BioC 2.13: CHECK report for ncdfFlow on zin1

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/ncdfFlow.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ncdfFlow/DESCRIPTION’ ... OK
* this is package ‘ncdfFlow’ version ‘2.8.22’
* 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 ... [7s/7s] 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
‘:::’ calls which should be ‘::’:
  ‘base:::system.file’ ‘flowCore:::read.FCSheader’
  ‘tools:::file_path_as_absolute’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ‘:::’ calls:
  ‘flowCore:::checkClass’ ‘flowCore:::makeFCSparameters’
  ‘flowCore:::readFCSgetPar’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of 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
addFrame,ncdfFlowSet-flowFrame: no visible binding for global variable
  ‘origData’
pData<-,ncdfFlowList-data.frame : <anonymous>: no visible binding for
  global variable ‘name’
* checking Rd files ... NOTE
prepare_Rd: addFrame-methods.Rd:13-17: Dropping empty section ‘Methods’
* 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 portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12s/12s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
ncdfFlowList-class  5.5  0.088   5.596
* 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 5 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/ncdfFlow.Rcheck/00check.log’
for details.

* 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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/include -I/usr/local/include    -fpic  -g -O2  -Wall -c bitOps.c -o bitOps.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/include -I/usr/local/include    -fpic  -g -O2  -Wall -c hdfFlow.c -o hdfFlow.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/include -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/include -I/usr/local/include    -fpic  -g -O2  -Wall -c wrappers.c -o wrappers.o
wrappers.c: In function ‘writeSlice’:
wrappers.c:49:2: warning: pointer targets in passing argument 4 of ‘_writeSlice’ differ in signedness [-Wpointer-sign]
hdfFlow.h:7:8: note: expected ‘unsigned int *’ but argument is of type ‘int *’
wrappers.c:38:23: warning: variable ‘nCol’ set but not used [-Wunused-but-set-variable]
wrappers.c: In function ‘readSlice’:
wrappers.c:86:14: warning: variable ‘status’ set but not used [-Wunused-but-set-variable]
wrappers.c:64:7: warning: unused variable ‘k’ [-Wunused-variable]
gcc -std=gnu99 -shared -L/usr/local/lib -o ncdfFlow.so bitOps.o hdfFlow.o init.o wrappers.o -L/usr/lib -lhdf5 -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-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)

name	user	system	elapsed
addFrame-methods	0.804	0.004	0.827
clone.ncdfFlowSet	0.676	0.004	0.680
ncdfFlowList-class	5.500	0.088	5.596
ncdfFlowSet-class	1.420	0.048	1.469
read.ncdfFlowSet	0.592	0.040	0.634

BioC 2.13: CHECK report for ncdfFlow on zin1

Summary

Command output