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CHECK report for HPAanalyze on malbec1

This page was generated on 2019-04-16 11:53:44 -0400 (Tue, 16 Apr 2019).

Package 733/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HPAanalyze 1.0.0
Anh Nhat Tran
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/HPAanalyze
Branch: RELEASE_3_8
Last Commit: 2d7785a
Last Changed Date: 2018-10-30 11:42:10 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: HPAanalyze
Version: 1.0.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:HPAanalyze.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings HPAanalyze_1.0.0.tar.gz
StartedAt: 2019-04-16 00:40:23 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:41:53 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 89.4 seconds
RetCode: 0
Status:  OK 
CheckDir: HPAanalyze.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:HPAanalyze.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings HPAanalyze_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/HPAanalyze.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 ‘1.0.0’
* 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 ‘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
hpaXmlTissueExpr 7.728      0   8.407
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/HPAanalyze.Rcheck/00check.log’
for details.



Installation output

HPAanalyze.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL HPAanalyze
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘HPAanalyze’ ...
** 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
* DONE (HPAanalyze)

Tests output


Example timings

HPAanalyze.Rcheck/HPAanalyze-Ex.timings

nameusersystemelapsed
hpaDownload1.9640.1402.271
hpaExport2.3600.1323.700
hpaListParam0.1400.0480.184
hpaVis1.5000.0361.554
hpaVisPatho3.8800.1604.231
hpaVisSubcell2.2640.1082.472
hpaVisTissue2.2760.1722.498
hpaXml0.4880.0121.387
hpaXmlAntibody0.0440.0000.163
hpaXmlGet0.0120.0000.131
hpaXmlProtClass0.0720.0000.196
hpaXmlTissueExpr7.7280.0008.407
hpaXmlTissueExprSum0.1280.0200.998
hpa_downloaded_histology_v181.9120.1322.050