Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2022-12-05 11:06:27 -0500 (Mon, 05 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4277
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-11-30 r83393 ucrt) -- "Unsuffered Consequences" 4193
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4236
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 rgsepd on nebbiolo1


To the developers/maintainers of the rgsepd package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rgsepd.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 1651/2155HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rgsepd 1.31.0  (landing page)
Karl Stamm
Snapshot Date: 2022-12-04 14:00:12 -0500 (Sun, 04 Dec 2022)
git_url: https://git.bioconductor.org/packages/rgsepd
git_branch: master
git_last_commit: cd0721e
git_last_commit_date: 2022-11-01 11:10:53 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'DESeq2' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'DESeq2' which is not available

Summary

Package: rgsepd
Version: 1.31.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:rgsepd.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings rgsepd_1.31.0.tar.gz
StartedAt: 2022-12-04 22:55:12 -0500 (Sun, 04 Dec 2022)
EndedAt: 2022-12-04 23:03:32 -0500 (Sun, 04 Dec 2022)
EllapsedTime: 499.8 seconds
RetCode: 0
Status:   OK  
CheckDir: rgsepd.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:rgsepd.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings rgsepd_1.31.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/rgsepd.Rcheck’
* using R Under development (unstable) (2022-11-30 r83393)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘rgsepd/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rgsepd’ version ‘1.31.0’
* 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 ‘rgsepd’ 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
ExtractProjection 65.076  2.496   67.57
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘rgsepd.Rnw’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

rgsepd.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL rgsepd
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘rgsepd’ ...
** using staged installation
** R
** data
** 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
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
** testing if installed package can be loaded from final location
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
** testing if installed package keeps a record of temporary installation path
* DONE (rgsepd)

Tests output


Example timings

rgsepd.Rcheck/rgsepd-Ex.timings

nameusersystemelapsed
DisplayName0.0020.0000.001
ExtractProjection65.076 2.49667.570
GSEPD_ChangeConditions0.2380.0000.238
GSEPD_ChangeOutput0.2460.0000.245
GSEPD_DEGHeatmap2.4120.0082.420
GSEPD_Export_DESeq0.4940.0040.498
GSEPD_Heatmap1.6490.0081.658
GSEPD_INIT0.230.000.23
GSEPD_PCA_Plot1.6930.0281.720
GSEPD_PCA_Spec1.6470.0081.656
GSEPD_Process0.3130.0000.312
GSEPD_ProcessAll0.2420.0040.245
GSEPD_PullDEG1.7420.0031.745
IlluminaBodymap0.2430.0040.247
IlluminaBodymapMeta0.0040.0040.009
Name_to_RefSeq000
rgsepd-package0.2490.0040.253