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CHECK report for ccTutorial on riesling1

This page was generated on 2021-01-21 16:01:25 -0500 (Thu, 21 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE ccTutorial PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 48/386HostnameOS / ArchINSTALLBUILDCHECK
ccTutorial 1.29.0
Joern Toedling
Snapshot Date: 2021-01-21 09:00:14 -0500 (Thu, 21 Jan 2021)
URL: https://git.bioconductor.org/packages/ccTutorial
Branch: master
Last Commit: edfce2d
Last Changed Date: 2020-10-27 09:49:38 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ]

Summary

Package: ccTutorial
Version: 1.29.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ccTutorial.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ccTutorial_1.29.0.tar.gz
StartedAt: 2021-01-21 11:14:09 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 11:18:06 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 237.2 seconds
RetCode: 0
Status:  OK  
CheckDir: ccTutorial.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ccTutorial.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ccTutorial_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/ccTutorial.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 'ccTutorial/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ccTutorial' 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 'ccTutorial' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 785.0Mb
  sub-directories of 1Mb or more:
    PairData       448.5Mb
    data            77.8Mb
    exonerateData  202.3Mb
    expression      49.9Mb
    vignettes        6.3Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'Biobase'
A package should be listed in only one of these fields.
* 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:
  'Ringo' 'affy' 'topGO'
  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 ... OK
* 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 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
Examples with CPU (user + system) or elapsed time > 5s
  user system elapsed
X 9.85   0.11    9.96
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
  user system elapsed
X 8.56   0.11    8.68
* 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
  'D:/biocbuild/bbs-3.13-data-experiment/meat/ccTutorial.Rcheck/00check.log'
for details.



Installation output

ccTutorial.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/ccTutorial_1.29.0.tar.gz && rm -rf ccTutorial.buildbin-libdir && mkdir ccTutorial.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ccTutorial.buildbin-libdir ccTutorial_1.29.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ccTutorial_1.29.0.zip && rm ccTutorial_1.29.0.tar.gz ccTutorial_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  277M    0  1211    0     0   1623      0 49:51:35 --:--:-- 49:51:35  1623
 11  277M   11 31.2M    0     0  23.7M      0  0:00:11  0:00:01  0:00:10 23.7M
 38  277M   38  107M    0     0  46.9M      0  0:00:05  0:00:02  0:00:03 46.9M
 62  277M   62  173M    0     0  52.6M      0  0:00:05  0:00:03  0:00:02 52.6M
 84  277M   84  233M    0     0  54.4M      0  0:00:05  0:00:04  0:00:01 54.4M
100  277M  100  277M    0     0  54.2M      0  0:00:05  0:00:05 --:--:-- 63.5M

install for i386

* installing *source* package 'ccTutorial' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
  converting help for package 'ccTutorial'
    finding HTML links ... done
    X                                       html  
REDIRECT:topic	 X -> X.html [ SUCCESS ]
    arrayGenesToProbeSets                   html  
REDIRECT:topic	 arrayGenesToProbeSets -> arrayGenesToProbeSets.html [ SUCCESS ]
    barreraExpressionX                      html  
REDIRECT:topic	 barreraExpressionX -> barreraExpressionX.html [ SUCCESS ]
    ccTutorial-package                      html  
REDIRECT:topic	 ccTutorial-package -> ccTutorial-package.html [ SUCCESS ]
REDIRECT:topic	 ccTutorial -> ccTutorial-package.html [ SUCCESS ]
    chersX                                  html  
REDIRECT:topic	 chersX -> chersX.html [ SUCCESS ]
    mm9g2p                                  html  
REDIRECT:topic	 mm9.g2p -> mm9g2p.html [ SUCCESS ]
REDIRECT:file	 mm9g2p.html -> mm9g2p.html [ SUCCESS ]
    mm9gene2GO                              html  
REDIRECT:topic	 mm9.gene2GO -> mm9gene2GO.html [ SUCCESS ]
REDIRECT:file	 mm9gene2GO.html -> mm9gene2GO.html [ SUCCESS ]
    mm9genes                                html  
REDIRECT:topic	 mm9genes -> mm9genes.html [ SUCCESS ]
    probeAnno                               html  
REDIRECT:topic	 probeAnno -> probeAnno.html [ SUCCESS ]
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package can be loaded from final location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'ccTutorial' ...
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* MD5 sums
packaged installation of 'ccTutorial' as ccTutorial_1.29.0.zip
* DONE (ccTutorial)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'ccTutorial' successfully unpacked and MD5 sums checked

Tests output


Example timings

ccTutorial.Rcheck/examples_i386/ccTutorial-Ex.timings

nameusersystemelapsed
X9.850.119.96
arrayGenesToProbeSets0.030.000.03
barreraExpressionX0.070.000.08
chersX0.50.00.5
mm9g2p0.680.000.67
mm9gene2GO0.010.000.01
mm9genes0.060.000.06
probeAnno000

ccTutorial.Rcheck/examples_x64/ccTutorial-Ex.timings

nameusersystemelapsed
X8.560.118.68
arrayGenesToProbeSets0.550.040.59
barreraExpressionX0.070.000.07
chersX0.340.020.36
mm9g2p0.470.010.48
mm9gene2GO0.030.000.03
mm9genes0.060.000.06
probeAnno000