BioC 3.2: CHECK report for inSilicoDb on oaxaca

Package: inSilicoDb

Version: 2.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings inSilicoDb_2.6.0.tar.gz

StartedAt: 2016-04-13 01:01:14 -0700 (Wed, 13 Apr 2016)

EndedAt: 2016-04-13 01:03:04 -0700 (Wed, 13 Apr 2016)

EllapsedTime: 110.0 seconds

RetCode: 0

Status:  OK

CheckDir: inSilicoDb.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings inSilicoDb_2.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/inSilicoDb.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘inSilicoDb/DESCRIPTION’ ... OK
* this is package ‘inSilicoDb’ version ‘2.6.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘inSilicoDb’ can be installed ... [3s/3s] 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [6s/84s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
getDatasets            1.613  0.709  30.301
getDataset             0.584  0.042  11.853
getDatasetPlatformList 0.407  0.018  12.280
getDatasetList         0.376  0.009  10.790
getDatasetInfo         0.295  0.006   7.336
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/inSilicoDb.Rcheck/00check.log’
for details.

* 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
* DONE (inSilicoDb)

name	user	system	elapsed
getAnnotations	0.133	0.007	1.513
getCurationInfo	0.078	0.003	1.522
getDataset	0.584	0.042	11.853
getDatasetInfo	0.295	0.006	7.336
getDatasetList	0.376	0.009	10.790
getDatasetPlatformList	0.407	0.018	12.280
getDatasets	1.613	0.709	30.301
getDefaultCuration	0.078	0.013	1.314
getPlatformList	0.218	0.004	3.544
getPlatforms	0.142	0.004	2.481