABSSeq_1.43.0.zip && rm ABSSeq_1.43.0.tar.gz ABSSeq_1.43.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0  223k    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  223k  100  223k    0     0   305k      0 --:--:-- --:--:-- --:--:--  306k

install for i386

* installing *source* package 'ABSSeq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ABSSeq'
    finding HTML links ... done
    ABSDataSet                              html  
    ABSSeq                                  html  
    ABSSeqlm                                html  
    LevelstoNormFC                          html  
    ReplaceOutliersByMAD                    html  
    aFoldcomplexDesign                      html  
    callDEs                                 html  
    callParameter                           html  
    callParameterwithoutReplicates          html  
    counts                                  html  
    estimateSizeFactorsForMatrix            html  
    excounts                                html  
    genAFold                                html  
    groups                                  html  
    maxRates                                html  
    minRates                                html  
    minimalDispersion                       html  
    normMethod                              html  
    normalFactors                           html  
    paired                                  html  
    plotDifftoBase                          html  
    qtotalNormalized                        html  
    results                                 html  
    sFactors                                html  
    simuN5                                  html  
** 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

install for x64

* installing *source* package 'ABSSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ABSSeq' as ABSSeq_1.43.0.zip
* DONE (ABSSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ABSSeq' successfully unpacked and MD5 sums checked

Tests output


Example timings

ABSSeq.Rcheck/examples_i386/ABSSeq-Ex.timings

nameusersystemelapsed
ABSDataSet0.130.000.12
ABSSeq12.79 0.1213.03
ABSSeqlm8.690.008.69
LevelstoNormFC0.060.000.06
ReplaceOutliersByMAD10.25 0.0010.25
aFoldcomplexDesign5.090.005.09
callDEs13.3 0.013.3
callParameter11.74 0.0011.73
callParameterwithoutReplicates1.510.001.52
counts0.050.000.04
estimateSizeFactorsForMatrix0.060.020.08
excounts7.520.007.52
genAFold3.910.003.90
groups0.050.000.05
maxRates0.030.010.04
minRates0.050.000.05
minimalDispersion0.060.000.06
normMethod0.050.000.05
normalFactors2.50.02.5
paired0.040.000.05
plotDifftoBase10.53 0.0010.53
qtotalNormalized2.880.002.87
results10.86 0.0210.88
sFactors2.650.032.68
simuN50.040.000.04

ABSSeq.Rcheck/examples_x64/ABSSeq-Ex.timings

nameusersystemelapsed
ABSDataSet0.160.000.15
ABSSeq12.90 0.0112.97
ABSSeqlm7.890.007.89
LevelstoNormFC0.050.000.04
ReplaceOutliersByMAD11.04 0.0211.07
aFoldcomplexDesign3.710.003.70
callDEs10.61 0.0010.61
callParameter10.03 0.0110.05
callParameterwithoutReplicates2.230.002.23
counts0.050.000.04
estimateSizeFactorsForMatrix0.080.000.08
excounts10.90 0.0010.91
genAFold4.350.004.34
groups0.040.000.05
maxRates0.030.000.03
minRates0.040.000.03
minimalDispersion0.030.010.05
normMethod0.030.000.03
normalFactors2.530.042.56
paired0.050.000.05
plotDifftoBase11.56 0.0011.56
qtotalNormalized3.560.003.56
results13.36 0.0313.39
sFactors2.940.002.94
simuN50.030.000.03