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BioC 3.0: CHECK report for SomatiCA on moscato1

This page was generated on 2015-04-10 09:48:36 -0700 (Fri, 10 Apr 2015).

Package 840/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SomatiCA 1.10.0
Mengjie Chen
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/SomatiCA
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  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: SomatiCA
Version: 1.10.0
Command: rm -rf SomatiCA.buildbin-libdir SomatiCA.Rcheck && mkdir SomatiCA.buildbin-libdir SomatiCA.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SomatiCA.buildbin-libdir SomatiCA_1.10.0.tar.gz >SomatiCA.Rcheck\00install.out 2>&1 && cp SomatiCA.Rcheck\00install.out SomatiCA-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=SomatiCA.buildbin-libdir --install="check:SomatiCA-install.out" --force-multiarch --no-vignettes --timings SomatiCA_1.10.0.tar.gz
StartedAt: 2015-04-10 05:47:40 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 05:53:04 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 323.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: SomatiCA.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SomatiCA.buildbin-libdir SomatiCA.Rcheck && mkdir SomatiCA.buildbin-libdir SomatiCA.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SomatiCA.buildbin-libdir SomatiCA_1.10.0.tar.gz >SomatiCA.Rcheck\00install.out 2>&1 && cp SomatiCA.Rcheck\00install.out SomatiCA-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=SomatiCA.buildbin-libdir --install="check:SomatiCA-install.out" --force-multiarch --no-vignettes --timings SomatiCA_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/SomatiCA.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 'SomatiCA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SomatiCA' version '1.10.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'SomatiCAData'

Depends: includes the non-default packages:
  'lars' 'DNAcopy' 'foreach' 'rebmix' 'GenomicRanges' 'IRanges'
  'doParallel'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'SomatiCA' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import by 'IRanges::sd' when loading 'SomatiCA'
See 'D:/biocbld/bbs-3.0-bioc/meat/SomatiCA.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'foreach' 'lars' 'DNAcopy' 'methods' 'rebmix' 'GenomicRanges' 'IRanges' 'sn'
A package should be listed in only one of these fields.
* 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
'library' or 'require' calls to packages already attached by Depends:
  'DNAcopy' 'doParallel' 'foreach' 'lars' 'rebmix'
  Please remove these calls from your code.
'library' or 'require' call to 'sn' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Package in Depends field not imported from: 'methods'
  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
refineSegment: no visible global function definition for 'sn.mle'
somaticRatio: no visible global function definition for 'sn.mle'
* 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' ... [63s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
SomatiCApipe  24.49   0.02   24.66
admixtureRate 21.84   0.01   21.86
** running examples for arch 'x64' ... [75s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
SomatiCApipe  30.08   0.04   30.57
admixtureRate 27.80   0.00   27.80
* 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

WARNING: There was 1 warning.
NOTE: There were 4 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/SomatiCA.Rcheck/00check.log'
for details.

SomatiCA.Rcheck/00install.out:


install for i386

* installing *source* package 'SomatiCA' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by 'IRanges::sd' when loading 'SomatiCA'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by 'IRanges::sd' when loading 'SomatiCA'

install for x64

* installing *source* package 'SomatiCA' ...
** testing if installed package can be loaded
Warning: replacing previous import by 'IRanges::sd' when loading 'SomatiCA'
* MD5 sums
packaged installation of 'SomatiCA' as SomatiCA_1.10.0.zip
* DONE (SomatiCA)

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

nameusersystemelapsed
GCbiasRemoval2.800.002.81
GCcount000
MergeSegment0.130.000.12
SomatiCA-package1.400.031.47
SomatiCAUsersGuide000
SomatiCApipe24.49 0.0224.66
admixtureRate21.84 0.0121.86
collapse000
copynumberCorrected0.030.000.03
denoise0.080.000.07
larsCBSsegment0.760.030.82
plotSegment0.140.030.17
plotSubclonality0.140.040.17
refineSegment0.460.000.45
segmentGCbiasRemoval2.650.012.66
somaticRatio0.210.000.21
subclonality1.940.031.97

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

nameusersystemelapsed
GCbiasRemoval3.650.023.66
GCcount000
MergeSegment0.150.020.17
SomatiCA-package1.170.001.19
SomatiCAUsersGuide000
SomatiCApipe30.08 0.0430.57
admixtureRate27.8 0.027.8
collapse0.010.000.02
copynumberCorrected0.050.000.05
denoise0.160.020.17
larsCBSsegment1.230.061.31
plotSegment0.090.080.36
plotSubclonality0.160.010.17
refineSegment0.560.000.56
segmentGCbiasRemoval1.580.021.59
somaticRatio0.140.000.14
subclonality1.420.021.44