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BioC 3.5: CHECK report for pepStat on tokay2

This page was generated on 2017-08-16 13:23:26 -0400 (Wed, 16 Aug 2017).

Package 968/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pepStat 1.10.0
Gregory C Imholte
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/pepStat
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: pepStat
Version: 1.10.0
Command: rm -rf pepStat.buildbin-libdir pepStat.Rcheck && mkdir pepStat.buildbin-libdir pepStat.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pepStat.buildbin-libdir pepStat_1.10.0.tar.gz >pepStat.Rcheck\00install.out 2>&1 && cp pepStat.Rcheck\00install.out pepStat-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=pepStat.buildbin-libdir --install="check:pepStat-install.out" --force-multiarch --no-vignettes --timings pepStat_1.10.0.tar.gz
StartedAt: 2017-08-16 01:53:00 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:56:49 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 229.4 seconds
RetCode: 0
Status:  OK  
CheckDir: pepStat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf pepStat.buildbin-libdir pepStat.Rcheck && mkdir pepStat.buildbin-libdir pepStat.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pepStat.buildbin-libdir pepStat_1.10.0.tar.gz >pepStat.Rcheck\00install.out 2>&1 && cp pepStat.Rcheck\00install.out pepStat-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=pepStat.buildbin-libdir --install="check:pepStat-install.out" --force-multiarch --no-vignettes --timings pepStat_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/pepStat.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.10.0'
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 or elapsed time > 5s
                  user system elapsed
makeCalls         7.96   0.09    8.72
normalizeArray    5.29   0.05    5.35
summarizePeptides 5.23   0.00    5.24
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
makeCalls      8.48   0.05    8.72
normalizeArray 5.36   0.06    5.42
plotArray      5.05   0.01    5.08
* 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-3.5-bioc/meat/pepStat.Rcheck/00check.log'
for details.


pepStat.Rcheck/00install.out:


install for i386

* installing *source* package 'pepStat' ...
** R
** inst
** preparing package for lazy loading
No methods found in "GenomicRanges" for requests: mcols<-
No methods found in "GenomicRanges" for requests: mcols
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "GenomicRanges" for requests: mcols<-
No methods found in "GenomicRanges" for requests: mcols

install for x64

* installing *source* package 'pepStat' ...
** testing if installed package can be loaded
No methods found in "GenomicRanges" for requests: mcols<-
No methods found in "GenomicRanges" for requests: mcols
* MD5 sums
packaged installation of 'pepStat' as pepStat_1.10.0.zip
* DONE (pepStat)

pepStat.Rcheck/examples_i386/pepStat-Ex.timings:

nameusersystemelapsed
create_db0.230.000.23
makeCalls7.960.098.72
makePeptideSet3.880.033.90
normalizeArray5.290.055.35
plotArray4.160.014.17
restab4.220.004.22
shinyPepStat0.010.000.01
slidingMean4.350.024.36
summarizePeptides5.230.005.24

pepStat.Rcheck/examples_x64/pepStat-Ex.timings:

nameusersystemelapsed
create_db0.250.000.27
makeCalls8.480.058.72
makePeptideSet4.030.024.05
normalizeArray5.360.065.42
plotArray5.050.015.08
restab4.690.074.75
shinyPepStat000
slidingMean4.650.014.67
summarizePeptides4.660.034.69