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BioC 3.2: CHECK report for ncdfFlow on moscato1

This page was generated on 2016-04-23 10:18:11 -0700 (Sat, 23 Apr 2016).

Package 697/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ncdfFlow 2.16.1
Mike Jiang
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/ncdfFlow
Last Changed Rev: 112037 / Revision: 116712
Last Changed Date: 2015-12-30 14:46:39 -0800 (Wed, 30 Dec 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ncdfFlow
Version: 2.16.1
Command: rm -rf ncdfFlow.buildbin-libdir ncdfFlow.Rcheck && mkdir ncdfFlow.buildbin-libdir ncdfFlow.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ncdfFlow.buildbin-libdir ncdfFlow_2.16.1.tar.gz >ncdfFlow.Rcheck\00install.out 2>&1 && cp ncdfFlow.Rcheck\00install.out ncdfFlow-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=ncdfFlow.buildbin-libdir --install="check:ncdfFlow-install.out" --force-multiarch --no-vignettes --timings ncdfFlow_2.16.1.tar.gz
StartedAt: 2016-04-23 05:17:42 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 05:30:38 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 775.5 seconds
RetCode: 0
Status:  OK  
CheckDir: ncdfFlow.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ncdfFlow.buildbin-libdir ncdfFlow.Rcheck && mkdir ncdfFlow.buildbin-libdir ncdfFlow.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ncdfFlow.buildbin-libdir ncdfFlow_2.16.1.tar.gz >ncdfFlow.Rcheck\00install.out 2>&1 && cp ncdfFlow.Rcheck\00install.out ncdfFlow-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=ncdfFlow.buildbin-libdir --install="check:ncdfFlow-install.out" --force-multiarch --no-vignettes --timings ncdfFlow_2.16.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/ncdfFlow.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ncdfFlow/DESCRIPTION' ... OK
* this is package 'ncdfFlow' version '2.16.1'
* 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 'ncdfFlow' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
* 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
* 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
* 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 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 ... 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-3.2-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/libs/i386/libhdf5ForBioC-7.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.2-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/libs/x64/libhdf5ForBioC-7.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.2-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/libs/i386/libsz-2.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.2-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/libs/x64/libsz-2.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.2-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/libs/i386/ncdfFlow.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.2-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/libs/x64/ncdfFlow.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' ... [31s] OK
** running examples for arch 'x64' ... [33s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
ncfsApply-ncdfFlowSet-method 1.59      0    5.17
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'run-all.R' [15s]
 [16s] OK
** running tests for arch 'x64' ...
  Running 'run-all.R' [19s]
 [19s] 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: 5 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/ncdfFlow.Rcheck/00check.log'
for details.

ncdfFlow.Rcheck/00install.out:


install for i386

* installing *source* package 'ncdfFlow' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
cp includeWin/i386/* includeWin/
cp libwin/i386/*.dll .
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/RcppArmadillo/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/BH/include" -I"d:/RCompile/r-compiling/local/local323/include"  -IincludeWin -DWINDOWS   -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/RcppArmadillo/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/BH/include" -I"d:/RCompile/r-compiling/local/local323/include"  -IincludeWin -DWINDOWS   -O2 -Wall  -mtune=core2 -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]
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/RcppArmadillo/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/BH/include" -I"d:/RCompile/r-compiling/local/local323/include"  -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c hdfFlow.c -o hdfFlow.o
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/RcppArmadillo/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/BH/include" -I"d:/RCompile/r-compiling/local/local323/include"  -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/RcppArmadillo/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/BH/include" -I"d:/RCompile/r-compiling/local/local323/include"  -IincludeWin -DWINDOWS   -O2 -Wall  -mtune=core2 -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]
readFrame.cpp:237:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readFrame.cpp: In function 'Rcpp::S4 readFrame(Rcpp::S4, Rcpp::RObject, Rcpp::RObject, bool)':
readFrame.cpp:379:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -shared -s -static-libgcc -o ncdfFlow.dll tmp.def RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o -L. -llibhdf5ForBioC-7 -Ld:/RCompile/r-compiling/local/local323/lib/i386 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/libs/i386
** 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

install for x64

* installing *source* package 'ncdfFlow' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
cp includeWin/x64/* includeWin/
cp libwin/x64/*.dll .
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/RcppArmadillo/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/BH/include" -I"d:/RCompile/r-compiling/local/local323/include"  -IincludeWin -DWINDOWS   -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/RcppArmadillo/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/BH/include" -I"d:/RCompile/r-compiling/local/local323/include"  -IincludeWin -DWINDOWS   -O2 -Wall  -mtune=core2 -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]
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/RcppArmadillo/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/BH/include" -I"d:/RCompile/r-compiling/local/local323/include"  -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c hdfFlow.c -o hdfFlow.o
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/RcppArmadillo/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/BH/include" -I"d:/RCompile/r-compiling/local/local323/include"  -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/RcppArmadillo/include" -I"D:/biocbld/bbs-3.2-bioc/R/library/BH/include" -I"d:/RCompile/r-compiling/local/local323/include"  -IincludeWin -DWINDOWS   -O2 -Wall  -mtune=core2 -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]
readFrame.cpp:237:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -shared -s -static-libgcc -o ncdfFlow.dll tmp.def RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o -L. -llibhdf5ForBioC-7 -Ld:/RCompile/r-compiling/local/local323/lib/x64 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ncdfFlow' as ncdfFlow_2.16.1.zip
* DONE (ncdfFlow)

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

nameusersystemelapsed
Indices1.970.054.75
as.flowSet1.340.061.40
clone.ncdfFlowSet0.620.004.80
extractFlowFrame1.110.051.56
ncdfFlowList-class1.140.001.14
ncdfFlowSet-constructor1.070.061.14
ncfsApply-ncdfFlowSet-method1.250.061.50
rbind2-method1.480.053.74
read.ncdfFlowSet0.570.000.57
replacement-method-for-ncdfFlowSet1.140.052.05
save_ncfs000
subset-methods1.150.021.19
unlink-ncdfFlowSet-method1.290.031.32

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

nameusersystemelapsed
Indices2.090.114.41
as.flowSet1.160.031.19
clone.ncdfFlowSet0.500.031.31
extractFlowFrame1.010.031.62
ncdfFlowList-class1.110.003.24
ncdfFlowSet-constructor1.120.001.12
ncfsApply-ncdfFlowSet-method1.590.005.17
rbind2-method1.640.054.12
read.ncdfFlowSet0.480.000.48
replacement-method-for-ncdfFlowSet1.110.033.82
save_ncfs000
subset-methods0.930.050.99
unlink-ncdfFlowSet-method0.770.040.81