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BioC 2.13: CHECK report for GLAD on perceval

This page was generated on 2014-04-05 09:51:42 -0700 (Sat, 05 Apr 2014).

Package 311/750HostnameOS / ArchBUILDCHECKBUILD BIN
GLAD 2.26.0
Philippe Hupe
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/GLAD
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: GLAD
Version: 2.26.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GLAD_2.26.0.tar.gz
StartedAt: 2014-04-05 01:39:39 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 01:40:31 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 52.1 seconds
RetCode: 0
Status:  OK 
CheckDir: GLAD.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/GLAD.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GLAD/DESCRIPTION’ ... OK
* this is package ‘GLAD’ version ‘2.26.0’
* 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 ‘GLAD’ can be installed ... [10s/11s] 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘GLAD/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage("\n")
    packageStartupMessage("######################################################################################\n")
    packageStartupMessage("\n")
    packageStartupMessage("Have fun with GLAD\n")
    packageStartupMessage("\n")
    packageStartupMessage("For smoothing it is possible to use either\n")
    packageStartupMessage("the AWS algorithm (Polzehl and Spokoiny, 2002)\n")
    packageStartupMessage("or the HaarSeg algorithm (Ben-Yaacov and Eldar, Bioinformatics,  2008)\n")
    packageStartupMessage("\n")
    packageStartupMessage("If you use the package with AWS, please cite:\n")
    packageStartupMessage("Hupe et al. (Bioinformatics, 2004) and Polzehl and Spokoiny (2002)\n")
    packageStartupMessage("\n")
    packageStartupMessage("If you use the package with HaarSeg, please cite:\n")
    packageStartupMessage("Hupe et al. (Bioinformatics, 2004) and (Ben-Yaacov and Eldar, Bioinformatics, 2008)\n")
    packageStartupMessage("\n")
    packageStartupMessage("For fast computation it is recommanded to use\n")
    packageStartupMessage("the daglad function with smoothfunc=haarseg\n")
    packageStartupMessage("\n")
    packageStartupMessage("######################################################################################\n")
    packageStartupMessage("\n")
    packageStartupMessage("New options are available in daglad: see help for details.")
    packageStartupMessage("\n")

See section ‘Good practice’ in '?.onAttach'.

arrayPersp.arrayCGH: warning in layout(matrix(c(1, 2), 1, 2), width =
  c(9, 1)): partial argument match of 'width' to 'widths'
arrayPersp.arrayCGH: warning in matrix("green", nr = nrow(z), nc =
  ncol(z)): partial argument match of 'nr' to 'nrow'
arrayPersp.arrayCGH: warning in matrix("green", nr = nrow(z), nc =
  ncol(z)): partial argument match of 'nc' to 'ncol'
arrayPersp.default: warning in layout(matrix(c(1, 2), 1, 2), width =
  c(9, 1)): partial argument match of 'width' to 'widths'
arrayPersp.default: warning in matrix("green", nr = nrow(z), nc =
  ncol(z)): partial argument match of 'nr' to 'nrow'
arrayPersp.default: warning in matrix("green", nr = nrow(z), nc =
  ncol(z)): partial argument match of 'nc' to 'ncol'
chrBreakpoints.profileCGH: no visible global function definition for
  ‘laws’
chrBreakpoints.profileCGH: possible error in aws(y =
  subsetdata[["LogRatio"]], x = x, hinit = hinit, hmax = hmax, sigma2 =
  sigma, NN = FALSE, symmetric = TRUE, ...): unused arguments (x = x,
  hinit = hinit, NN = FALSE, symmetric = TRUE)
chrBreakpoints.profileCGH: possible error in aws(y =
  subsetdata[["LogRatio"]], hinit = hinit, hmax = hmax, sigma2 = sigma,
  symmetric = TRUE, ...): unused arguments (hinit = hinit, symmetric =
  TRUE)
* 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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/Users/biocbuild/bbs-2.13-bioc/meat/GLAD.Rcheck/GLAD/libs/GLAD.so’:
  Found ‘__ZSt4cout’, possibly from ‘std::cout’ (C++)
    Object: ‘glad-utils.o’
  Found ‘_printf’, possibly from ‘printf’ (C)
    Object: ‘chrBreakpoints.o’
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Objects: ‘OutliersGNL.o’, ‘chrBreakpoints.o’, ‘findCluster.o’,
      ‘glad-utils.o’, ‘hclust.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘GLAD.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [6s/6s] 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/GLAD.Rcheck/00check.log’
for details.

GLAD.Rcheck/00install.out:

* installing *source* package ‘GLAD’ ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
GSL has been found on the operating system
operating system: Darwin
configure: creating ./config.status
config.status: creating src/Makevars

src/Makevars file

PKG_LIBS = -L/usr/local/lib -lgsl -lgslcblas -lm  
PKG_CPPFLAGS += -DIS_MAC_OS

** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c BkpInfo.cpp -o BkpInfo.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c HaarSeg.cpp -o HaarSeg.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c MoveBkp.cpp -o MoveBkp.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c OutliersGNL.cpp -o OutliersGNL.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c chrBreakpoints.cpp -o chrBreakpoints.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c cutree.cpp -o cutree.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c daglad.cpp -o daglad.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c distance.cpp -o distance.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c filterBkp.cpp -o filterBkp.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c findCluster.cpp -o findCluster.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c glad-utils.cpp -o glad-utils.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c hclust.cpp -o hclust.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c laws.c -o laws.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c loopRemove.cpp -o loopRemove.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o GLAD.so BkpInfo.o HaarSeg.o MoveBkp.o OutliersGNL.o chrBreakpoints.o cutree.o daglad.o distance.o filterBkp.o findCluster.o glad-utils.o hclust.o laws.o loopRemove.o -L/usr/local/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.13-bioc/meat/GLAD.Rcheck/GLAD/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GLAD)

GLAD.Rcheck/GLAD-Ex.timings:

nameusersystemelapsed
ChrNumeric0.0090.0010.009
ColorBar0.0310.0020.034
arrayCGH0.1070.0080.115
arrayPersp0.0060.0000.007
arrayPlot0.1080.0140.123
as.data.frame.profileCGH0.8260.0220.847
as.profileCGH0.1770.0100.188
bladder0.0310.0060.038
cytoband0.0990.0160.115
daglad1.2350.0411.284
glad0.8870.0390.934
hclust0.0500.0050.056
myPalette0.0660.0040.071
plotProfile1.1160.0391.169
profileCGH0.0880.0150.105
snijders0.0750.0130.090
tkdaglad0.1640.0160.184
veltman0.1740.0680.244