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BioC 3.0: CHECK report for ncdfFlow on perceval

This page was generated on 2015-04-10 09:56:30 -0700 (Fri, 10 Apr 2015).

Package 596/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ncdfFlow 2.12.0
Mike Jiang
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/ncdfFlow
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  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: ncdfFlow
Version: 2.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ncdfFlow_2.12.0.tar.gz
StartedAt: 2015-04-10 04:17:52 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 04:20:43 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 171.1 seconds
RetCode: 0
Status:  OK 
CheckDir: ncdfFlow.Rcheck
Warnings: 0

Command output

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ncdfFlow_2.12.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/ncdfFlow.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ncdfFlow/DESCRIPTION’ ... OK
* this is package ‘ncdfFlow’ version ‘2.12.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... NOTE
Found the following apparent object files/libraries:
  src/libwin/i386/libhdf5ForBioC-7.dll src/libwin/i386/libsz-2.dll
  src/libwin/x64/libhdf5ForBioC-7.dll src/libwin/x64/libsz-2.dll
Object files/libraries should not be included in a source package.
* 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 ‘ncdfFlow’ can be installed ... [31s/35s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘flowCore’ ‘flowViz’
A package should be listed in only one of these fields.
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘BH’ ‘RcppArmadillo’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘flowCore:::makeFCSparameters’ ‘flowCore:::readFCSgetPar’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
pData<-,ncdfFlowList-data.frame : <anonymous>: no visible binding for
  global variable ‘name’
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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 ... [21s/22s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘run-all.R’ [16s/17s]
 [17s/17s] 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

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/ncdfFlow.Rcheck/00check.log’
for details.

ncdfFlow.Rcheck/00install.out:

* installing *source* package ‘ncdfFlow’ ...
configure: search for hdf5 library in: /usr/lib
configure: found hdf5 library in: /usr/lib
configure: creating ./config.status
config.status: creating src/Makevars
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c RcppExports.cpp -o RcppExports.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bitOps.cpp -o bitOps.o
bitOps.cpp: In function ‘Rcpp::LogicalVector toLogical(Rcpp::RawVector)’:
bitOps.cpp:23: warning: unused variable ‘nByte’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c hdfFlow.c -o hdfFlow.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c init.c -o init.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c readFrame.cpp -o readFrame.o
readFrame.cpp: In function ‘Rcpp::NumericVector readSlice_cpp(std::string, std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, unsigned int&)’:
readFrame.cpp:140: warning: comparison between signed and unsigned integer expressions
readFrame.cpp:237: warning: comparison between signed and unsigned integer expressions
readFrame.cpp: In function ‘Rcpp::S4 readFrame(Rcpp::S4, Rcpp::RObject, Rcpp::RObject, bool)’:
readFrame.cpp:373: warning: comparison between signed and unsigned integer expressions
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c wrappers.c -o wrappers.o
wrappers.c: In function ‘readSlice’:
wrappers.c:535: warning: unused variable ‘data_out’
llvm-g++-4.2 -arch x86_64 -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 -L/usr/local/lib -o ncdfFlow.so RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o wrappers.o -L/usr/lib -lhdf5 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/ncdfFlow.Rcheck/ncdfFlow/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘lapply’ from package ‘base’ in package ‘ncdfFlow’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ncdfFlow)

ncdfFlow.Rcheck/ncdfFlow-Ex.timings:

nameusersystemelapsed
as.flowSet2.4750.1593.001
clone.ncdfFlowSet0.5910.0600.738
getIndices-ncdfFlowSet-character-method1.6430.1191.802
ncdfFlowList-class1.4010.0871.492
ncdfFlowSet-constructor1.3170.0971.420
ncfsApply-ncdfFlowSet-method1.6210.0801.760
rbind2-method1.6350.0891.752
read.ncdfFlowSet0.5730.0470.641
replacement-method-for-ncdfFlowSet1.3910.1131.520
save_ncfs0.0010.0000.000
sub-ncdfFlowSet-ANY-method0.9150.0741.057
sub-sub-ncdfFlowSet-ANY-method0.9240.0661.137
unlink-ncdfFlowSet-method0.8750.0640.960