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This page was generated on 2024-03-04 11:39:48 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 1725/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rgsepd 1.35.0  (landing page)
Karl Stamm
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/rgsepd
git_branch: devel
git_last_commit: 850590c
git_last_commit_date: 2023-10-24 10:40:48 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for rgsepd on merida1


To the developers/maintainers of the rgsepd package:
- 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 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: rgsepd
Version: 1.35.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rgsepd.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rgsepd_1.35.0.tar.gz
StartedAt: 2024-03-02 09:26:22 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 09:44:07 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 1065.1 seconds
RetCode: 0
Status:   OK  
CheckDir: rgsepd.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rgsepd.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rgsepd_1.35.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/rgsepd.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rgsepd/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rgsepd’ version ‘1.35.0’
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    Rebuilt for R 3.2.2
* 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 whether startup messages can be suppressed ... NOTE
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
ExtractProjection 144.532  9.244 197.534
GSEPD_DEGHeatmap    7.174  0.106   8.797
GSEPD_PCA_Plot      4.343  0.063   5.365
GSEPD_Heatmap       4.289  0.055   5.288
GSEPD_PullDEG       4.226  0.062   5.168
GSEPD_PCA_Spec      4.163  0.048   5.057
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/rgsepd.Rcheck/00check.log’
for details.



Installation output

rgsepd.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rgsepd
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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
DisplayName0.0020.0010.006
ExtractProjection144.532 9.244197.534
GSEPD_ChangeConditions0.5830.0150.724
GSEPD_ChangeOutput0.5810.0130.736
GSEPD_DEGHeatmap7.1740.1068.797
GSEPD_Export_DESeq1.3310.0181.629
GSEPD_Heatmap4.2890.0555.288
GSEPD_INIT0.5960.0150.742
GSEPD_PCA_Plot4.3430.0635.365
GSEPD_PCA_Spec4.1630.0485.057
GSEPD_Process0.5750.0140.728
GSEPD_ProcessAll0.5910.0160.759
GSEPD_PullDEG4.2260.0625.168
IlluminaBodymap0.5600.0170.707
IlluminaBodymapMeta0.0150.0050.024
Name_to_RefSeq000
rgsepd-package0.5750.0130.709