BioC 3.4: CHECK report for RImmPort on morelia

Package: RImmPort

Version: 1.1.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RImmPort_1.1.2.tar.gz

StartedAt: 2016-09-20 12:22:16 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 12:22:55 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 39.2 seconds

RetCode: 0

Status:  OK

CheckDir: RImmPort.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 RImmPort_1.1.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/RImmPort.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RImmPort/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RImmPort’ version ‘1.1.2’
* 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 ‘RImmPort’ 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
* 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
getCellularQuantification: no visible binding for global variable
  ‘experiment_sample_accession’
getCellularQuantification: no visible binding for global variable
  ‘control_files_names’
getCellularQuantification: no visible binding for global variable
  ‘ZBREFIDP’
getGeneticsFindings: no visible binding for global variable
  ‘experiment_sample_accession’
getNucleicAcidQuantification: no visible binding for global variable
  ‘experiment_sample_accession’
getProteinQuantification: no visible binding for global variable
  ‘experiment_sample_accession’
getTiterAssayResults: no visible binding for global variable
  ‘experiment_sample_accession’
Undefined global functions or variables:
  ZBREFIDP control_files_names experiment_sample_accession
* 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 ... OK
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/RImmPort.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
Events-class	0.460	0.035	0.684
Findings-class	0.309	0.016	0.324
Interventions-class	0.300	0.013	0.313
SpecialPurpose-class	0.307	0.013	0.320
Study-class	0.370	0.017	0.388
TrialDesign-class	0.427	0.018	0.446
buildNewSqliteDb	0.001	0.001	0.001
getAssayDataOfStudies	0.139	0.008	0.147
getDomainCode	0.001	0.000	0.001
getDomainDataOfStudies	0.033	0.003	0.037
getListOfAssayTypes	0.001	0.000	0.000
getListOfDomains	0	0	0
getListOfStudies	0.030	0.003	0.033
getStudiesWithSpecificAssayData	0.038	0.004	0.042
getStudiesWithSpecificDomainData	0.038	0.003	0.043
getStudy	0.330	0.017	0.348
loadSerializedStudyData	0.004	0.000	0.004
mergeDomainAndSupplemental	0.073	0.007	0.079
serialzeStudyData	0.508	0.036	0.544
setImmPortDataSource	0.032	0.003	0.035