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CHECK report for MAQCsubset on riesling1

This page was generated on 2021-01-11 15:59:31 -0500 (Mon, 11 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE MAQCsubset PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 209/385HostnameOS / ArchINSTALLBUILDCHECK
MAQCsubset 1.29.0
VJ Carey
Snapshot Date: 2021-01-11 09:00:09 -0500 (Mon, 11 Jan 2021)
URL: https://git.bioconductor.org/packages/MAQCsubset
Branch: master
Last Commit: 9b3813f
Last Changed Date: 2020-10-27 09:46:43 -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: MAQCsubset
Version: 1.29.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MAQCsubset.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MAQCsubset_1.29.0.tar.gz
StartedAt: 2021-01-11 11:32:10 -0500 (Mon, 11 Jan 2021)
EndedAt: 2021-01-11 11:37:12 -0500 (Mon, 11 Jan 2021)
EllapsedTime: 302.0 seconds
RetCode: 0
Status:  OK  
CheckDir: MAQCsubset.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:MAQCsubset.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MAQCsubset_1.29.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/MAQCsubset.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 'MAQCsubset/DESCRIPTION' ... OK
* this is package 'MAQCsubset' 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 'MAQCsubset' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 64.5Mb
  sub-directories of 1Mb or more:
    data  64.1Mb
* 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 'genefilter' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Biobase' 'affy' 'lumi' '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
proboscis: no visible global function definition for 'rowttests'
proboscis: no visible global function definition for 'exprs'
Undefined global functions or variables:
  exprs rowttests
* 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
** 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: 3 NOTEs
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/MAQCsubset.Rcheck/00check.log'
for details.



Installation output

MAQCsubset.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/MAQCsubset_1.29.0.tar.gz && rm -rf MAQCsubset.buildbin-libdir && mkdir MAQCsubset.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MAQCsubset.buildbin-libdir MAQCsubset_1.29.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL MAQCsubset_1.29.0.zip && rm MAQCsubset_1.29.0.tar.gz MAQCsubset_1.29.0.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
 63 64.6M   63 40.7M    0     0  67.7M      0 --:--:-- --:--:-- --:--:-- 67.6M
100 64.6M  100 64.6M    0     0  78.4M      0 --:--:-- --:--:-- --:--:-- 78.4M

install for i386

* installing *source* package 'MAQCsubset' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
** help
*** installing help indices
  converting help for package 'MAQCsubset'
    finding HTML links ... done
    MAQCsubset                              html  
REDIRECT:topic	 afxsubRMAES -> MAQCsubset.html [ SUCCESS ]
REDIRECT:topic	 afxsubRMA -> MAQCsubset.html [ SUCCESS ]
REDIRECT:topic	 ilmMAQCsubR -> MAQCsubset.html [ SUCCESS ]
REDIRECT:topic	 afxsub -> MAQCsubset.html [ SUCCESS ]
REDIRECT:topic	 MAQCsubset -> MAQCsubset.html [ SUCCESS ]
    gehMAQCsubDef                           html  
REDIRECT:topic	 gehMAQCsubDef -> gehMAQCsubDef.html [ SUCCESS ]
REDIRECT:topic	 gehSubRaw -> gehMAQCsubDef.html [ SUCCESS ]
    gnfCerebHi                              html  
REDIRECT:topic	 gnfCerebHi -> gnfCerebHi.html [ SUCCESS ]
REDIRECT:topic	 gnfCerebLow -> gnfCerebHi.html [ SUCCESS ]
    proboStruct-class                       html  
REDIRECT:topic	 proboStruct-class -> proboStruct-class.html [ SUCCESS ]
REDIRECT:topic	 lines,proboStruct-method -> proboStruct-class.html [ SUCCESS ]
REDIRECT:topic	 plot,proboStruct-method -> proboStruct-class.html [ SUCCESS ]
REDIRECT:topic	 plot,proboStruct,ANY-method -> proboStruct-class.html [ SUCCESS ]
REDIRECT:topic	 show,proboStruct-method -> proboStruct-class.html [ SUCCESS ]
    proboscis                               html  
REDIRECT:topic	 proboscis -> proboscis.html [ SUCCESS ]
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
** testing if installed package can be loaded from final location
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'MAQCsubset' ...
** testing if installed package can be loaded
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
* MD5 sums
packaged installation of 'MAQCsubset' as MAQCsubset_1.29.0.zip
* DONE (MAQCsubset)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'MAQCsubset' successfully unpacked and MD5 sums checked

Tests output


Example timings

MAQCsubset.Rcheck/examples_i386/MAQCsubset-Ex.timings

nameusersystemelapsed
MAQCsubset0.780.000.78
gehMAQCsubDef0.320.010.33
gnfCerebHi0.010.000.02
proboStruct-class1.500.031.53
proboscis1.420.021.44

MAQCsubset.Rcheck/examples_x64/MAQCsubset-Ex.timings

nameusersystemelapsed
MAQCsubset0.590.040.64
gehMAQCsubDef0.250.020.26
gnfCerebHi000
proboStruct-class1.450.011.46
proboscis0.710.030.75