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BioC 3.5: CHECK report for erma on tokay2

This page was generated on 2017-08-16 13:24:41 -0400 (Wed, 16 Aug 2017).

Package 413/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
erma 0.8.0
VJ Carey
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/erma
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  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
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: erma
Version: 0.8.0
Command: rm -rf erma.buildbin-libdir erma.Rcheck && mkdir erma.buildbin-libdir erma.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=erma.buildbin-libdir erma_0.8.0.tar.gz >erma.Rcheck\00install.out 2>&1 && cp erma.Rcheck\00install.out erma-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=erma.buildbin-libdir --install="check:erma-install.out" --force-multiarch --no-vignettes --timings erma_0.8.0.tar.gz
StartedAt: 2017-08-15 23:34:49 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:42:15 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 446.9 seconds
RetCode: 0
Status:  OK  
CheckDir: erma.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf erma.buildbin-libdir erma.Rcheck && mkdir erma.buildbin-libdir erma.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=erma.buildbin-libdir erma_0.8.0.tar.gz >erma.Rcheck\00install.out 2>&1 && cp erma.Rcheck\00install.out erma-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=erma.buildbin-libdir --install="check:erma-install.out" --force-multiarch --no-vignettes --timings erma_0.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/erma.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 'erma/DESCRIPTION' ... OK
* this is package 'erma' version '0.8.0'
* 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 'erma' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 199.6Mb
  sub-directories of 1Mb or more:
    bed_tabix  161.4Mb
    data        37.1Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
** 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 ... 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
geneTxRange: no visible global function definition for 'select'
geneTxRange: no visible global function definition for 'IRanges'
genemodel: no visible global function definition for 'IRanges'
genemodelOLD: no visible binding for global variable 'exonsBy'
map2range: no visible global function definition for 'IRanges'
mapmeta: no visible global function definition for 'read.csv'
stateProf: no visible global function definition for 'keys'
stateProfOLD: no visible global function definition for 'keys'
stateProfOLD : server: possible error in stateProfile(ermaset,
  input$sym, ctsize = 12, width = input$scope): unused argument (width
  = input$scope)
stateProfile: no visible binding for global variable 'i'
stateProfile: no visible global function definition for 'genome'
stateProfile: no visible global function definition for 'seqlevels<-'
stateProfile: no visible global function definition for 'seqlevels'
stateProfile : <anonymous>: no visible global function definition for
  'IRanges'
stateProfile: no visible global function definition for 'data'
stateProfile: no visible binding for global variable 'short_celltype'
stateProfile: no visible binding for global variable 'states_25'
stateProfile: no visible binding for global variable 'name'
subsetByRanges : <anonymous>: no visible global function definition for
  'genome'
subsetByRanges : <anonymous>: no visible global function definition for
  'seqlevels<-'
subsetByRanges : <anonymous>: no visible global function definition for
  'seqlevels'
Undefined global functions or variables:
  IRanges data exonsBy genome i keys name read.csv select seqlevels
  seqlevels<- short_celltype states_25
Consider adding
  importFrom("utils", "data", "read.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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
erma-package 9.94   0.38   10.36
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
erma-package 10.14   0.20   10.34
stateProfile  3.67   0.04    6.05
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/erma.Rcheck/00check.log'
for details.


erma.Rcheck/00install.out:


install for i386

* installing *source* package 'erma' ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery

install for x64

* installing *source* package 'erma' ...
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* MD5 sums
packaged installation of 'erma' as erma_0.8.0.zip
* DONE (erma)

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

nameusersystemelapsed
ErmaSet-class0.950.041.00
erma-package 9.94 0.3810.36
genemodel1.670.091.94
mapmeta0.110.020.12
stateProfile3.580.163.74
states_250.010.000.01

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

nameusersystemelapsed
ErmaSet-class0.720.000.72
erma-package10.14 0.2010.34
genemodel1.890.051.94
mapmeta0.090.000.09
stateProfile3.670.046.05
states_250.000.020.01