BioC 3.4: CHECK report for RImmPort on morelia

Package: RImmPort

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RImmPort_1.2.0.tar.gz

StartedAt: 2017-04-15 07:21:13 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 07:22:24 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 70.8 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_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/RImmPort.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.2.0’
* 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 ‘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	0.673	0.053	2.506
Findings-class	0.468	0.022	0.489
Interventions-class	0.432	0.020	0.451
SpecialPurpose-class	0.526	0.019	0.544
Study-class	0.444	0.024	0.466
TrialDesign-class	0.379	0.016	0.394
buildNewSqliteDb	0.001	0.000	0.001
getAssayDataOfStudies	0.101	0.009	0.109
getDomainCode	0.001	0.000	0.001
getDomainDataOfStudies	0.052	0.004	0.055
getListOfAssayTypes	0	0	0
getListOfDomains	0.001	0.000	0.000
getListOfStudies	0.060	0.006	0.066
getStudiesWithSpecificAssayData	0.046	0.005	0.049
getStudiesWithSpecificDomainData	0.042	0.004	0.047
getStudy	0.421	0.021	0.441
loadSerializedStudyData	0.004	0.000	0.005
mergeDomainAndSupplemental	0.068	0.006	0.074
serialzeStudyData	0.487	0.028	1.170
setImmPortDataSource	0.032	0.004	0.035