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This page was generated on 2021-12-03 13:04:52 -0500 (Fri, 03 Dec 2021).

CHECK results for loci2path on nebbiolo2

To the developers/maintainers of the loci2path package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/loci2path.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 1008/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
loci2path 1.14.0  (landing page)
Tianlei Xu
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/loci2path
git_branch: RELEASE_3_14
git_last_commit: 47ab6ff
git_last_commit_date: 2021-10-26 12:40:18 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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: loci2path
Version: 1.14.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:loci2path.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings loci2path_1.14.0.tar.gz
StartedAt: 2021-12-02 07:45:52 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 07:47:16 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 83.4 seconds
RetCode: 0
Status:   OK  
CheckDir: loci2path.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:loci2path.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings loci2path_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/loci2path.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘loci2path/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘loci2path’ 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 for sufficient/correct file permissions ... OK
* checking whether package ‘loci2path’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 ... OK
* 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: OK


Installation output

loci2path.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL loci2path
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘loci2path’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** 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 (loci2path)

Tests output


Example timings

loci2path.Rcheck/loci2path-Ex.timings

nameusersystemelapsed
biocarta0.0060.0000.006
check.geneid0.0130.0000.013
eqtlSet-class0.210.000.21
eset.list0.0010.0000.001
geneSet-class0.0120.0080.021
getHeatmap-methods0.5390.0160.533
getMat-methods0.3220.0000.301
getPathDescription-methods0.3700.0040.340
getPval-methods0.3070.0370.315
getTissueDegree-methods0.2990.0030.281
getWordcloud-methods0.8200.0320.831
loci2pathResult-class0.2340.0000.212
query-methods0.3740.0050.344
query.gr0.0010.0000.001