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CHECK report for XhybCasneuf on riesling1

This page was generated on 2021-01-21 16:01:40 -0500 (Thu, 21 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE XhybCasneuf PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 379/386HostnameOS / ArchINSTALLBUILDCHECK
XhybCasneuf 1.29.0
Tineke Casneuf
Snapshot Date: 2021-01-21 09:00:14 -0500 (Thu, 21 Jan 2021)
URL: https://git.bioconductor.org/packages/XhybCasneuf
Branch: master
Last Commit: e8fd05c
Last Changed Date: 2020-10-27 09:48:27 -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: XhybCasneuf
Version: 1.29.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:XhybCasneuf.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings XhybCasneuf_1.29.0.tar.gz
StartedAt: 2021-01-21 11:52:54 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 11:54:03 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 69.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: XhybCasneuf.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:XhybCasneuf.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings XhybCasneuf_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/XhybCasneuf.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 'XhybCasneuf/DESCRIPTION' ... OK
* this is package 'XhybCasneuf' version '1.29.0'
* 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 'XhybCasneuf' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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:
  'RColorBrewer' 'affy' 'ath1121501cdf' 'grid' 'methods' 'tinesath1cdf'
  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
runSimulation : ourmedianpolish: no visible global function definition
  for 'medpolish'
runSimulation: no visible global function definition for 'hsv'
runSimulation: no visible global function definition for 'rnorm'
runSimulation: no visible global function definition for 'layout'
runSimulation: no visible global function definition for 'par'
runSimulation: no visible global function definition for 'matplot'
runSimulation: no visible binding for global variable
  'generateExprVal.method.mas'
runSimulation: no visible binding for global variable
  'generateExprVal.method.liwong'
runSimulation: no visible global function definition for 'legend'
runSimulation: no visible global function definition for 'cor'
plotExample,XhybExamples: no visible global function definition for
  'par'
plotExample,XhybExamples: no visible global function definition for
  'brewer.pal'
plotExample,XhybExamples: no visible global function definition for
  'matplot'
plotExample,XhybExamples: no visible global function definition for
  'lines'
plotExample,XhybExamples: no visible global function definition for
  'legend'
plotExample,XhybExamples : <anonymous>: no visible global function
  definition for 'cor'
plotExample,XhybExamples: no visible global function definition for
  'abline'
Undefined global functions or variables:
  abline brewer.pal cor generateExprVal.method.liwong
  generateExprVal.method.mas hsv layout legend lines matplot medpolish
  par rnorm
Consider adding
  importFrom("grDevices", "hsv")
  importFrom("graphics", "abline", "layout", "legend", "lines",
             "matplot", "par")
  importFrom("stats", "cor", "medpolish", "rnorm")
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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                         old_size new_size compress
  AffysTissue.noBl.rda      202Kb    154Kb       xz
  AffysTissue.rda           741Kb    491Kb       xz
  AffysTissueMC.rda         886Kb    589Kb       xz
  CustomsTissue.noBl.rda    153Kb    120Kb       xz
  CustomsTissue.rda         552Kb    373Kb       xz
  CustomsTissueMC.rda       688Kb    468Kb       xz
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 1 WARNING, 3 NOTEs
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/XhybCasneuf.Rcheck/00check.log'
for details.



Installation output

XhybCasneuf.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/XhybCasneuf_1.29.0.tar.gz && rm -rf XhybCasneuf.buildbin-libdir && mkdir XhybCasneuf.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=XhybCasneuf.buildbin-libdir XhybCasneuf_1.29.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL XhybCasneuf_1.29.0.zip && rm XhybCasneuf_1.29.0.tar.gz XhybCasneuf_1.29.0.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
  0 3166k    0  1215    0     0   3007      0  0:17:58 --:--:--  0:17:58  3000
100 3166k  100 3166k    0     0  3720k      0 --:--:-- --:--:-- --:--:-- 3716k

install for i386

* installing *source* package 'XhybCasneuf' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Warning messages:
1: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'ath1121501cdf' 
2: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'ath1121501cdf' 
** help
*** installing help indices
  converting help for package 'XhybCasneuf'
    finding HTML links ... done
    AffysTissue                             html  
REDIRECT:topic	 AffysTissue -> AffysTissue.html [ SUCCESS ]
REDIRECT:topic	 AffysTissueMC -> AffysTissue.html [ SUCCESS ]
REDIRECT:topic	 AffysTissue.noBl -> AffysTissue.html [ SUCCESS ]
    CustomsTissue                           html  
REDIRECT:topic	 CustomsTissue -> CustomsTissue.html [ SUCCESS ]
REDIRECT:topic	 CustomsTissueMC -> CustomsTissue.html [ SUCCESS ]
REDIRECT:topic	 CustomsTissue.noBl -> CustomsTissue.html [ SUCCESS ]
    XhybExamples-class                      html  
REDIRECT:topic	 XhybExamples-class -> XhybExamples-class.html [ SUCCESS ]
REDIRECT:topic	 plotExample -> XhybExamples-class.html [ SUCCESS ]
REDIRECT:topic	 plotExample,XhybExamples-method -> XhybExamples-class.html [ SUCCESS ]
    ex1                                     html  
REDIRECT:topic	 ex1 -> ex1.html [ SUCCESS ]
REDIRECT:topic	 ex2 -> ex1.html [ SUCCESS ]
REDIRECT:topic	 ex3 -> ex1.html [ SUCCESS ]
    runSimulation                           html  
REDIRECT:topic	 runSimulation -> runSimulation.html [ SUCCESS ]
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'ath1121501cdf'
Warning: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'ath1121501cdf'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'ath1121501cdf'
Warning: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'ath1121501cdf'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'XhybCasneuf' ...
** testing if installed package can be loaded
Warning: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'ath1121501cdf'
Warning: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'ath1121501cdf'
* MD5 sums
packaged installation of 'XhybCasneuf' as XhybCasneuf_1.29.0.zip
* DONE (XhybCasneuf)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'XhybCasneuf' successfully unpacked and MD5 sums checked

Tests output


Example timings

XhybCasneuf.Rcheck/examples_i386/XhybCasneuf-Ex.timings

nameusersystemelapsed
AffysTissue0.140.000.14
CustomsTissue0.060.000.06
XhybExamples-class0.040.000.06
ex10.000.000.03
runSimulation0.020.000.03

XhybCasneuf.Rcheck/examples_x64/XhybCasneuf-Ex.timings

nameusersystemelapsed
AffysTissue0.120.000.13
CustomsTissue0.050.010.10
XhybExamples-class0.060.000.06
ex10.020.020.05
runSimulation0.030.000.03