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

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### Running command:
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###   /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.

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### Running command:
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###   /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)

name	user	system	elapsed
hpaDownload	2.300	0.180	2.788
hpaExport	0.596	0.056	0.758
hpaListParam	0.148	0.020	0.301
hpaVis	1.484	0.008	1.894
hpaVisPatho	4.904	0.212	5.842
hpaVisSubcell	2.644	0.220	3.186
hpaVisTissue	2.772	0.156	3.193
hpaXml	0.228	0.004	1.938
hpaXmlAntibody	0	0	0
hpaXmlGet	0	0	0
hpaXmlProtClass	0	0	0
hpaXmlTissueExpr	0.000	0.000	0.001
hpaXmlTissueExprSum	0	0	0
hpa_downloaded_histology_v18	1.780	0.108	2.167
hpa_histology_data	2.140	0.188	2.896