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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 939/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HIPPO 1.12.0  (landing page)
Tae Kim
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/HIPPO
git_branch: RELEASE_3_17
git_last_commit: 9976bac
git_last_commit_date: 2023-04-25 11:16:38 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for HIPPO on kjohnson2


To the developers/maintainers of the HIPPO 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: HIPPO
Version: 1.12.0
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_1.12.0.tar.gz
StartedAt: 2023-10-18 00:51:28 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 00:56:21 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 293.0 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_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/HIPPO.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 ‘HIPPO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HIPPO’ version ‘1.12.0’
* 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-3.17-bioc-mac-arm64/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/4.3-arm64/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_sce0.4910.0110.767
get_hippo0.2530.0160.415
get_hippo_diffexp1.3720.0452.146
hippo0.2100.0150.349
hippo_diagnostic_plot0.3490.0210.570
hippo_diffexp0.8250.0341.315
hippo_dimension_reduction1.2420.0341.946
hippo_feature_heatmap0.4730.0150.739
hippo_pca_plot0.4840.0130.748
hippo_tsne_plot0.7340.0251.149
hippo_umap_plot1.5360.0522.404
nb_prob_zero0.0000.0000.001
pois_prob_zero000
preprocess_heterogeneous0.0860.0070.141
preprocess_homogeneous0.0880.0080.157
zero_proportion_plot0.9300.0271.511
zinb_prob_zero000