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BioC 3.0: CHECK report for biomvRCNS on perceval

This page was generated on 2015-04-10 09:57:49 -0700 (Fri, 10 Apr 2015).

Package 98/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biomvRCNS 1.6.0
Yang Du
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/biomvRCNS
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: biomvRCNS
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch biomvRCNS_1.6.0.tar.gz
StartedAt: 2015-04-09 23:10:35 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:18:57 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 502.2 seconds
RetCode: 0
Status:  OK 
CheckDir: biomvRCNS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch biomvRCNS_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/biomvRCNS.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biomvRCNS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘biomvRCNS’ version ‘1.6.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘biomvRCNS’ can be installed ... [44s/47s] OK
* checking installed package size ... OK
* 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
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘cluster’ ‘dynamicTreeCut’ ‘GenomicFeatures’ ‘parallel’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
biomvRhsmm: no visible binding for global variable ‘mclapply’
biomvRhsmm : <anonymous> : <anonymous>: no visible global function
  definition for ‘DataFrame’
biomvRhsmm : <anonymous> : <anonymous>: no visible global function
  definition for ‘Rle’
biomvRhsmm: no visible global function definition for ‘DataFrame’
biomvRhsmm: no visible binding for global variable ‘DataFrame’
biomvRmgmr: no visible global function definition for ‘seqlevels<-’
biomvRmgmr: no visible global function definition for ‘DataFrame’
biomvRseg: no visible global function definition for ‘seqlevels<-’
biomvRseg: no visible global function definition for ‘DataFrame’
estEmis: no visible global function definition for ‘clara’
hsmmRun: no visible global function definition for ‘Rle’
hsmmRun : <anonymous>: no visible global function definition for ‘Rle’
hsmmRun: no visible global function definition for ‘seqlevels<-’
maxGapminRun: no visible global function definition for ‘Rle’
maxGapminRun: no visible global function definition for ‘runValue’
preClustGrp: no visible global function definition for ‘cutreeDynamic’
regionSegAlphaNB: no visible global function definition for ‘mclapply’
regionSegCost: no visible global function definition for ‘mclapply’
simSegData: no visible global function definition for ‘runValue’
simSegData: no visible global function definition for ‘Rle’
sojournAnno: no visible global function definition for ‘transcripts’
sojournAnno: no visible global function definition for ‘seqlengths’
sojournAnno: no visible global function definition for ‘exons’
sojournAnno: no visible global function definition for
  ‘intronsByTranscript’
splitFarNeighbouryhat: no visible global function definition for
  ‘runValue’
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [44s/39s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
biomvRhsmm 5.731  0.647    7.73
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/biomvRCNS.Rcheck/00check.log’
for details.

biomvRCNS.Rcheck/00install.out:

* installing *source* package ‘biomvRCNS’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c biomvRCNS.c -o biomvRCNS.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o biomvRCNS.so biomvRCNS.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/biomvRCNS.Rcheck/biomvRCNS/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (biomvRCNS)

biomvRCNS.Rcheck/biomvRCNS-Ex.timings:

nameusersystemelapsed
biomvRCNS-class0.0020.0000.001
biomvRGviz3.4820.0513.534
biomvRhsmm5.7310.6477.730
biomvRmgmr1.1100.0181.129
biomvRseg4.1970.0364.235
hsmmRun0.1340.0020.136
maxGapminRun0.0060.0000.006
regionSegAlphaNB0.1420.0010.144
regionSegCost0.0020.0010.002
simSegData0.0060.0020.009
sojournAnno0.0910.0020.093
splitFarNeighbour0.0020.0000.002