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BioC 3.0: CHECK report for ADaCGH2 on oaxaca

This page was generated on 2015-04-10 10:04:29 -0700 (Fri, 10 Apr 2015).

Package 11/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ADaCGH2 2.6.0
Ramon Diaz-Uriarte
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/ADaCGH2
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: ADaCGH2
Version: 2.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ADaCGH2_2.6.0.tar.gz
StartedAt: 2015-04-09 21:08:55 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 21:12:51 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 236.0 seconds
RetCode: 0
Status:  OK 
CheckDir: ADaCGH2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ADaCGH2_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/ADaCGH2.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ADaCGH2/DESCRIPTION’ ... OK
* this is package ‘ADaCGH2’ version ‘2.6.0’
* 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 ‘ADaCGH2’ can be installed ... [17s/18s] 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' call to ‘Cairo’ in package code.
  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
cutFile: no visible global function definition for ‘detectCores’
distribute: no visible global function definition for ‘clusterApply’
imagemap3: no visible global function definition for ‘CairoPNG’
inputToADaCGH: no visible global function definition for ‘detectCores’
pChromPlot: no visible global function definition for ‘detectCores’
pSegmentBioHMM: no visible global function definition for ‘detectCores’
pSegmentCGHseg: no visible global function definition for ‘detectCores’
pSegmentDNAcopy: no visible global function definition for
  ‘detectCores’
pSegmentGLAD: no visible global function definition for ‘detectCores’
pSegmentHMM: no visible global function definition for ‘detectCores’
pSegmentHaarSeg: no visible global function definition for
  ‘detectCores’
pSegmentWavelets: no visible global function definition for
  ‘detectCores’
* 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 ... [73s/60s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
pChromPlot         15.577  9.683   6.095
pSegment           13.800  4.390  25.848
outputToCGHregions 11.776  2.791  10.942
inputToADaCGH       2.391  0.289   9.559
* 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/ADaCGH2.Rcheck/00check.log’
for details.

ADaCGH2.Rcheck/00install.out:

* installing *source* package ‘ADaCGH2’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c init.c -o init.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c r_haarseg.c -o r_haarseg.o
r_haarseg.c:65:12: warning: unused variable 'totalNorm' [-Wunused-variable]
    double totalNorm;
           ^
r_haarseg.c:152:8: warning: '/*' within block comment [-Wcomment]
                                         }/* for j */
                                          ^
r_haarseg.c:176:8: warning: '/*' within block comment [-Wcomment]
                                         }/* for j */
                                          ^
r_haarseg.c:128:9: warning: unused variable 'j' [-Wunused-variable]
         int k,j;
               ^
4 warnings generated.
clang -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 -o ADaCGH2.so init.o r_haarseg.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/ADaCGH2.Rcheck/ADaCGH2/libs
** R
** data
** inst
** preparing package for lazy loading
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc,  :
  No generic function found corresponding to requested imported methods for "as.list" from package "multtest" (malformed exports?)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc,  :
  No generic function found corresponding to requested imported methods for "as.list" from package "multtest" (malformed exports?)
* DONE (ADaCGH2)

ADaCGH2.Rcheck/ADaCGH2-Ex.timings:

nameusersystemelapsed
cutFile0.0050.0010.005
inputToADaCGH2.3910.2899.559
outputToCGHregions11.776 2.79110.942
pChromPlot15.577 9.683 6.095
pSegment13.800 4.39025.848