BioC 3.3: CHECK report for sRAP on windows2.bioconductor.org

Package: sRAP

Version: 1.11.0

Command: rm -rf sRAP.buildbin-libdir sRAP.Rcheck && mkdir sRAP.buildbin-libdir sRAP.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sRAP.buildbin-libdir sRAP_1.11.0.tar.gz >sRAP.Rcheck\00install.out 2>&1 && cp sRAP.Rcheck\00install.out sRAP-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=sRAP.buildbin-libdir --install="check:sRAP-install.out" --force-multiarch --no-vignettes --timings sRAP_1.11.0.tar.gz

StartedAt: 2015-10-27 06:19:15 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:23:22 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 247.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: sRAP.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf sRAP.buildbin-libdir sRAP.Rcheck && mkdir sRAP.buildbin-libdir sRAP.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sRAP.buildbin-libdir sRAP_1.11.0.tar.gz >sRAP.Rcheck\00install.out 2>&1 && cp sRAP.Rcheck\00install.out sRAP-install.out  && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=sRAP.buildbin-libdir --install="check:sRAP-install.out" --force-multiarch --no-vignettes --timings sRAP_1.11.0.tar.gz
###
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/sRAP.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'sRAP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sRAP' version '1.11.0'
* 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 'sRAP' can be installed ... OK
* checking installed package size ... OK
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
RNA.bdfunc.fc: no visible binding for global variable
  'bdfunc.enrichment.human'
RNA.bdfunc.fc: no visible binding for global variable
  'bdfunc.enrichment.mouse'
RNA.bdfunc.signal: no visible binding for global variable
  'bdfunc.enrichment.human'
RNA.bdfunc.signal: no visible binding for global variable
  'bdfunc.enrichment.mouse'
Undefined global functions or variables:
  bdfunc.enrichment.human bdfunc.enrichment.mouse
* 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
  bdfunc.enrichment.human.rda    1.3Mb    951Kb    bzip2
  bdfunc.enrichment.mouse.rda     31Kb     26Kb       xz
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... NOTE
The following files look like leftovers/mistakes:
  'sRAP.bbl'
Please remove them from your package.
* checking examples ...
** running examples for arch 'i386' ... [96s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
RNA.bdfunc.signal 56.00   0.05   60.61
RNA.bdfunc.fc      9.17   0.02   14.75
RNA.deg            8.48   0.01   13.33
** running examples for arch 'x64' ... [118s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
RNA.bdfunc.signal 75.48   0.04   80.09
RNA.bdfunc.fc     10.82   0.00   15.25
RNA.deg            9.16   0.02   13.66
* 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: 1 WARNING, 2 NOTEs
See
  'c:/biocbld/bbs-3.3-bioc/meat/sRAP.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'sRAP' ...
** 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 'sRAP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sRAP' as sRAP_1.11.0.zip
* DONE (sRAP)

name	user	system	elapsed
RNA.bdfunc.fc	9.17	0.02	14.75
RNA.bdfunc.signal	56.00	0.05	60.61
RNA.deg	8.48	0.01	13.33
RNA.norm	1.85	0.00	3.34
RNA.prepare.input	0.00	0.00	0.24
RNA.qc	1.86	0.02	3.36

name	user	system	elapsed
RNA.bdfunc.fc	10.82	0.00	15.25
RNA.bdfunc.signal	75.48	0.04	80.09
RNA.deg	9.16	0.02	13.66
RNA.norm	1.65	0.00	3.92
RNA.prepare.input	0.02	0.00	0.24
RNA.qc	1.64	0.00	3.73