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CHECK report for alsace on tokay1

This page was generated on 2020-08-07 12:03:38 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE alsace PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 46/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
alsace 1.25.0
Ron Wehrens
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/alsace
Branch: master
Last Commit: 1b7cacd
Last Changed Date: 2020-04-27 14:38:51 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: alsace
Version: 1.25.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:alsace.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings alsace_1.25.0.tar.gz
StartedAt: 2020-08-07 01:22:12 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 01:24:04 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 112.0 seconds
RetCode: 0
Status:  OK  
CheckDir: alsace.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:alsace.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings alsace_1.25.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/alsace.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'alsace/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'alsace' version '1.25.0'
* 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 'alsace' 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 'lattice' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getPeakTable : clusterPeaks: no visible global function definition for
  'stripplot'
getPeakTable : clusterPeaks : <anonymous>: no visible global function
  definition for 'panel.stripplot'
getPeakTable : clusterPeaks : <anonymous>: no visible global function
  definition for 'panel.abline'
Undefined global functions or variables:
  panel.abline panel.stripplot stripplot
* 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
components 9.86   0.03    9.89
teaMerged  5.76   0.00    5.77
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
components   14.45   0.00   14.46
teaMerged     8.41   0.03    8.43
fitpeaks      6.50   0.02    6.54
doALS         6.30   0.03    6.33
correctPeaks  6.28   0.00    6.28
* 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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/alsace.Rcheck/00check.log'
for details.



Installation output

alsace.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/alsace_1.25.0.tar.gz && rm -rf alsace.buildbin-libdir && mkdir alsace.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=alsace.buildbin-libdir alsace_1.25.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL alsace_1.25.0.zip && rm alsace_1.25.0.tar.gz alsace_1.25.0.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
100 1067k  100 1067k    0     0  23.5M      0 --:--:-- --:--:-- --:--:-- 26.0M

install for i386

* installing *source* package 'alsace' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'alsace'
    finding HTML links ... done
    alsace-package                          html  
    components                              html  
    correctPeaks                            html  
    correctRT                               html  
    finding level-2 HTML links ... done

    doALS                                   html  
    filterPeaks                             html  
    fitpeaks                                html  
    getAllPeaks                             html  
    getPeakTable                            html  
    opa                                     html  
    preprocess                              html  
    showALSresult                           html  
    tea                                     html  
    teaMerged                               html  
    windows                                 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 'alsace' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'alsace' as alsace_1.25.0.zip
* DONE (alsace)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'alsace' successfully unpacked and MD5 sums checked

Tests output


Example timings

alsace.Rcheck/examples_i386/alsace-Ex.timings

nameusersystemelapsed
components9.860.039.89
correctPeaks3.880.023.89
correctRT1.980.001.98
doALS4.330.024.35
filterPeaks0.030.000.03
fitpeaks4.220.014.23
getAllPeaks0.050.000.05
getPeakTable1.870.001.87
opa1.140.001.14
preprocess0.130.000.13
showALSresult0.110.020.12
tea0.130.000.12
teaMerged5.760.005.77
windows0.110.030.14

alsace.Rcheck/examples_x64/alsace-Ex.timings

nameusersystemelapsed
components14.45 0.0014.46
correctPeaks6.280.006.28
correctRT3.010.013.03
doALS6.300.036.33
filterPeaks0.060.000.06
fitpeaks6.500.026.54
getAllPeaks0.030.020.04
getPeakTable2.770.002.77
opa1.780.011.79
preprocess0.110.000.11
showALSresult0.110.000.11
tea0.120.050.18
teaMerged8.410.038.43
windows0.190.020.21