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This page was generated on 2024-12-24 11:41 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 971/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HPAanalyze 1.25.0  (landing page)
Anh Nhat Tran
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/HPAanalyze
git_branch: devel
git_last_commit: d90d2c8
git_last_commit_date: 2024-10-29 10:30:52 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for HPAanalyze on palomino7

To the developers/maintainers of the HPAanalyze package:
- 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 Troubleshooting Build Report for more information.
- 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: 1.25.0
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HPAanalyze.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings HPAanalyze_1.25.0.tar.gz
StartedAt: 2024-12-24 01:39:34 -0500 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 01:41:05 -0500 (Tue, 24 Dec 2024)
EllapsedTime: 90.9 seconds
RetCode: 0
Status:   OK  
CheckDir: HPAanalyze.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HPAanalyze.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings HPAanalyze_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/HPAanalyze.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'HPAanalyze/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HPAanalyze' version '1.25.0'
* 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 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 code 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 ... 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
  'E:/biocbuild/bbs-3.21-bioc/meat/HPAanalyze.Rcheck/00check.log'
for details.


Installation output

HPAanalyze.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL HPAanalyze
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-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
hpaDownload1.480.141.63
hpaExport0.560.080.84
hpaListParam0.120.030.15
hpaVis1.320.031.35
hpaVisPatho3.370.233.61
hpaVisSubcell1.470.241.70
hpaVisTissue1.980.222.20
hpaXml0.180.031.88
hpaXmlAntibody000
hpaXmlGet000
hpaXmlProtClass000
hpaXmlTissueExpr000
hpaXmlTissueExprSum000
hpa_histology_data1.300.181.49