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This page was generated on 2024-12-24 11:45 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1521/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pepStat 1.41.0  (landing page)
Gregory C Imholte
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/pepStat
git_branch: devel
git_last_commit: 42e8f77
git_last_commit_date: 2024-10-29 09:53:04 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
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 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for pepStat on kjohnson3

To the developers/maintainers of the pepStat package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pepStat.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: pepStat
Version: 1.41.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pepStat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pepStat_1.41.0.tar.gz
StartedAt: 2024-12-23 20:40:51 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 20:41:42 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 50.7 seconds
RetCode: 0
Status:   OK  
CheckDir: pepStat.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pepStat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pepStat_1.41.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/pepStat.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pepStat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pepStat’ version ‘1.41.0’
* 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 ‘pepStat’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘pepStat’ for: ‘end’, ‘start’, ‘values’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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
.findFDR : <anonymous>: no visible global function definition for
  ‘median’
.sanitize_mapping_file2: no visible global function definition for
  ‘read.csv’
create_db: no visible global function definition for ‘mcols<-’
create_db: no visible global function definition for ‘mcols’
getPlotCoords: no visible global function definition for ‘values’
getWeightedEstimator : <anonymous>: no visible global function
  definition for ‘lm.fit’
getWeightedEstimator : <anonymous>: no visible global function
  definition for ‘lm.wfit’
getWeightedEstimator : <anonymous> : <anonymous>: no visible global
  function definition for ‘sd’
getZpep: no visible global function definition for ‘values’
getZpep : <anonymous>: no visible global function definition for
  ‘values’
plotArrayImage: no visible global function definition for
  ‘dev.interactive’
plotArrayImage: no visible global function definition for
  ‘devAskNewPage’
plotArrayImage: no visible global function definition for ‘dev.hold’
plotArrayImage: no visible global function definition for ‘dev.flush’
plotArrayResiduals: no visible global function definition for
  ‘dev.interactive’
plotArrayResiduals: no visible global function definition for
  ‘devAskNewPage’
plotArrayResiduals: no visible global function definition for
  ‘dev.hold’
plotArrayResiduals: no visible global function definition for
  ‘dev.flush’
summarizePeptides: no visible global function definition for ‘values<-’
summarizePeptides: no visible global function definition for ‘values’
coerce,peptideSet-ExpressionSet: no visible global function definition
  for ‘annotation’
end,peptideSet: no visible global function definition for ‘end’
featureID,peptideSet: no visible global function definition for
  ‘values’
pepZscore,GRanges: no visible global function definition for ‘values’
peptide,peptideSet: no visible global function definition for ‘values’
peptide<-,peptideSet-character: no visible global function definition
  for ‘values’
peptide<-,peptideSet-character: no visible global function definition
  for ‘values<-’
position,peptideSet: no visible global function definition for ‘start’
position,peptideSet: no visible global function definition for ‘end’
start,peptideSet: no visible global function definition for ‘start’
values,peptideSet: no visible global function definition for ‘values’
values<-,peptideSet: no visible global function definition for
  ‘values<-’
write.pSet,peptideSet: no visible global function definition for
  ‘start’
write.pSet,peptideSet: no visible global function definition for ‘end’
write.pSet,peptideSet: no visible global function definition for
  ‘write.csv’
Undefined global functions or variables:
  annotation dev.flush dev.hold dev.interactive devAskNewPage end
  lm.fit lm.wfit mcols mcols<- median read.csv sd start values values<-
  write.csv
Consider adding
  importFrom("grDevices", "dev.flush", "dev.hold", "dev.interactive",
             "devAskNewPage")
  importFrom("stats", "end", "lm.fit", "lm.wfit", "median", "sd",
             "start")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  create_db.Rd: GRanges
  makePeptideSet.Rd: read.maimages, backgroundCorrect
  peptideSet.Rd: ExpressionSet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/pepStat.Rcheck/00check.log’
for details.


Installation output

pepStat.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘pepStat’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘GenomicRanges’ for request: ‘mcols<-’ when loading ‘pepStat’
No methods found in package ‘GenomicRanges’ for request: ‘mcols’ when loading ‘pepStat’
No methods found in package ‘IRanges’ for request: ‘values<-’ when loading ‘pepStat’
No methods found in package ‘IRanges’ for request: ‘values’ when loading ‘pepStat’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘GenomicRanges’ for request: ‘mcols<-’ when loading ‘pepStat’
No methods found in package ‘GenomicRanges’ for request: ‘mcols’ when loading ‘pepStat’
No methods found in package ‘IRanges’ for request: ‘values<-’ when loading ‘pepStat’
No methods found in package ‘IRanges’ for request: ‘values’ when loading ‘pepStat’
** testing if installed package can be loaded from final location
No methods found in package ‘GenomicRanges’ for request: ‘mcols<-’ when loading ‘pepStat’
No methods found in package ‘GenomicRanges’ for request: ‘mcols’ when loading ‘pepStat’
No methods found in package ‘IRanges’ for request: ‘values<-’ when loading ‘pepStat’
No methods found in package ‘IRanges’ for request: ‘values’ when loading ‘pepStat’
** testing if installed package keeps a record of temporary installation path
* DONE (pepStat)

Tests output


Example timings

pepStat.Rcheck/pepStat-Ex.timings

nameusersystemelapsed
create_db0.0270.0010.027
makeCalls1.3590.0281.398
makePeptideSet0.4860.0160.504
normalizeArray1.1070.0221.131
plotArray1.1030.0191.123
restab1.1330.0201.157
shinyPepStat000
slidingMean1.1200.0251.146
summarizePeptides1.1660.0271.207