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BioC 3.1: CHECK report for ncdfFlow on zin2

This page was generated on 2015-10-09 09:24:47 -0700 (Fri, 09 Oct 2015).

Package 648/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ncdfFlow 2.14.2
Mike Jiang
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/ncdfFlow
Last Changed Rev: 108512 / Revision: 109384
Last Changed Date: 2015-09-14 15:42:01 -0700 (Mon, 14 Sep 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ncdfFlow
Version: 2.14.2
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings ncdfFlow_2.14.2.tar.gz
StartedAt: 2015-10-09 03:55:24 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 03:56:47 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 82.4 seconds
RetCode: 0
Status:  OK 
CheckDir: ncdfFlow.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings ncdfFlow_2.14.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/ncdfFlow.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ncdfFlow/DESCRIPTION’ ... OK
* this is package ‘ncdfFlow’ version ‘2.14.2’
* 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 ... [22s/23s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
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
'library' or 'require' call to ‘parallel’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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
ncdfFlowSet,flowSet : .local: warning in assign(guid, new("flowFrame",
  exprs = matrix(numeric(0), nrow = 0, ncol = 0),
  parameters(x[[guid]]), description(x[[guid]])), env = e1): partial
  argument match of 'env' to 'envir'
rbind2,ncdfFlowList-ANY : .local : <anonymous> : <anonymous>: warning
  in assign(curSample, NA, env = indiceEnv): partial argument match of
  'env' to 'envir'
read.ncdfFlowSet: no visible global function definition for ‘mclapply’
* 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 ... [11s/11s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run-all.R’ [7s/7s]
 [7s/7s] 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

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/ncdfFlow.Rcheck/00check.log’
for details.


ncdfFlow.Rcheck/00install.out:

* installing *source* package ‘ncdfFlow’ ...
configure: No directory was specified for --with-hdf5. Trying to find hdf5 using pkg-config.
checking for pkg-config... /usr/bin/pkg-config
Package hdf5 was not found in the pkg-config search path.
Perhaps you should add the directory containing `hdf5.pc'
to the PKG_CONFIG_PATH environment variable
No package 'hdf5' found
configure: pkg-config was not able to find the hdf5 library.
configure: Trying some common locations."
configure: search for hdf5 library in: /usr/local/lib
configure: search for hdf5 library in: /usr/local/lib64
configure: search for hdf5 library in: /usr/local/lib/x86_64-linux-gnu
configure: search for hdf5 library in: /usr/local/lib64/x86_64-linux-gnu
checking for h5cc... /usr/bin/h5cc
configure: PKG_CPPFLAGS =  
configure: PKG_LIBS = -lhdf5
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c bitOps.cpp -o bitOps.o
bitOps.cpp: In function ‘Rcpp::LogicalVector toLogical(Rcpp::RawVector)’:
bitOps.cpp:23:11: warning: unused variable ‘nByte’ [-Wunused-variable]
  unsigned nByte = bytes.size();
           ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c hdfFlow.c -o hdfFlow.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c init.c -o init.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/BH/include"   -fpic  -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:140:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i = 0; i < chCount; i++){
                  ^
readFrame.cpp:237:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(i = 0; i < chCount; i++){
                   ^
g++ -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o ncdfFlow.so RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o -lhdf5 -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-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
Indices1.2970.0241.342
as.flowSet0.7490.0160.765
clone.ncdfFlowSet0.3680.0000.404
extractFlowFrame0.6920.0120.704
ncdfFlowList-class0.7930.0120.805
ncdfFlowSet-constructor0.7370.0000.736
ncfsApply-ncdfFlowSet-method0.7580.0080.765
rbind2-method1.0460.0081.053
read.ncdfFlowSet0.2750.0120.288
replacement-method-for-ncdfFlowSet0.7900.0080.797
save_ncfs0.0010.0000.000
subset-methods0.6650.0080.674
unlink-ncdfFlowSet-method0.6690.0120.680