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This page was generated on 2025-03-17 11:39 -0400 (Mon, 17 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
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 1130/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LPE 1.81.0  (landing page)
Nitin Jain
Snapshot Date: 2025-03-16 13:40 -0400 (Sun, 16 Mar 2025)
git_url: https://git.bioconductor.org/packages/LPE
git_branch: devel
git_last_commit: 8bda3fa
git_last_commit_date: 2024-10-29 09:22:14 -0400 (Tue, 29 Oct 2024)
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for LPE on lconway

To the developers/maintainers of the LPE package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/LPE.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: LPE
Version: 1.81.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:LPE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings LPE_1.81.0.tar.gz
StartedAt: 2025-03-16 21:45:46 -0400 (Sun, 16 Mar 2025)
EndedAt: 2025-03-16 21:46:21 -0400 (Sun, 16 Mar 2025)
EllapsedTime: 34.3 seconds
RetCode: 0
Status:   OK  
CheckDir: LPE.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:LPE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings LPE_1.81.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/LPE.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LPE/DESCRIPTION’ ... OK
* this is package ‘LPE’ version ‘1.81.0’
* 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 ‘LPE’ 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:
    Updated the file am.trans.R for faster computations.
* 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 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
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/LPE.Rcheck/00check.log’
for details.


Installation output

LPE.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘LPE’ ...
** this is package ‘LPE’ version ‘1.81.0’
** using staged installation
** R
** data
** 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 (LPE)

Tests output


Example timings

LPE.Rcheck/LPE-Ex.timings

nameusersystemelapsed
am.trans0.0010.0010.002
baseOlig.error0.2540.0370.291
baseOlig.error.step10.1420.0120.155
baseOlig.error.step20.2180.0170.239
fdr.adjust1.3440.1101.480
fixbounds.predict.smooth.spline0.2890.0070.301
iqr0.0000.0000.001
lowess.normalize0.0460.0030.049
lpe0.4830.0150.505
mt.rawp2adjp0.4200.0140.440
n.genes.adaptive.int0.1390.0050.146
permute0.0000.0000.001
preprocess0.0910.0040.099
quan.norm0.0010.0000.001
quartile.normalize0.0410.0020.045
resamp.adj1.6200.0741.707