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CHECK report for pepStat on tokay2

This page was generated on 2020-10-17 11:57:22 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE pepStat PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1293/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pepStat 1.22.0
Gregory C Imholte
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/pepStat
Branch: RELEASE_3_11
Last Commit: 6e21a03
Last Changed Date: 2020-04-27 14:41:23 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: pepStat
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pepStat.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings pepStat_1.22.0.tar.gz
StartedAt: 2020-10-17 06:49:57 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:53:49 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 232.0 seconds
RetCode: 0
Status:  OK  
CheckDir: pepStat.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pepStat.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings pepStat_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/pepStat.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.22.0'
* 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'

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'

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'
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'
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'
coerce,peptideSet-ExpressionSet: no visible global function definition
  for 'annotation'
end,peptideSet: no visible global function definition for 'end'
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'
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 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   5.55   0.18    7.36
slidingMean 5.12   0.04    5.16
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
plotArray 5.48   0.02    5.52
* 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-3.11-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 https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/pepStat_1.22.0.tar.gz && rm -rf pepStat.buildbin-libdir && mkdir pepStat.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pepStat.buildbin-libdir pepStat_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL pepStat_1.22.0.zip && rm pepStat_1.22.0.tar.gz pepStat_1.22.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 56  395k   56  224k    0     0  3120k      0 --:--:-- --:--:-- --:--:-- 3446k
100  395k  100  395k    0     0  5392k      0 --:--:-- --:--:-- --:--:-- 5908k

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'
** 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  
    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'
** 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'
** 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'
* MD5 sums
packaged installation of 'pepStat' as pepStat_1.22.0.zip
* DONE (pepStat)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'pepStat' successfully unpacked and MD5 sums checked

Tests output


Example timings

pepStat.Rcheck/examples_i386/pepStat-Ex.timings

nameusersystemelapsed
create_db0.140.000.14
makeCalls5.550.187.36
makePeptideSet2.310.022.33
normalizeArray3.970.034.08
plotArray4.830.044.87
restab4.080.004.08
shinyPepStat000
slidingMean5.120.045.16
summarizePeptides4.580.034.62

pepStat.Rcheck/examples_x64/pepStat-Ex.timings

nameusersystemelapsed
create_db0.090.000.10
makeCalls4.560.034.59
makePeptideSet2.390.022.42
normalizeArray4.450.004.45
plotArray5.480.025.52
restab4.250.024.26
shinyPepStat000
slidingMean4.100.064.16
summarizePeptides4.530.004.53