ncdfFlow 1.5.14
M. Jiang
| Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ncdfFlow | | Last Changed Rev: 72511 / Revision: 72575 | | Last Changed Date: 2013-01-14 12:17:57 -0800 (Mon, 14 Jan 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | ERROR | skipped | |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | [ ERROR ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | ERROR | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | ERROR | skipped | skipped |
* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/ncdfFlow.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.5.14’
* 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 ‘ncdfFlow’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 for unstated 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 ... OK
* 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 ... WARNING
Warning: parse error in file ‘ncdfFlow-Ex.R’:
1: unexpected symbol
90: GvHD <- GvHD[pData(GvHD)$Patient
91: nc1
^
* checking line endings in C/C++/Fortran sources/headers ... WARNING
Found the following sources/headers with CR or CRLF line endings:
src/trimmed_netcdf-4.2.1.1/include/ncaux.h
src/trimmed_netcdf-4.2.1.1/libdispatch/ncaux.c
Some Unix compilers require LF line endings.
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... ERROR
Running examples in ‘ncdfFlow-Ex.R’ failed
The error most likely occurred in:
> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ncdfFlowList-class
> ### Title: 'ncdfFlowList': a class that stores multiple ncdfFlowSet objects
> ### Aliases: ncdfFlowList ncdfFlowList-class show,ncdfFlowList-method
> ### rbind2,ncdfFlowList-method rbind2,ncdfFlowList,ANY-method
> ### Keywords: classes
>
> ### ** Examples
>
> data(GvHD)
> GvHD <- GvHD[pData(GvHD)$Patient
+ nc1<-ncdfFlowSet(GvHD)
Error: unexpected symbol in:
"GvHD <- GvHD[pData(GvHD)$Patient
nc1"
Execution halted
* installing *source* package ‘ncdfFlow’ ...
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
untarring netcdf include tree...
configure: compiling netcdf library...
configure: Using the following compilation and linking flags for ncdfFlow
configure: PKG_CPPFLAGS=
configure: PKG_LIBS=trimmed_netcdf-4.2.1.1/build/*.o -L/usr/lib64 -L/usr/local/lib64 -lhdf5 -lhdf5_hl -L/usr/local/lib64
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c bitOps.c -o bitOps.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c netCDF.c -o netCDF.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o ncdfFlow.so bitOps.o init.o netCDF.o trimmed_netcdf-4.2.1.1/build/attr.o trimmed_netcdf-4.2.1.1/build/datt.o trimmed_netcdf-4.2.1.1/build/dattget.o trimmed_netcdf-4.2.1.1/build/dattinq.o trimmed_netcdf-4.2.1.1/build/dattput.o trimmed_netcdf-4.2.1.1/build/dcompound.o trimmed_netcdf-4.2.1.1/build/dcopy.o trimmed_netcdf-4.2.1.1/build/ddim.o trimmed_netcdf-4.2.1.1/build/ddispatch.o trimmed_netcdf-4.2.1.1/build/denum.o trimmed_netcdf-4.2.1.1/build/derror.o trimmed_netcdf-4.2.1.1/build/dfile.o trimmed_netcdf-4.2.1.1/build/dgroup.o trimmed_netcdf-4.2.1.1/build/dim.o trimmed_netcdf-4.2.1.1/build/dnclog.o trimmed_netcdf-4.2.1.1/build/dopaque.o trimmed_netcdf-4.2.1.1/build/dparallel.o trimmed_netcdf-4.2.1.1/build/dstring.o trimmed_netcdf-4.2.1.1/build/dsubstrate.o trimmed_netcdf-4.2.1.1/build/dtype.o trimmed_netcdf-4.2.1.1/build/dutf8proc.o trimmed_netcdf-4.2.1.1/build/dv2i.o trimmed_netcdf-4.2.1.1/build/dvar.o trimmed_netcdf-4.2.1.1/build/dvarget.o trimmed_netcdf-4.2.1.1/build/dvarinq.o trimmed_netcdf-4.2.1.1/build/dvarput.o trimmed_netcdf-4.2.1.1/build/dvlen.o trimmed_netcdf-4.2.1.1/build/error4.o trimmed_netcdf-4.2.1.1/build/lookup3.o trimmed_netcdf-4.2.1.1/build/memio.o trimmed_netcdf-4.2.1.1/build/mmapio.o trimmed_netcdf-4.2.1.1/build/nc.o trimmed_netcdf-4.2.1.1/build/nc3dispatch.o trimmed_netcdf-4.2.1.1/build/nc4attr.o trimmed_netcdf-4.2.1.1/build/nc4dim.o trimmed_netcdf-4.2.1.1/build/nc4dispatch.o trimmed_netcdf-4.2.1.1/build/nc4file.o trimmed_netcdf-4.2.1.1/build/nc4grp.o trimmed_netcdf-4.2.1.1/build/nc4hdf.o trimmed_netcdf-4.2.1.1/build/nc4internal.o trimmed_netcdf-4.2.1.1/build/nc4type.o trimmed_netcdf-4.2.1.1/build/nc4var.o trimmed_netcdf-4.2.1.1/build/nc_uri.o trimmed_netcdf-4.2.1.1/build/ncaux.o trimmed_netcdf-4.2.1.1/build/ncbytes.o trimmed_netcdf-4.2.1.1/build/ncfunc.o trimmed_netcdf-4.2.1.1/build/nchashmap.o trimmed_netcdf-4.2.1.1/build/ncio.o trimmed_netcdf-4.2.1.1/build/nclist.o trimmed_netcdf-4.2.1.1/build/nclistmgr.o trimmed_netcdf-4.2.1.1/build/nctime.o trimmed_netcdf-4.2.1.1/build/ncx.o trimmed_netcdf-4.2.1.1/build/posixio.o trimmed_netcdf-4.2.1.1/build/putget.o trimmed_netcdf-4.2.1.1/build/stub.o trimmed_netcdf-4.2.1.1/build/v1hpg.o trimmed_netcdf-4.2.1.1/build/var.o -L/usr/lib64 -L/usr/local/lib64 -lhdf5 -lhdf5_hl -L/usr/local/lib64 -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/ncdfFlow.Rcheck/ncdfFlow/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘ncdfFlow.Rnw’
** testing if installed package can be loaded
* DONE (ncdfFlow)