BioC experimental data: CHECK report for PREDAsampledata on linux2.bioconductor.org

Package: PREDAsampledata

Version: 0.11.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings PREDAsampledata_0.11.0.tar.gz

StartedAt: 2015-10-24 12:35:04 -0400 (Sat, 24 Oct 2015)

EndedAt: 2015-10-24 12:44:03 -0400 (Sat, 24 Oct 2015)

EllapsedTime: 538.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: PREDAsampledata.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings PREDAsampledata_0.11.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-data-experiment/meat/PREDAsampledata.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PREDAsampledata/DESCRIPTION’ ... OK
* this is package ‘PREDAsampledata’ version ‘0.11.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘PREDA’ ‘Biobase’ ‘affy’ ‘annotate’ ‘gahgu133plus2.db’
  ‘gahgu133plus2cdf’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘PREDAsampledata’ can be installed ... [9s/9s] OK
* checking installed package size ... NOTE
  installed size is 116.5Mb
  sub-directories of 1Mb or more:
    data        95.8Mb
    sampledata  20.7Mb
* checking package 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
* 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:
  ‘Biobase’ ‘PREDA’ ‘affy’ ‘annotate’ ‘gahgu133plus2.db’
  ‘gahgu133plus2cdf’ ‘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 ... 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                                 old_size new_size compress
  AffybatchRCC.RData               61.4Mb   37.4Mb       xz
  ExpressionSetRCC.RData            9.1Mb    7.7Mb       xz
  GEanalysisResults.RData           1.1Mb    596Kb       xz
  SODEGIRCNDataForPREDA.RData      10.6Mb    4.7Mb       xz
  SODEGIRCNanalysisResults.RData    3.1Mb    2.3Mb       xz
  SODEGIRGEDataForPREDA.RData       2.1Mb    1.8Mb       xz
  SODEGIRGEanalysisResults.RData    5.1Mb    4.0Mb       xz
  gaExpressionSetRCC.RData          3.3Mb    2.8Mb       xz
* checking examples ... [9s/9s] OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-data-experiment/meat/PREDAsampledata.Rcheck/00check.log’
for details.

* installing *source* package ‘PREDAsampledata’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (PREDAsampledata)

name	user	system	elapsed
AffybatchRCC	4.178	0.132	4.417
ExpressionSetRCC	0.308	0.004	0.312
GEanalysisResults	0.183	0.004	0.188
SODEGIRCNDataForPREDA	0.596	0.004	0.599
SODEGIRCNanalysisResults	0.290	0.012	0.301
SODEGIRGEDataForPREDA	0.117	0.000	0.117
SODEGIRGEanalysisResults	0.219	0.004	0.224
gaExpressionSetRCC	0.107	0.000	0.109