Package: HPAanalyze

Version: 1.1.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HPAanalyze.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HPAanalyze_1.1.1.tar.gz

StartedAt: 2019-04-09 02:44:43 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:46:21 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 97.9 seconds

RetCode: 0

Status:  OK

CheckDir: HPAanalyze.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HPAanalyze.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HPAanalyze_1.1.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/HPAanalyze.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HPAanalyze/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HPAanalyze’ version ‘1.1.1’
* package encoding: UTF-8
* 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 ‘HPAanalyze’ 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 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
hpaDownload: no visible binding for global variable ‘hpaNormalTissue’
hpaDownload: no visible binding for global variable ‘hpaCancer’
hpaDownload: no visible binding for global variable ‘Total.patients’
hpaDownload: no visible binding for global variable ‘Level’
hpaDownload: no visible binding for global variable ‘Count.patients’
hpaDownload: no visible binding for global variable ‘hpaSubcellularLoc’
hpaDownload: no visible binding for global variable ‘rnaGeneTissue’
hpaDownload: no visible binding for global variable ‘rnaGeneCellLine’
hpaSubset: no visible binding for global variable ‘gene’
hpaSubset: no visible binding for global variable ‘tissue’
hpaSubset: no visible binding for global variable ‘cell_type’
hpaSubset: no visible binding for global variable ‘cancer’
hpaSubset: no visible binding for global variable ‘cell_line’
hpaVisPatho: no visible binding for global variable ‘gene’
hpaVisPatho: no visible binding for global variable ‘cancer’
hpaVisPatho: no visible binding for global variable ‘high’
hpaVisPatho: no visible binding for global variable ‘medium’
hpaVisPatho: no visible binding for global variable ‘low’
hpaVisPatho: no visible binding for global variable ‘not_detected’
hpaVisPatho: no visible binding for global variable ‘patient_count’
hpaVisPatho: no visible binding for global variable ‘level’
hpaVisSubcell: no visible binding for global variable ‘gene’
hpaVisSubcell: no visible binding for global variable ‘go_id’
hpaVisSubcell: no visible binding for global variable ‘sub_location’
hpaVisTissue: no visible binding for global variable ‘gene’
hpaVisTissue: no visible binding for global variable ‘tissue’
hpaVisTissue: no visible binding for global variable ‘cell_type’
hpaVisTissue: no visible binding for global variable ‘level’
hpaVisTissue: no visible binding for global variable ‘tissue_cell’
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
  ‘patientId’
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
  ‘age’
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
  ‘sex’
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
  ‘staining’
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
  ‘intensity’
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
  ‘quantity’
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
  ‘imageUrl’
hpaXmlTissueExprSum: no visible binding for global variable ‘tissue’
hpaXmlTissueExprSum: no visible binding for global variable ‘imageUrl’
named_vector_list_to_tibble: no visible binding for global variable
  ‘index’
named_vector_list_to_tibble: no visible binding for global variable
  ‘value’
Undefined global functions or variables:
  Count.patients Level Total.patients age cancer cell_line cell_type
  gene go_id high hpaCancer hpaNormalTissue hpaSubcellularLoc imageUrl
  index intensity level low medium not_detected patientId patient_count
  quantity rnaGeneCellLine rnaGeneTissue sex staining sub_location
  tissue tissue_cell value
* 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 ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
hpaVisPatho 4.528  0.368   5.563
* 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-3.9-bioc/meat/HPAanalyze.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL HPAanalyze
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘HPAanalyze’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HPAanalyze)

name	user	system	elapsed
hpaDownload	1.930	0.408	2.502
hpaExport	0.881	0.145	1.106
hpaListParam	0.175	0.064	0.258
hpaVis	2.184	0.131	2.522
hpaVisPatho	4.528	0.368	5.563
hpaVisSubcell	2.334	0.174	2.693
hpaVisTissue	2.407	0.181	2.700
hpaXml	0.476	0.031	1.289
hpaXmlAntibody	0	0	0
hpaXmlGet	0.000	0.000	0.001
hpaXmlProtClass	0.001	0.001	0.001
hpaXmlTissueExpr	0.000	0.001	0.000
hpaXmlTissueExprSum	0.001	0.000	0.000
hpa_downloaded_histology_v18	1.643	0.314	2.192