Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:21:38 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 palomino3


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 901/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HIPPO 1.8.0  (landing page)
Tae Kim
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/HIPPO
git_branch: RELEASE_3_15
git_last_commit: 5eb3f20
git_last_commit_date: 2022-04-26 12:03:49 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: HIPPO
Version: 1.8.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HIPPO.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings HIPPO_1.8.0.tar.gz
StartedAt: 2022-10-19 01:00:29 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 01:03:42 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 192.7 seconds
RetCode: 0
Status:   OK  
CheckDir: HIPPO.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HIPPO.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings HIPPO_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/HIPPO.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.8.0'
* 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-3.15-bioc/meat/HIPPO.Rcheck/00check.log'
for details.



Installation output

HIPPO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL HIPPO
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-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_sce0.730.020.75
get_hippo0.270.000.27
get_hippo_diffexp0.800.040.84
hippo0.810.000.81
hippo_diagnostic_plot0.440.000.44
hippo_diffexp0.650.000.66
hippo_dimension_reduction1.460.071.51
hippo_feature_heatmap0.510.010.53
hippo_pca_plot0.520.000.52
hippo_tsne_plot0.650.020.67
hippo_umap_plot1.060.081.14
nb_prob_zero000
pois_prob_zero000
preprocess_heterogeneous0.080.010.10
preprocess_homogeneous0.760.000.76
zero_proportion_plot0.750.030.78
zinb_prob_zero000