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CHECK report for HPAanalyze on malbec1

This page was generated on 2020-04-15 12:14:38 -0400 (Wed, 15 Apr 2020).

Package 799/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HPAanalyze 1.4.3
Anh Nhat Tran
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/HPAanalyze
Branch: RELEASE_3_10
Last Commit: 6c129f5
Last Changed Date: 2020-01-17 14:17:38 -0400 (Fri, 17 Jan 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  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: 1.4.3
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:HPAanalyze.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings HPAanalyze_1.4.3.tar.gz
StartedAt: 2020-04-15 05:58:21 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 06:00:03 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 101.4 seconds
RetCode: 0
Status:  OK 
CheckDir: HPAanalyze.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:HPAanalyze.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings HPAanalyze_1.4.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/HPAanalyze.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.4.3’
* 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 ... NOTE
Found the following non-portable file paths:
  HPAanalyze/docs/articles/a_HPAanalyze_quick_start_files/elevate-section-attrs-2.0/elevate-section-attrs.js
  HPAanalyze/docs/articles/b_HPAanalyze_indepth_files/elevate-section-attrs-2.0/elevate-section-attrs.js
  HPAanalyze/docs/articles/c_HPAanalyze_case_query_files/elevate-section-attrs-2.0/elevate-section-attrs.js
  HPAanalyze/docs/articles/d_HPAanalyze_case_offline_xml_files/elevate-section-attrs-2.0/elevate-section-attrs.js
  HPAanalyze/docs/articles/e_HPAanalyze_case_json_files/elevate-section-attrs-2.0/elevate-section-attrs.js
  HPAanalyze/docs/articles/f_HPAanalyze_case_images_files/elevate-section-attrs-2.0/elevate-section-attrs.js
  HPAanalyze/docs/articles/z_HPAanalyze_paper_figures_files/elevate-section-attrs-2.0/elevate-section-attrs.js

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HPAanalyze’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
* 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
hpaListParam: no visible binding for global variable
  ‘hpa_histology_data’
hpaSubset: no visible binding for global variable ‘hpa_histology_data’
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’
hpaVis: no visible binding for global variable ‘hpa_histology_data’
hpaVisPatho: no visible binding for global variable
  ‘hpa_histology_data’
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
  ‘hpa_histology_data’
hpaVisSubcell: no visible binding for global variable ‘gene’
hpaVisSubcell: no visible binding for global variable ‘sub_location’
hpaVisSubcell: no visible binding for global variable ‘enhanced’
hpaVisSubcell: no visible binding for global variable ‘supported’
hpaVisSubcell: no visible binding for global variable ‘approved’
hpaVisSubcell: no visible binding for global variable ‘uncertain’
hpaVisTissue: no visible binding for global variable
  ‘hpa_histology_data’
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’
Undefined global functions or variables:
  age approved cancer cell_line cell_type enhanced gene high
  hpa_histology_data imageUrl index intensity level low medium
  not_detected patientId patient_count quantity sex staining
  sub_location supported tissue tissue_cell uncertain
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
hpaVisPatho 4.904  0.212   5.842
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/HPAanalyze.Rcheck/00check.log’
for details.



Installation output

HPAanalyze.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL HPAanalyze
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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)

Tests output


Example timings

HPAanalyze.Rcheck/HPAanalyze-Ex.timings

nameusersystemelapsed
hpaDownload2.3000.1802.788
hpaExport0.5960.0560.758
hpaListParam0.1480.0200.301
hpaVis1.4840.0081.894
hpaVisPatho4.9040.2125.842
hpaVisSubcell2.6440.2203.186
hpaVisTissue2.7720.1563.193
hpaXml0.2280.0041.938
hpaXmlAntibody000
hpaXmlGet000
hpaXmlProtClass000
hpaXmlTissueExpr0.0000.0000.001
hpaXmlTissueExprSum000
hpa_downloaded_histology_v181.7800.1082.167
hpa_histology_data2.1400.1882.896