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This page was generated on 2021-10-15 15:06:15 -0400 (Fri, 15 Oct 2021).

CHECK results for pepStat on tokay2

To the developers/maintainers of the pepStat package:
- Please 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 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 1370/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pepStat 1.26.0  (landing page)
Gregory C Imholte
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/pepStat
git_branch: RELEASE_3_13
git_last_commit: a3472cb
git_last_commit_date: 2021-05-19 12:05:52 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: pepStat
Version: 1.26.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pepStat.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings pepStat_1.26.0.tar.gz
StartedAt: 2021-10-15 03:17:26 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 03:20:58 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 211.6 seconds
RetCode: 0
Status:   OK  
CheckDir: pepStat.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pepStat.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings pepStat_1.26.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/pepStat.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pepStat/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pepStat' version '1.26.0'
* 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 '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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
makeCalls 5.33   0.20    6.14
plotArray 5.28   0.03    5.32
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
makeCalls 5.32   0.03    5.36
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/pepStat.Rcheck/00check.log'
for details.



Installation output

pepStat.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/pepStat_1.26.0.tar.gz && rm -rf pepStat.buildbin-libdir && mkdir pepStat.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pepStat.buildbin-libdir pepStat_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL pepStat_1.26.0.zip && rm pepStat_1.26.0.tar.gz pepStat_1.26.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  395k  100  395k    0     0   936k      0 --:--:-- --:--:-- --:--:--  939k

install for i386

* 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
  converting help for package 'pepStat'
    finding HTML links ... done
    baselineCorrect.pSet                    html  
    baseline_correct                        html  
    create_db                               html  
    finding level-2 HTML links ... done

    makeCalls                               html  
    makePeptideSet                          html  
    normalizeArray                          html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/pepStat.buildbin-libdir/00LOCK-pepStat/00new/pepStat/help/normalizeArray.html
    peptideSet-methods                      html  
    peptideSet                              html  
    plotArray                               html  
    restab                                  html  
    shinyPepStat                            html  
    slidingMean                             html  
    summarizePeptides                       html  
** building package indices
** installing vignettes
   'pepStat.Rnw' 
** 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

install for x64

* installing *source* package 'pepStat' ...
** testing if installed package can be loaded
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'
* MD5 sums
packaged installation of 'pepStat' as pepStat_1.26.0.zip
* DONE (pepStat)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'pepStat' successfully unpacked and MD5 sums checked

Tests output


Example timings

pepStat.Rcheck/examples_i386/pepStat-Ex.timings

nameusersystemelapsed
create_db0.110.000.11
makeCalls5.330.206.14
makePeptideSet2.100.032.12
normalizeArray4.860.054.91
plotArray5.280.035.32
restab4.480.034.52
shinyPepStat000
slidingMean4.410.024.42
summarizePeptides4.510.014.53

pepStat.Rcheck/examples_x64/pepStat-Ex.timings

nameusersystemelapsed
create_db0.150.010.16
makeCalls5.320.035.36
makePeptideSet2.110.022.13
normalizeArray4.550.004.55
plotArray4.610.014.62
restab4.270.054.32
shinyPepStat000
slidingMean4.360.034.39
summarizePeptides4.780.024.79