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 2.12: CHECK report for ADaCGH2 on george2

This page was generated on 2013-10-09 09:37:40 -0700 (Wed, 09 Oct 2013).

Package 10/671HostnameOS / ArchBUILDCHECKBUILD BIN
ADaCGH2 1.10.0
Ramon Diaz-Uriarte
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/ADaCGH2
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: ADaCGH2
Version: 1.10.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings ADaCGH2_1.10.0.tar.gz
StartedAt: 2013-10-08 23:51:37 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 23:57:35 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 357.8 seconds
RetCode: 0
Status:  OK 
CheckDir: ADaCGH2.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/ADaCGH2.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ADaCGH2/DESCRIPTION’ ... OK
* this is package ‘ADaCGH2’ version ‘1.10.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  ‘Rmpi’ ‘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 for sufficient/correct file permissions ... OK
* checking whether package ‘ADaCGH2’ can be installed ... [26s/28s] OK
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls with ‘PACKAGE’ argument in a different package:
  .Fortran("fndcpt", ..., PACKAGE = "DNAcopy")
  .Fortran("wfindcpt", ..., PACKAGE = "DNAcopy")
See the chapter ‘System and foreign language interfaces’ of the
‘Writing R Extensions’ manual.
* checking R code for possible problems ... NOTE
mpi.clean.quit.Web: no visible global function definition for
  ‘mpi.comm.size’
mpi.clean.quit.Web: no visible global function definition for
  ‘mpi.close.Rslaves’
mpi.clean.quit.Web: no visible global function definition for
  ‘mpi.exit’
snowfallInit: no visible global function definition for
  ‘mpi.universe.size’
* 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [27s/125s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
outputToCGHregions    4.093  0.120  25.521
pSegment              3.796  0.140  33.794
pChromPlot            3.088  0.084  23.423
inputDataToADaCGHData 2.368  0.008   9.400
snowfallInit          0.116  0.044  18.400
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/ADaCGH2.Rcheck/00check.log’
for details.

ADaCGH2.Rcheck/00install.out:

* installing *source* package ‘ADaCGH2’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c r_haarseg.c -o r_haarseg.o
r_haarseg.c: In function ‘ad_HaarConv’:
r_haarseg.c:65:12: warning: unused variable ‘totalNorm’ [-Wunused-variable]
r_haarseg.c: In function ‘ad_FindLocalPeaks’:
r_haarseg.c:152:8: warning: "/*" within comment [-Wcomment]
r_haarseg.c:176:8: warning: "/*" within comment [-Wcomment]
r_haarseg.c:128:9: warning: unused variable ‘j’ [-Wunused-variable]
r_haarseg.c: In function ‘ad_HaarConv’:
r_haarseg.c:97:27: warning: ‘highNonNormed’ may be used uninitialized in this function [-Wuninitialized]
r_haarseg.c:96:26: warning: ‘lowNonNormed’ may be used uninitialized in this function [-Wuninitialized]
r_haarseg.c:99:27: warning: ‘highWeightSum’ may be used uninitialized in this function [-Wuninitialized]
r_haarseg.c:98:26: warning: ‘lowWeightSum’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -shared -L/usr/local/lib -o ADaCGH2.so r_haarseg.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/ADaCGH2.Rcheck/ADaCGH2/libs
** R
** data
** inst
** preparing package for lazy loading
Setting adacgh_changepoints to DNAcopy:::changepoints
Setting adacgh_trimmed.variance to DNAcopy:::trimmed.variance
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ADaCGH2)

ADaCGH2.Rcheck/ADaCGH2-Ex.timings:

nameusersystemelapsed
inputDataToADaCGHData2.3680.0089.400
outputToCGHregions 4.093 0.12025.521
pChromPlot 3.088 0.08423.423
pSegment 3.796 0.14033.794
snowfallInit 0.116 0.04418.400