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BioC experimental data: CHECK report for dyebiasexamples on moscato1

This page was generated on 2014-04-04 17:29:00 -0700 (Fri, 04 Apr 2014).

Package 49/181HostnameOS / ArchBUILDCHECKBUILD BIN
dyebiasexamples 1.0.12
Philip Lijnzaad
Snapshot Date: 2014-04-04 06:15:32 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_13/experiment/pkgs/dyebiasexamples
Last Changed Rev: 2557 / Revision: 2768
Last Changed Date: 2013-11-01 13:36:05 -0700 (Fri, 01 Nov 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ WARNINGS ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  WARNINGS  OK 

Summary

Package: dyebiasexamples
Version: 1.0.12
Command: rm -rf dyebiasexamples.buildbin-libdir && mkdir dyebiasexamples.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=dyebiasexamples.buildbin-libdir dyebiasexamples_1.0.12.tar.gz >dyebiasexamples-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=dyebiasexamples.buildbin-libdir --install="check:dyebiasexamples-install.out" --force-multiarch --no-vignettes --timings dyebiasexamples_1.0.12.tar.gz && mv dyebiasexamples.buildbin-libdir/* dyebiasexamples.Rcheck/ && rmdir dyebiasexamples.buildbin-libdir
StartedAt: 2014-04-04 11:30:17 -0700 (Fri, 04 Apr 2014)
EndedAt: 2014-04-04 11:33:07 -0700 (Fri, 04 Apr 2014)
EllapsedTime: 169.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: dyebiasexamples.Rcheck
Warnings: 4

Command output

* using log directory 'D:/biocbld/bbs-2.13-data-experiment/meat/dyebiasexamples.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'dyebiasexamples/DESCRIPTION' ... OK
* this is package 'dyebiasexamples' version '1.0.12'
* 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 'dyebiasexamples' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 40.2Mb
  sub-directories of 1Mb or more:
    data        5.3Mb
    extradata  34.8Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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:
  'GEOquery' 'marray'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of 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 ... OK
* checking Rd files ... WARNING
checkRd: (3) dyebias.geo2marray.Rd:10-17: \synopsis will be removed in R 3.1.0
checkRd: (3) dyebias.umcu.proper.estimators.Rd:11-13: \synopsis will be removed in R 3.1.0
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'dyebias.geo2marray':
dyebias.geo2marray
  Code: function(gse, slide.ids = NULL, type = "norm", gene.selector =
                 function(table) { T}, reporterid.name, cy3.name,
                 cy5.name, R.name = NULL, G.name = NULL, M.name = NULL,
                 A.name = NULL, Rf.name = NULL, Gf.name = NULL, Rb.name
                 = NULL, Gb.name = NULL)
  Docs: function(gse, slide.ids = NULL, type = "norm", gene.selector =
                 function(table) { TRUE}, reporterid.name, cy3.name,
                 cy5.name, R.name = NULL, G.name = NULL, M.name = NULL,
                 A.name = NULL, Rf.name = NULL, Gf.name = NULL, Rb.name
                 = NULL, Gb.name = NULL)
  Mismatches in argument default values:
    Name: 'gene.selector'
    Code: function(table) {
          T
      }
    Docs: function(table) {
          TRUE
      }

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... WARNING
Files not of a type allowed in a 'data' directory:
  'README'
Please use e.g. 'inst/extdata' for non-R data files
* 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
  data.norm.rda    2.1Mb    1.5Mb       xz
  data.raw.rda     3.2Mb    2.2Mb       xz
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [6s] OK
** running examples for arch 'x64' ... [7s] OK
* checking PDF version of manual ... OK

WARNING: There were 4 warnings.
NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-2.13-data-experiment/meat/dyebiasexamples.Rcheck/00check.log'
for details.

dyebiasexamples.Rcheck/00install.out:


install for i386

* installing *source* package 'dyebiasexamples' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'dyebiasexamples' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'dyebiasexamples' as dyebiasexamples_1.0.12.zip
* DONE (dyebiasexamples)

dyebiasexamples.Rcheck/examples_i386/dyebiasexamples-Ex.timings:

nameusersystemelapsed
data.raw0.920.000.92
dyebias.geo2marray000
dyebias.umcu.proper.estimators2.490.022.57

dyebiasexamples.Rcheck/examples_x64/dyebiasexamples-Ex.timings:

nameusersystemelapsed
data.raw1.080.021.09
dyebias.geo2marray0.10.00.1
dyebias.umcu.proper.estimators3.370.033.40