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BioC 3.0: CHECK report for CNVrd2 on moscato1

This page was generated on 2015-04-10 09:49:50 -0700 (Fri, 10 Apr 2015).

Package 181/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNVrd2 1.4.0
Hoang Tan Nguyen
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/CNVrd2
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: CNVrd2
Version: 1.4.0
Command: rm -rf CNVrd2.buildbin-libdir CNVrd2.Rcheck && mkdir CNVrd2.buildbin-libdir CNVrd2.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CNVrd2.buildbin-libdir CNVrd2_1.4.0.tar.gz >CNVrd2.Rcheck\00install.out 2>&1 && cp CNVrd2.Rcheck\00install.out CNVrd2-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=CNVrd2.buildbin-libdir --install="check:CNVrd2-install.out" --force-multiarch --no-vignettes --timings CNVrd2_1.4.0.tar.gz
StartedAt: 2015-04-09 23:58:19 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-10 00:05:02 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 403.0 seconds
RetCode: 0
Status:  OK  
CheckDir: CNVrd2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CNVrd2.buildbin-libdir CNVrd2.Rcheck && mkdir CNVrd2.buildbin-libdir CNVrd2.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CNVrd2.buildbin-libdir CNVrd2_1.4.0.tar.gz >CNVrd2.Rcheck\00install.out 2>&1 && cp CNVrd2.Rcheck\00install.out CNVrd2-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=CNVrd2.buildbin-libdir --install="check:CNVrd2-install.out" --force-multiarch --no-vignettes --timings CNVrd2_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/CNVrd2.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CNVrd2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNVrd2' version '1.4.0'
* 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 'CNVrd2' can be installed ... 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
* 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
** 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 ... 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
Namespaces in Imports field not imported from:
  'DNAcopy' 'Rsamtools'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'VariantAnnotation' 'ggplot2' 'gridExtra' 'methods' 'parallel'
  'rjags'
  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
calculateLDSNPandCNV: no visible global function definition for
  'TabixFile'
calculateLDSNPandCNV : readChunkVCF: no visible global function
  definition for 'GRanges'
calculateLDSNPandCNV : readChunkVCF: no visible global function
  definition for 'readVcf'
calculateLDSNPandCNV : readChunkVCF: no visible global function
  definition for 'geno'
calculateLDSNPandCNV: no visible global function definition for
  'mclapply'
groupBayesianCNVs: no visible global function definition for
  'jags.model'
groupBayesianCNVs: no visible global function definition for
  'coda.samples'
* 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' ... [18s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
calculateLDSNPandCNV 4.28   0.84    5.29
** running examples for arch 'x64' ... [26s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
calculateLDSNPandCNV 5.99   1.12    7.32
* 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
  'D:/biocbld/bbs-3.0-bioc/meat/CNVrd2.Rcheck/00check.log'
for details.

CNVrd2.Rcheck/00install.out:


install for i386

* installing *source* package 'CNVrd2' ...
** 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 'CNVrd2' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNVrd2' as CNVrd2_1.4.0.zip
* DONE (CNVrd2)

CNVrd2.Rcheck/examples_i386/CNVrd2-Ex.timings:

nameusersystemelapsed
CNVrd2-class000
calculateLDSNPandCNV4.280.845.29
clusteringCNVs-class0.010.000.02
countReadInWindow-methods000
countReadInWindow000
emnormalCNV0.190.000.19
groupBayesianCNVs000
groupCNVs0.130.020.14
identifyPolymorphicRegion000
plotCNVrd20.060.000.06
plotPolymorphicRegion000
segmentSamples0.010.000.01

CNVrd2.Rcheck/examples_x64/CNVrd2-Ex.timings:

nameusersystemelapsed
CNVrd2-class000
calculateLDSNPandCNV5.991.127.32
clusteringCNVs-class000
countReadInWindow-methods000
countReadInWindow000
emnormalCNV0.140.000.14
groupBayesianCNVs000
groupCNVs0.110.020.12
identifyPolymorphicRegion000
plotCNVrd20.060.000.06
plotPolymorphicRegion000
segmentSamples000