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BioC 3.0: CHECK report for inSilicoDb on moscato1

This page was generated on 2015-04-10 09:47:11 -0700 (Fri, 10 Apr 2015).

Package 456/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
inSilicoDb 2.2.1
InSilico DB
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/inSilicoDb
Last Changed Rev: 99533 / Revision: 102249
Last Changed Date: 2015-02-17 01:04:51 -0800 (Tue, 17 Feb 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: inSilicoDb
Version: 2.2.1
Command: rm -rf inSilicoDb.buildbin-libdir inSilicoDb.Rcheck && mkdir inSilicoDb.buildbin-libdir inSilicoDb.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=inSilicoDb.buildbin-libdir inSilicoDb_2.2.1.tar.gz >inSilicoDb.Rcheck\00install.out 2>&1 && cp inSilicoDb.Rcheck\00install.out inSilicoDb-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=inSilicoDb.buildbin-libdir --install="check:inSilicoDb-install.out" --force-multiarch --no-vignettes --timings inSilicoDb_2.2.1.tar.gz
StartedAt: 2015-04-10 02:22:25 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:25:58 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 213.1 seconds
RetCode: 0
Status:  OK  
CheckDir: inSilicoDb.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf inSilicoDb.buildbin-libdir inSilicoDb.Rcheck && mkdir inSilicoDb.buildbin-libdir inSilicoDb.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=inSilicoDb.buildbin-libdir inSilicoDb_2.2.1.tar.gz >inSilicoDb.Rcheck\00install.out 2>&1 && cp inSilicoDb.Rcheck\00install.out inSilicoDb-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=inSilicoDb.buildbin-libdir --install="check:inSilicoDb-install.out" --force-multiarch --no-vignettes --timings inSilicoDb_2.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/inSilicoDb.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'inSilicoDb/DESCRIPTION' ... OK
* this is package 'inSilicoDb' version '2.2.1'
* 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 whether package 'inSilicoDb' 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
* 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:
  'Biobase' 'RCurl' 'rjson'
  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
checkBinary: no visible global function definition for 'fromJSON'
getInSilicoBinary: no visible global function definition for
  'basicHeaderGatherer'
getInSilicoBinary: no visible global function definition for
  'getCurlHandle'
getInSilicoBinary: no visible global function definition for
  'getBinaryURL'
getInSilicoJSON: no visible global function definition for
  'basicHeaderGatherer'
getInSilicoJSON: no visible global function definition for
  'getCurlHandle'
getInSilicoJSON: no visible global function definition for 'postForm'
getInSilicoJSON: no visible global function definition for 'fromJSON'
writeInSilicoCache: no visible binding for global variable 'cache'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [83s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
getDatasets            2.70   0.31   24.34
getDataset             0.69   0.02   14.15
getDatasetList         0.36   0.02   10.85
getDatasetPlatformList 0.34   0.00   12.25
getDatasetInfo         0.31   0.00    7.46
** running examples for arch 'x64' ... [84s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
getDatasets            3.31   0.34   25.43
getDataset             0.80   0.02   14.36
getDatasetPlatformList 0.44   0.00   12.44
getDatasetList         0.37   0.00   10.78
getDatasetInfo         0.28   0.03    7.38
* 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

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/inSilicoDb.Rcheck/00check.log'
for details.

inSilicoDb.Rcheck/00install.out:


install for i386

* installing *source* package 'inSilicoDb' ...
** R
** 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 'inSilicoDb' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'inSilicoDb' as inSilicoDb_2.2.1.zip
* DONE (inSilicoDb)

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

nameusersystemelapsed
getAnnotations0.300.011.89
getCurationInfo0.070.001.51
getDataset 0.69 0.0214.15
getDatasetInfo0.310.007.46
getDatasetList 0.36 0.0210.85
getDatasetPlatformList 0.34 0.0012.25
getDatasets 2.70 0.3124.34
getDefaultCuration0.070.001.49
getPlatformList0.160.004.37
getPlatforms0.090.003.05

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

nameusersystemelapsed
getAnnotations0.280.061.78
getCurationInfo0.080.001.52
getDataset 0.80 0.0214.36
getDatasetInfo0.280.037.38
getDatasetList 0.37 0.0010.78
getDatasetPlatformList 0.44 0.0012.44
getDatasets 3.31 0.3425.43
getDefaultCuration0.090.021.56
getPlatformList0.230.004.43
getPlatforms0.170.033.03