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BioC 3.2: CHECK report for sRAP on windows1.bioconductor.org

This page was generated on 2015-10-27 17:30:52 -0400 (Tue, 27 Oct 2015).

Package 1015/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sRAP 1.10.0
Charles Warden
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/sRAP
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: sRAP
Version: 1.10.0
Command: rm -rf sRAP.buildbin-libdir sRAP.Rcheck && mkdir sRAP.buildbin-libdir sRAP.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sRAP.buildbin-libdir sRAP_1.10.0.tar.gz >sRAP.Rcheck\00install.out 2>&1 && cp sRAP.Rcheck\00install.out sRAP-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=sRAP.buildbin-libdir --install="check:sRAP-install.out" --force-multiarch --no-vignettes --timings sRAP_1.10.0.tar.gz
StartedAt: 2015-10-27 05:53:39 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 05:57:44 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 244.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: sRAP.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf sRAP.buildbin-libdir sRAP.Rcheck && mkdir sRAP.buildbin-libdir sRAP.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sRAP.buildbin-libdir sRAP_1.10.0.tar.gz >sRAP.Rcheck\00install.out 2>&1 && cp sRAP.Rcheck\00install.out sRAP-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=sRAP.buildbin-libdir --install="check:sRAP-install.out" --force-multiarch --no-vignettes --timings sRAP_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/sRAP.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* 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 '1.10.0'
* 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'
* 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' ... [94s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
RNA.bdfunc.signal 54.71   0.06   59.42
RNA.bdfunc.fc      9.54   0.03   14.00
RNA.deg            7.97   0.02   12.51
** running examples for arch 'x64' ... [115s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
RNA.bdfunc.signal 74.46   0.03   78.83
RNA.bdfunc.fc     10.92   0.01   15.13
RNA.deg            9.56   0.07   14.11
* 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-3.2-bioc/meat/sRAP.Rcheck/00check.log'
for details.


sRAP.Rcheck/00install.out:


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_1.10.0.zip
* DONE (sRAP)

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

nameusersystemelapsed
RNA.bdfunc.fc 9.54 0.0314.00
RNA.bdfunc.signal54.71 0.0659.42
RNA.deg 7.97 0.0212.51
RNA.norm1.790.013.38
RNA.prepare.input0.000.000.22
RNA.qc1.950.003.46

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

nameusersystemelapsed
RNA.bdfunc.fc10.92 0.0115.13
RNA.bdfunc.signal74.46 0.0378.83
RNA.deg 9.56 0.0714.11
RNA.norm1.760.003.28
RNA.prepare.input0.020.000.23
RNA.qc1.500.003.09