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This page was generated on 2023-10-20 09:38:04 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 946/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HPAanalyze 1.18.1  (landing page)
Anh Nhat Tran
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/HPAanalyze
git_branch: RELEASE_3_17
git_last_commit: 142bb5a
git_last_commit_date: 2023-06-02 15:51:14 -0400 (Fri, 02 Jun 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for HPAanalyze on kjohnson2


To the developers/maintainers of the HPAanalyze package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: HPAanalyze
Version: 1.18.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HPAanalyze.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HPAanalyze_1.18.1.tar.gz
StartedAt: 2023-10-18 01:02:03 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 01:04:52 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 168.6 seconds
RetCode: 0
Status:   OK  
CheckDir: HPAanalyze.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HPAanalyze.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HPAanalyze_1.18.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/HPAanalyze.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HPAanalyze/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HPAanalyze’ version ‘1.18.1’
* 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 ‘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
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
hpaVisPatho 3.546  0.123   5.438
* 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-3.17-bioc-mac-arm64/meat/HPAanalyze.Rcheck/00check.log’
for details.



Installation output

HPAanalyze.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HPAanalyze
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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)

Tests output


Example timings

HPAanalyze.Rcheck/HPAanalyze-Ex.timings

nameusersystemelapsed
hpaDownload1.9430.1093.128
hpaExport0.4980.0440.829
hpaListParam0.1190.0160.200
hpaVis1.2480.0631.990
hpaVisPatho3.5460.1235.438
hpaVisSubcell2.2470.1123.576
hpaVisTissue2.3240.1193.732
hpaXml0.1790.0174.970
hpaXmlAntibody0.0000.0000.001
hpaXmlGet0.0000.0010.000
hpaXmlProtClass000
hpaXmlTissueExpr0.0000.0000.003
hpaXmlTissueExprSum000
hpa_histology_data1.7890.1072.878