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CHECK report for davidTiling on riesling1

This page was generated on 2021-01-14 15:59:07 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE davidTiling PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 89/385HostnameOS / ArchINSTALLBUILDCHECK
davidTiling 1.31.0
Wolfgang Huber
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/davidTiling
Branch: master
Last Commit: 0c228f3
Last Changed Date: 2020-10-27 09:45:05 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ WARNINGS ]

Summary

Package: davidTiling
Version: 1.31.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:davidTiling.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings davidTiling_1.31.0.tar.gz
StartedAt: 2021-01-14 11:13:35 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:17:33 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 237.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: davidTiling.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:davidTiling.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings davidTiling_1.31.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/davidTiling.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'davidTiling/DESCRIPTION' ... OK
* this is package 'davidTiling' version '1.31.0'
* 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 'davidTiling' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 538.1Mb
  sub-directories of 1Mb or more:
    celfiles  305.9Mb
    data      229.5Mb
    website     2.3Mb
* checking package 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
Packages in Depends field not imported from:
  'Biobase' 'GO.db' 'tilingArray'
  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
GOHyperG: no visible global function definition for 'phyper'
GOHyperG: no visible binding for global variable 'GOTERM'
GOHyperG: no visible global function definition for
  'replaceSystematicByCommonName'
GOHyperG: no visible global function definition for 'Term'
GOHyperG: no visible global function definition for 'abline'
colMedians: no visible binding for global variable 'median'
getAllGO: no visible binding for global variable 'GOMFANCESTOR'
getAllGO: no visible binding for global variable 'GOBPANCESTOR'
getAllGO: no visible binding for global variable 'GOCCANCESTOR'
movingWindow: no visible global function definition for 'median'
movingWindow : <anonymous>: no visible global function definition for
  'median'
scatterWithHist: no visible global function definition for 'hist'
scatterWithHist: no visible global function definition for 'layout'
scatterWithHist: no visible global function definition for 'par'
scatterWithHist: no visible global function definition for 'barplot'
scatterWithHist: no visible global function definition for 'text'
scoreSegments: no visible global function definition for 'data'
scoreSegments: no visible binding for global variable 'yeastFeatures'
scoreSegments: no visible binding for global variable 'chrs'
scoreSegments: no visible global function definition for 'otherStrand'
scoreSegments: no visible global function definition for 'median'
scoreSegments: no visible global function definition for 'posMin'
showDens: no visible global function definition for 'hist'
showDens: no visible global function definition for 'axis'
showDens: no visible global function definition for 'polygon'
zscore: no visible global function definition for 'sd'
Undefined global functions or variables:
  GOBPANCESTOR GOCCANCESTOR GOMFANCESTOR GOTERM Term abline axis
  barplot chrs data hist layout median otherStrand par phyper polygon
  posMin replaceSystematicByCommonName sd text yeastFeatures
Consider adding
  importFrom("graphics", "abline", "axis", "barplot", "hist", "layout",
             "par", "polygon", "text")
  importFrom("stats", "median", "phyper", "sd")
  importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: GOHyperG.Rd:34-35: Dropping empty section \examples
prepare_Rd: getGO.Rd:32-33: Dropping empty section \examples
prepare_Rd: scatterWithHist.Rd:19-20: Dropping empty section \details
prepare_Rd: scoreSegments.Rd:103-104: Dropping empty section \examples
* 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' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  'Archi_RT_positions.txt', 'strongConservedNovelIsolated.txt',
    'utrmap-GOcategories.txt'
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
davidTiling 22.2   0.31   22.52
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
davidTiling 18.09   0.55   18.64
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/davidTiling.Rcheck/00check.log'
for details.



Installation output

davidTiling.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/davidTiling_1.31.0.tar.gz && rm -rf davidTiling.buildbin-libdir && mkdir davidTiling.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=davidTiling.buildbin-libdir davidTiling_1.31.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL davidTiling_1.31.0.zip && rm davidTiling_1.31.0.tar.gz davidTiling_1.31.0.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
 17  537M   17 94.2M    0     0   101M      0  0:00:05 --:--:--  0:00:05  101M
 37  537M   37  202M    0     0   105M      0  0:00:05  0:00:01  0:00:04  104M
 51  537M   51  279M    0     0  95.4M      0  0:00:05  0:00:02  0:00:03 95.4M
 72  537M   72  392M    0     0  99.9M      0  0:00:05  0:00:03  0:00:02 99.8M
 93  537M   93  501M    0     0   101M      0  0:00:05  0:00:04  0:00:01  101M
100  537M  100  537M    0     0   102M      0  0:00:05  0:00:05 --:--:--  102M

install for i386

* installing *source* package 'davidTiling' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'davidTiling'
    finding HTML links ... done
    GOHyperG                                html  
REDIRECT:topic	 GOHyperG -> GOHyperG.html [ SUCCESS ]
    davidTiling                             html  
REDIRECT:topic	 data:davidTiling -> davidTiling.html [ FAIL ]
REDIRECT:topic	 davidTiling -> davidTiling.html [ SUCCESS ]
    getAttributeField                       html  
REDIRECT:topic	 getAttributeField -> getAttributeField.html [ SUCCESS ]
    getGO                                   html  
REDIRECT:topic	 getAllGO -> getGO.html [ SUCCESS ]
REDIRECT:file	 getGO.html -> getGO.html [ SUCCESS ]
    gff                                     html  
REDIRECT:topic	 data:gff -> gff.html [ FAIL ]
REDIRECT:topic	 gff -> gff.html [ SUCCESS ]
    probeAnno                               html  
REDIRECT:topic	 data:probeAnno -> probeAnno.html [ FAIL ]
REDIRECT:topic	 probeAnno -> probeAnno.html [ SUCCESS ]
    scatterWithHist                         html  
REDIRECT:topic	 scatterWithHist -> scatterWithHist.html [ SUCCESS ]
    scoreSegments                           html  
REDIRECT:topic	 scoreSegments -> scoreSegments.html [ SUCCESS ]
    showDens                                html  
REDIRECT:topic	 showDens -> showDens.html [ SUCCESS ]
    yeastFeatures                           html  
REDIRECT:topic	 yeastFeatures -> yeastFeatures.html [ SUCCESS ]
** 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 'davidTiling' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'davidTiling' as davidTiling_1.31.0.zip
* DONE (davidTiling)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'davidTiling' successfully unpacked and MD5 sums checked

Tests output


Example timings

davidTiling.Rcheck/examples_i386/davidTiling-Ex.timings

nameusersystemelapsed
davidTiling22.20 0.3122.52
getAttributeField000
gff0.360.000.36
probeAnno4.230.174.40
scatterWithHist0.020.000.02
showDens000
yeastFeatures0.010.000.02

davidTiling.Rcheck/examples_x64/davidTiling-Ex.timings

nameusersystemelapsed
davidTiling18.09 0.5518.64
getAttributeField000
gff0.300.020.32
probeAnno3.500.183.68
scatterWithHist0.020.000.02
showDens000
yeastFeatures0.000.010.01