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This page was generated on 2024-04-17 11:36:52 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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 963/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HIPPO 1.14.0  (landing page)
Tae Kim
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/HIPPO
git_branch: RELEASE_3_18
git_last_commit: 7d5a5b2
git_last_commit_date: 2023-10-24 11:20:42 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for HIPPO on palomino4


To the developers/maintainers of the HIPPO package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HIPPO.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: HIPPO
Version: 1.14.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HIPPO.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings HIPPO_1.14.0.tar.gz
StartedAt: 2024-04-16 01:41:34 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 01:44:48 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 194.0 seconds
RetCode: 0
Status:   OK  
CheckDir: HIPPO.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HIPPO.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings HIPPO_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/HIPPO.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'HIPPO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HIPPO' version '1.14.0'
* 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 'HIPPO' can be installed ... OK
* checking installed package size ... OK
* checking package 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
ensg_to_hgnc: no visible global function definition for 'data'
ensg_to_hgnc: no visible binding for global variable 'ensg_hgnc'
hippo: no visible global function definition for 'is'
hippo_feature_heatmap: no visible binding for global variable 'zvalue'
hippo_tsne_plot: no visible binding for global variable 'K'
hippo_umap_plot: no visible binding for global variable 'K'
preprocess_homogeneous: no visible global function definition for 'is'
zero_proportion_plot: no visible binding for global variable 'K'
zero_proportion_plot: no visible binding for global variable 'zvalue'
zero_proportion_plot: no visible binding for global variable
  'featurecount'
Undefined global functions or variables:
  K data ensg_hgnc featurecount is zvalue
Consider adding
  importFrom("methods", "is")
  importFrom("utils", "data")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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
  'F:/biocbuild/bbs-3.18-bioc/meat/HIPPO.Rcheck/00check.log'
for details.



Installation output

HIPPO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL HIPPO
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'HIPPO' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (HIPPO)

Tests output


Example timings

HIPPO.Rcheck/HIPPO-Ex.timings

nameusersystemelapsed
get_data_from_sce0.080.000.08
get_hippo0.810.010.82
get_hippo_diffexp1.180.031.22
hippo0.280.020.30
hippo_diagnostic_plot1.210.081.28
hippo_diffexp0.790.010.81
hippo_dimension_reduction0.770.050.81
hippo_feature_heatmap0.700.010.72
hippo_pca_plot1.330.021.34
hippo_tsne_plot0.720.020.74
hippo_umap_plot1.230.061.30
nb_prob_zero000
pois_prob_zero000
preprocess_heterogeneous0.100.000.09
preprocess_homogeneous0.080.010.09
zero_proportion_plot1.610.001.61
zinb_prob_zero000