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This page was generated on 2021-10-15 15:05:42 -0400 (Fri, 15 Oct 2021).

CHECK results for HPAanalyze on nebbiolo1

To the developers/maintainers of the HPAanalyze package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HPAanalyze.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 873/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HPAanalyze 1.10.0  (landing page)
Anh Nhat Tran
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/HPAanalyze
git_branch: RELEASE_3_13
git_last_commit: d9bcfdb
git_last_commit_date: 2021-05-19 12:37:33 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: HPAanalyze
Version: 1.10.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:HPAanalyze.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings HPAanalyze_1.10.0.tar.gz
StartedAt: 2021-10-14 10:11:51 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 10:13:09 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 77.6 seconds
RetCode: 0
Status:   OK  
CheckDir: HPAanalyze.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:HPAanalyze.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings HPAanalyze_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/HPAanalyze.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.10.0’
* 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 ‘datasetnames’
hpaDownload: no visible binding for global variable
  ‘hpa_histology_data’
hpaDownload: no visible binding for global variable ‘.’
hpaSubset : subsetting: no visible binding for global variable ‘gene’
hpaSubset : subsetting: no visible binding for global variable ‘tissue’
hpaSubset : subsetting: no visible binding for global variable
  ‘cell_type’
hpaSubset : subsetting: no visible binding for global variable ‘cancer’
hpaSubset : subsetting: 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 ‘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 ‘sub_location’
hpaVisTissue: no visible binding for global variable ‘gene’
hpaVisTissue: no visible binding for global variable ‘.’
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’
is_null_data: no visible binding for global variable
  ‘hpa_histology_data’
named_vector_list_to_tibble: no visible binding for global variable
  ‘index’
Undefined global functions or variables:
  . age cancer cell_line cell_type datasetnames gene high
  hpa_histology_data imageUrl index intensity level low medium
  not_detected patientId patient_count quantity sex staining
  sub_location tissue tissue_cell
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... 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
  ‘/home/biocbuild/bbs-3.13-bioc/meat/HPAanalyze.Rcheck/00check.log’
for details.



Installation output

HPAanalyze.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL HPAanalyze
###
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* installing to library ‘/home/biocbuild/bbs-3.13-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
hpaDownload1.5980.2081.806
hpaExport0.4820.0510.534
hpaListParam0.1140.0350.150
hpaVis0.8600.0320.893
hpaVisPatho2.8360.2163.053
hpaVisSubcell1.8280.2232.053
hpaVisTissue1.9060.2322.138
hpaXml0.2400.0432.858
hpaXmlAntibody000
hpaXmlGet0.0010.0000.000
hpaXmlProtClass0.0000.0000.001
hpaXmlTissueExpr000
hpaXmlTissueExprSum000
hpa_histology_data1.3770.2111.587