Back to the "Multiple platform build/check report"

BioC experimental data: CHECK report for leeBamViews on moscato2

This page was generated on 2016-10-08 19:30:47 -0700 (Sat, 08 Oct 2016).

Package 157/293HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
leeBamViews 1.8.0
VJ Carey
Snapshot Date: 2016-10-08 07:15:25 -0700 (Sat, 08 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_3/experiment/pkgs/leeBamViews
Last Changed Rev: 3760 / Revision: 3935
Last Changed Date: 2016-05-03 14:35:06 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 

Summary

Package: leeBamViews
Version: 1.8.0
Command: rm -rf leeBamViews.buildbin-libdir leeBamViews.Rcheck && mkdir leeBamViews.buildbin-libdir leeBamViews.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=leeBamViews.buildbin-libdir leeBamViews_1.8.0.tar.gz >leeBamViews.Rcheck\00install.out 2>&1 && cp leeBamViews.Rcheck\00install.out leeBamViews-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=leeBamViews.buildbin-libdir --install="check:leeBamViews-install.out" --force-multiarch --no-vignettes --timings leeBamViews_1.8.0.tar.gz
StartedAt: 2016-10-08 12:43:37 -0700 (Sat, 08 Oct 2016)
EndedAt: 2016-10-08 12:48:50 -0700 (Sat, 08 Oct 2016)
EllapsedTime: 312.9 seconds
RetCode: 0
Status:  OK  
CheckDir: leeBamViews.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf leeBamViews.buildbin-libdir leeBamViews.Rcheck && mkdir leeBamViews.buildbin-libdir leeBamViews.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=leeBamViews.buildbin-libdir leeBamViews_1.8.0.tar.gz >leeBamViews.Rcheck\00install.out 2>&1 && cp leeBamViews.Rcheck\00install.out leeBamViews-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=leeBamViews.buildbin-libdir --install="check:leeBamViews-install.out" --force-multiarch --no-vignettes --timings leeBamViews_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-data-experiment/meat/leeBamViews.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'leeBamViews/DESCRIPTION' ... OK
* this is package 'leeBamViews' version '1.8.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'multicore'
* 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 'leeBamViews' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.3Mb
  sub-directories of 1Mb or more:
    bam  10.1Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Non-standard license specification:
  Artistic 2.0
Standardizable: TRUE
Standardized license specification:
  Artistic-2.0
* 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 ... NOTE
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'BSgenome' 'Biobase' 'Rsamtools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.tabulateReads: no visible global function definition for 'bamRanges'
.tabulateReads: no visible global function definition for
  'elementMetadata'
.tabulateReads : alignByFirstRange: no visible global function
  definition for 'ScanBamParam'
.tabulateReads : alignByFirstRange: no visible global function
  definition for 'bamRanges'
.tabulateReads : alignByFirstRange: no visible global function
  definition for 'bamPaths'
.tabulateReads: no visible global function definition for 'start'
.tabulateReads: no visible global function definition for 'bamSamples'
.tabulateReads: no visible global function definition for 'IRanges'
.tabulateReads: no visible global function definition for 'GRanges'
.tabulateReads: no visible global function definition for 'seqnames'
.tabulateReads: no visible global function definition for 'values'
.tabulateReads: no visible global function definition for 'values<-'
.tabulateReads: no visible global function definition for 'DataFrame'
tabulateReads,BamViews-characterORNULL-missing-missing: no visible
  binding for global variable 'mclapply'
tabulateReads,BamViews-missing-missing-missing: no visible binding for
  global variable 'mclapply'
totalReadCounts,BamViews: no visible global function definition for
  'bamPaths'
totalReadCounts,BamViews: no visible binding for global variable
  'scanBam'
totalReadCounts,BamViews: no visible global function definition for
  'ScanBamParam'
Undefined global functions or variables:
  DataFrame GRanges IRanges ScanBamParam bamPaths bamRanges bamSamples
  elementMetadata mclapply scanBam seqnames start values values<-
Consider adding
  importFrom("stats", "start")
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
tabulateReads 4.65   0.06    5.94
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
tabulateReads  5.2   0.06    5.26
bs1            1.0   0.03    7.58
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'lbvtest.R'
 OK
** running tests for arch 'x64' ...
  Running 'lbvtest.R'
 OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'IRanges'
* 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: 6 NOTEs
See
  'E:/biocbld/bbs-3.3-data-experiment/meat/leeBamViews.Rcheck/00check.log'
for details.


leeBamViews.Rcheck/00install.out:


install for i386

* installing *source* package 'leeBamViews' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'leeBamViews' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'leeBamViews' as leeBamViews_1.8.0.zip
* DONE (leeBamViews)

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

nameusersystemelapsed
bs11.220.033.14
leeRPKM0.030.020.04
leeUnn0.090.000.10
tabulateReads4.650.065.94
totalReadCounts1.330.021.38

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

nameusersystemelapsed
bs11.000.037.58
leeRPKM0.060.000.07
leeUnn0.110.020.12
tabulateReads5.200.065.26
totalReadCounts0.950.051.00