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BioC 3.0: CHECK report for ADaCGH2 on moscato1

This page was generated on 2015-04-10 09:46:42 -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: rm -rf ADaCGH2.buildbin-libdir ADaCGH2.Rcheck && mkdir ADaCGH2.buildbin-libdir ADaCGH2.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ADaCGH2.buildbin-libdir ADaCGH2_2.6.0.tar.gz >ADaCGH2.Rcheck\00install.out 2>&1 && cp ADaCGH2.Rcheck\00install.out ADaCGH2-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=ADaCGH2.buildbin-libdir --install="check:ADaCGH2-install.out" --force-multiarch --no-vignettes --timings ADaCGH2_2.6.0.tar.gz
StartedAt: 2015-04-09 22:19:22 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 22:26:34 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 432.4 seconds
RetCode: 0
Status:  OK  
CheckDir: ADaCGH2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ADaCGH2.buildbin-libdir ADaCGH2.Rcheck && mkdir ADaCGH2.buildbin-libdir ADaCGH2.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ADaCGH2.buildbin-libdir ADaCGH2_2.6.0.tar.gz >ADaCGH2.Rcheck\00install.out 2>&1 && cp ADaCGH2.Rcheck\00install.out ADaCGH2-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=ADaCGH2.buildbin-libdir --install="check:ADaCGH2-install.out" --force-multiarch --no-vignettes --timings ADaCGH2_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/ADaCGH2.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 '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 whether package 'ADaCGH2' 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
'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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.0-bioc/meat/ADaCGH2.buildbin-libdir/ADaCGH2/libs/i386/ADaCGH2.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.0-bioc/meat/ADaCGH2.buildbin-libdir/ADaCGH2/libs/x64/ADaCGH2.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [80s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
pSegment           12.19   0.04   32.23
pChromPlot         10.71   0.03   12.41
outputToCGHregions  9.57   0.07   15.46
inputToADaCGH       1.98   0.03   12.66
** running examples for arch 'x64' ... [92s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
pSegment           14.87   0.06   35.35
outputToCGHregions 11.73   0.03   18.75
pChromPlot         11.37   0.08   18.50
inputToADaCGH       2.84   0.03   11.33
* 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 3 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/ADaCGH2.Rcheck/00check.log'
for details.

ADaCGH2.Rcheck/00install.out:


install for i386

* installing *source* package 'ADaCGH2' ...
** libs
gcc -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -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 -m32 -shared -s -static-libgcc -o ADaCGH2.dll tmp.def init.o r_haarseg.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/ADaCGH2.buildbin-libdir/ADaCGH2/libs/i386
** 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?)

install for x64

* installing *source* package 'ADaCGH2' ...
** libs
gcc -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -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 -m64 -shared -s -static-libgcc -o ADaCGH2.dll tmp.def init.o r_haarseg.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/ADaCGH2.buildbin-libdir/ADaCGH2/libs/x64
** 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?)
* MD5 sums
packaged installation of 'ADaCGH2' as ADaCGH2_2.6.0.zip
* DONE (ADaCGH2)

ADaCGH2.Rcheck/examples_i386/ADaCGH2-Ex.timings:

nameusersystemelapsed
cutFile000
inputToADaCGH 1.98 0.0312.66
outputToCGHregions 9.57 0.0715.46
pChromPlot10.71 0.0312.41
pSegment12.19 0.0432.23

ADaCGH2.Rcheck/examples_x64/ADaCGH2-Ex.timings:

nameusersystemelapsed
cutFile0.020.000.01
inputToADaCGH 2.84 0.0311.33
outputToCGHregions11.73 0.0318.75
pChromPlot11.37 0.0818.50
pSegment14.87 0.0635.35