Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 968/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HIPPO 1.18.0  (landing page)
Tae Kim
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/HIPPO
git_branch: RELEASE_3_20
git_last_commit: 126e595
git_last_commit_date: 2024-10-29 10:44:57 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for HIPPO on nebbiolo2

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: 1.18.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:HIPPO.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings HIPPO_1.18.0.tar.gz
StartedAt: 2024-12-20 01:05:23 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 01:11:57 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 394.3 seconds
RetCode: 0
Status:   OK  
CheckDir: HIPPO.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:HIPPO.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings HIPPO_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/HIPPO.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘HIPPO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HIPPO’ version ‘1.18.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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 loading without being on the library search path ... 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/HIPPO.Rcheck/00check.log’
for details.


Installation output

HIPPO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL HIPPO
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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_sce0.0380.0050.043
get_hippo0.6530.0140.667
get_hippo_diffexp0.6670.0130.681
hippo0.1760.0110.188
hippo_diagnostic_plot0.7690.0190.790
hippo_diffexp0.5790.0400.620
hippo_dimension_reduction0.5890.0100.600
hippo_feature_heatmap0.3790.0030.382
hippo_pca_plot0.3680.0200.388
hippo_tsne_plot1.5740.0841.659
hippo_umap_plot0.8390.0030.842
nb_prob_zero000
pois_prob_zero000
preprocess_heterogeneous0.0620.0010.064
preprocess_homogeneous0.0670.0110.079
zero_proportion_plot0.6490.0020.652
zinb_prob_zero000