Back to the "Multiple platform build/check report" A  B [C] D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.2: CHECK report for CGHcall on moscato1

This page was generated on 2016-04-23 10:16:24 -0700 (Sat, 23 Apr 2016).

Package 154/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CGHcall 2.32.0
Mark van de Wiel
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/CGHcall
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CGHcall
Version: 2.32.0
Command: rm -rf CGHcall.buildbin-libdir CGHcall.Rcheck && mkdir CGHcall.buildbin-libdir CGHcall.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CGHcall.buildbin-libdir CGHcall_2.32.0.tar.gz >CGHcall.Rcheck\00install.out 2>&1 && cp CGHcall.Rcheck\00install.out CGHcall-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=CGHcall.buildbin-libdir --install="check:CGHcall-install.out" --force-multiarch --no-vignettes --timings CGHcall_2.32.0.tar.gz
StartedAt: 2016-04-23 00:27:49 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 00:29:32 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 103.1 seconds
RetCode: 0
Status:  OK  
CheckDir: CGHcall.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CGHcall.buildbin-libdir CGHcall.Rcheck && mkdir CGHcall.buildbin-libdir CGHcall.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CGHcall.buildbin-libdir CGHcall_2.32.0.tar.gz >CGHcall.Rcheck\00install.out 2>&1 && cp CGHcall.Rcheck\00install.out CGHcall-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=CGHcall.buildbin-libdir --install="check:CGHcall-install.out" --force-multiarch --no-vignettes --timings CGHcall_2.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/CGHcall.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CGHcall/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CGHcall' version '2.32.0'
* 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 'CGHcall' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Non-standard license specification:
  GPL (http://www.gnu.org/copyleft/gpl.html)
Standardizable: FALSE
* 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
'library' or 'require' call to 'snowfall' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'DNAcopy' 'methods' 'snowfall'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'DNAcopy:::getbdry'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'Biobase:::assayDataDims' 'DNAcopy:::trimmed.variance'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.MakeData' '.alpha0all' '.assignNames' '.callFromSeg' '.countcl'
  '.posteriorp' '.reallik4' '.segFromRaw' '.sumreg' '.sumsqreg'
  '.totallik' '.varproffun' '.varregtimescount'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Fortran("fndcpt", ..., PACKAGE = "DNAcopy")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
.changepoints2: no visible global function definition for
  'changepoints.prune'
.segment2: no visible binding for global variable
  'default.DNAcopy.bdry'
.totallik: no visible global function definition for 'sfExport'
.totallik: no visible global function definition for 'sfSapply'
CGHcall: no visible global function definition for 'sfInit'
CGHcall: no visible global function definition for 'sfLibrary'
CGHcall: no visible global function definition for 'sfExport'
CGHcall: no visible global function definition for 'sfRemoveAll'
CGHcall: no visible global function definition for 'sfStop'
* 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' ... [7s] OK
** running examples for arch 'x64' ... [4s] OK
* 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: 4 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/CGHcall.Rcheck/00check.log'
for details.


CGHcall.Rcheck/00install.out:


install for i386

* installing *source* package 'CGHcall' ...
** 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 'CGHcall' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CGHcall' as CGHcall_2.32.0.zip
* DONE (CGHcall)

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

nameusersystemelapsed
CGHcall0.440.000.44
ExpandCGHcall0.270.000.26
normalize0.250.010.27
postsegnormalize0.220.000.22
preprocess0.080.001.34
segmentData0.010.021.92

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

nameusersystemelapsed
CGHcall0.370.000.40
ExpandCGHcall0.250.000.25
normalize0.300.001.08
postsegnormalize0.230.020.25
preprocess0.050.000.05
segmentData0.030.000.03