Back to the "Multiple platform build/check report"

BioC experimental data: CHECK report for dyebiasexamples on perceval

This page was generated on 2015-04-08 17:41:25 -0700 (Wed, 08 Apr 2015).

Package 65/219HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dyebiasexamples 1.3.1
Philip Lijnzaad
Snapshot Date: 2015-04-08 06:15:26 -0700 (Wed, 08 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_0/experiment/pkgs/dyebiasexamples
Last Changed Rev: 3075 / Revision: 3266
Last Changed Date: 2014-10-13 14:52:40 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ WARNINGS ] OK 

Summary

Package: dyebiasexamples
Version: 1.3.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch dyebiasexamples_1.3.1.tar.gz
StartedAt: 2015-04-08 09:31:40 -0700 (Wed, 08 Apr 2015)
EndedAt: 2015-04-08 09:35:18 -0700 (Wed, 08 Apr 2015)
EllapsedTime: 217.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: dyebiasexamples.Rcheck
Warnings: 4

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch dyebiasexamples_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-data-experiment/meat/dyebiasexamples.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dyebiasexamples/DESCRIPTION’ ... OK
* this is package ‘dyebiasexamples’ version ‘1.3.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘dyebiasexamples’ can be installed ... [7s/18s] WARNING
Found the following significant warnings:
  Warning: /Users/biocbuild/bbs-3.0-data-experiment/meat/dyebiasexamples.Rcheck/00_pkg_src/dyebiasexamples/man/dyebias.geo2marray.Rd:10-17: Section \synopsis is unrecognized and will be dropped
  Warning: /Users/biocbuild/bbs-3.0-data-experiment/meat/dyebiasexamples.Rcheck/00_pkg_src/dyebiasexamples/man/dyebias.umcu.proper.estimators.Rd:11-13: Section \synopsis is unrecognized and will be dropped
See ‘/Users/biocbuild/bbs-3.0-data-experiment/meat/dyebiasexamples.Rcheck/00install.out’ for details.
* 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
* 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.extract.measurements: no visible global function definition for
  ‘GSMList’
.extract.measurements : <anonymous>: no visible global function
  definition for ‘Table’
.extract.meta: no visible global function definition for ‘GSMList’
.extract.meta : <anonymous>: no visible global function definition for
  ‘Meta’
.gsmlist2targetinfo: no visible global function definition for
  ‘GSMList’
.gsmlist2targetinfo: no visible global function definition for ‘Meta’
.have.umcu.version: no visible global function definition for
  ‘package.version’
dyebias.geo2marray: no visible global function definition for ‘GSMList’
dyebias.geo2marray : <anonymous>: no visible global function definition
  for ‘Meta’
dyebias.geo2marray: no visible global function definition for ‘Meta’
dyebias.geo2marray: no visible global function definition for ‘GPLList’
dyebias.geo2marray: no visible global function definition for ‘Table’
dyebias.geo2marray: no visible global function definition for
  ‘read.marrayLayout’
dyebias.geo2marray: no visible global function definition for
  ‘Accession’
dyebias.geo2marray: no visible global function definition for
  ‘maControls<-’
dyebias.geo2marray: no visible global function definition for
  ‘maLabels<-’
dyebias.geo2marray: no visible global function definition for
  ‘maInfo<-’
dyebias.geo2marray: no visible global function definition for ‘maRf’
dyebias.geo2marray: no visible global function definition for ‘maRb<-’
dyebias.geo2marray: no visible global function definition for ‘maGb<-’
dyebias.geo2marray: no visible global function definition for
  ‘maTargets<-’
dyebias.geo2marray: no visible global function definition for
  ‘maLayout<-’
dyebias.geo2marray: no visible global function definition for
  ‘maGnames<-’
* checking Rd files ... WARNING
prepare_Rd: dyebias.geo2marray.Rd:10-17: Section \synopsis is unrecognized and will be dropped
prepare_Rd: dyebias.umcu.proper.estimators.Rd:11-13: Section \synopsis is unrecognized and will be dropped
* 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 ... 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 ... [10s/17s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
dyebias.umcu.proper.estimators 4.022  0.074   6.842
* checking PDF version of manual ... OK
* DONE

WARNING: There were 4 warnings.
NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-3.0-data-experiment/meat/dyebiasexamples.Rcheck/00check.log’
for details.

dyebiasexamples.Rcheck/00install.out:

* installing *source* package ‘dyebiasexamples’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
Warning: /Users/biocbuild/bbs-3.0-data-experiment/meat/dyebiasexamples.Rcheck/00_pkg_src/dyebiasexamples/man/dyebias.geo2marray.Rd:10-17: Section \synopsis is unrecognized and will be dropped
Warning: /Users/biocbuild/bbs-3.0-data-experiment/meat/dyebiasexamples.Rcheck/00_pkg_src/dyebiasexamples/man/dyebias.umcu.proper.estimators.Rd:11-13: Section \synopsis is unrecognized and will be dropped
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (dyebiasexamples)

dyebiasexamples.Rcheck/dyebiasexamples-Ex.timings:

nameusersystemelapsed
data.raw1.6920.0462.578
dyebias.geo2marray0.0010.0000.002
dyebias.umcu.proper.estimators4.0220.0746.842