Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:09 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for HIPPO on machv2


To the developers/maintainers of the HIPPO package:
- Please 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 How and When does the builder pull? When will my changes propagate? 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 876/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HIPPO 1.6.0  (landing page)
Tae Kim
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/HIPPO
git_branch: RELEASE_3_14
git_last_commit: c9e2f06
git_last_commit_date: 2021-10-26 12:58:22 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: HIPPO
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HIPPO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HIPPO_1.6.0.tar.gz
StartedAt: 2022-04-12 14:16:43 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 14:20:55 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 252.4 seconds
RetCode: 0
Status:   OK  
CheckDir: HIPPO.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HIPPO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HIPPO_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/HIPPO.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HIPPO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HIPPO’ version ‘1.6.0’
* 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 ‘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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/HIPPO.Rcheck/00check.log’
for details.



Installation output

HIPPO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HIPPO
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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_sce0.1890.0160.385
get_hippo0.9060.0231.241
get_hippo_diffexp1.7400.0661.824
hippo0.3620.0090.371
hippo_diagnostic_plot0.5130.0290.544
hippo_diffexp1.0550.0221.079
hippo_dimension_reduction1.2670.0511.538
hippo_feature_heatmap1.1850.0291.673
hippo_pca_plot0.7110.0160.730
hippo_tsne_plot1.0990.0291.130
hippo_umap_plot2.2540.0822.995
nb_prob_zero0.0010.0000.001
pois_prob_zero0.0000.0000.001
preprocess_heterogeneous0.1570.0020.160
preprocess_homogeneous0.1650.0210.188
zero_proportion_plot1.1270.0261.156
zinb_prob_zero000