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This page was generated on 2023-10-20 09:38:09 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 1579/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PSEA 1.34.0  (landing page)
Alexandre Kuhn
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/PSEA
git_branch: RELEASE_3_17
git_last_commit: 9f436e4
git_last_commit_date: 2023-04-25 10:34:53 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for PSEA on kjohnson2


To the developers/maintainers of the PSEA package:
- 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: PSEA
Version: 1.34.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PSEA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PSEA_1.34.0.tar.gz
StartedAt: 2023-10-18 16:14:11 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 16:15:15 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 64.0 seconds
RetCode: 0
Status:   OK  
CheckDir: PSEA.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PSEA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PSEA_1.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/PSEA.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PSEA/DESCRIPTION’ ... OK
* this is package ‘PSEA’ version ‘1.34.0’
* 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 ‘PSEA’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... NOTE
crplot: no visible global function definition for ‘residuals’
crplot: no visible global function definition for ‘dev.new’
crplot: no visible global function definition for ‘abline’
crplot: no visible global function definition for ‘points’
lmfitst: no visible global function definition for ‘is’
lmfitst : <anonymous>: no visible global function definition for
  ‘lm.fit’
marker: no visible global function definition for ‘is’
swlm: no visible global function definition for ‘formula’
swlm: no visible global function definition for ‘is’
swlm: no visible global function definition for ‘lm’
Undefined global functions or variables:
  abline dev.new formula is lm lm.fit points residuals
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "points")
  importFrom("methods", "is")
  importFrom("stats", "formula", "lm", "lm.fit", "residuals")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/PSEA.Rcheck/00check.log’
for details.



Installation output

PSEA.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PSEA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘PSEA’ ...
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (PSEA)

Tests output


Example timings

PSEA.Rcheck/PSEA-Ex.timings

nameusersystemelapsed
coefmat0.1190.0090.196
crplot0.0110.0040.022
em_quantvg0.0120.0040.023
fmm0.0110.0050.025
lmfitst0.0230.0050.042
marker0.0050.0010.009
pvalmat0.0460.0050.079
slt0.0030.0000.005
swlm0.0370.0020.061