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This page was generated on 2022-01-21 11:08:26 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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 riesling1


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? 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 1591/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rgsepd 1.27.0  (landing page)
Karl Stamm
Snapshot Date: 2022-01-20 13:55:17 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/rgsepd
git_branch: master
git_last_commit: 517eb1e
git_last_commit_date: 2021-10-26 12:18:10 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
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  UNNEEDED, same version is already published

Summary

Package: rgsepd
Version: 1.27.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rgsepd.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings rgsepd_1.27.0.tar.gz
StartedAt: 2022-01-20 19:52:04 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 19:58:09 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 365.2 seconds
RetCode: 0
Status:   OK  
CheckDir: rgsepd.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rgsepd.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings rgsepd_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/rgsepd.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rgsepd/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rgsepd' version '1.27.0'
* 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 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 49.4   7.28   56.97
* 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

rgsepd.Rcheck/00install.out

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


* installing to library 'D:/biocbuild/bbs-3.15-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
  converting help for package 'rgsepd'
    finding HTML links ... done
    DisplayName                             html  
    ExtractProjection                       html  
    GSEPD_ChangeConditions                  html  
    GSEPD_ChangeOutput                      html  
    GSEPD_DEGHeatmap                        html  
    GSEPD_Export_DESeq                      html  
    GSEPD_Heatmap                           html  
    GSEPD_INIT                              html  
    GSEPD_PCA_Plot                          html  
    GSEPD_PCA_Spec                          html  
    GSEPD_Process                           html  
    GSEPD_ProcessAll                        html  
    GSEPD_PullDEG                           html  
    IlluminaBodymap                         html  
    IlluminaBodymapMeta                     html  
    Name_to_RefSeq                          html  
    rgsepd-package                          html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'tLOH' is missing or broken
 done

Tests output


Example timings

rgsepd.Rcheck/rgsepd-Ex.timings

nameusersystemelapsed
DisplayName000
ExtractProjection49.40 7.2856.97
GSEPD_ChangeConditions0.20.00.2
GSEPD_ChangeOutput0.170.010.19
GSEPD_DEGHeatmap2.550.052.59
GSEPD_Export_DESeq0.410.000.41
GSEPD_Heatmap1.970.021.98
GSEPD_INIT0.180.010.20
GSEPD_PCA_Plot1.970.082.05
GSEPD_PCA_Spec1.950.031.99
GSEPD_Process0.210.000.20
GSEPD_ProcessAll0.20.00.2
GSEPD_PullDEG2.020.032.05
IlluminaBodymap0.180.000.19
IlluminaBodymapMeta0.020.000.01
Name_to_RefSeq000
rgsepd-package0.190.000.19