ncdfFlow 1.6.1
M. Jiang
| Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/ncdfFlow | | Last Changed Rev: 78304 / Revision: 81334 | | Last Changed Date: 2013-07-10 16:03:19 -0700 (Wed, 10 Jul 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | N O T S U P P O R T E D |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/ncdfFlow.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.6.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... NOTE
Found the following apparent object files/libraries:
inst/lib/libncdfFlow.so
Object files/libraries should not be included in a source package.
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ncdfFlow’ can be installed ... [29s/30s] OK
* checking installed package size ... NOTE
installed size is 5.1Mb
sub-directories of 1Mb or more:
lib 2.3Mb
libs 2.3Mb
* 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 ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* 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 ... [19s/19s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ncdfFlowList-class 7.281 0.284 7.661
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There were 3 notes.
See
‘/home/biocbuild/bbs-2.12-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: using bundled netcdf4 library
configure: 'found ' trimmed_netcdf-4.2.1.1 ' header sources and tar archive;using what is there.'
configure: Using the following compilation and linking flags for ncdfFlow
configure: PKG_CPPFLAGS=-I/usr/include
configure: PKG_LIBS=-L/usr/lib -lhdf5 -lhdf5_hl
configure: creating ./config.status
config.status: creating src/Makevars
** libs
/home/biocbuild/bbs-2.12-bioc/R/share/make/shlib.mk:6: warning: overriding commands for target `ncdfFlow.so'
Makevars:32: warning: ignoring old commands for target `ncdfFlow.so'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c bitOps.c -o bitOps.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c netCDF.c -o netCDF.o
netCDF.c: In function ‘readSlice’:
netCDF.c:168:61: warning: unused variable ‘failcount’ [-Wunused-variable]
netCDF.c:166:11: warning: unused variable ‘estack’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/liblib/stub.c -o trimmed_netcdf-4.2.1.1/liblib/stub.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/datt.c -o trimmed_netcdf-4.2.1.1/libdispatch/datt.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/dattget.c -o trimmed_netcdf-4.2.1.1/libdispatch/dattget.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/dattinq.c -o trimmed_netcdf-4.2.1.1/libdispatch/dattinq.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/dattput.c -o trimmed_netcdf-4.2.1.1/libdispatch/dattput.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/dcompound.c -o trimmed_netcdf-4.2.1.1/libdispatch/dcompound.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/dcopy.c -o trimmed_netcdf-4.2.1.1/libdispatch/dcopy.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/ddim.c -o trimmed_netcdf-4.2.1.1/libdispatch/ddim.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/ddispatch.c -o trimmed_netcdf-4.2.1.1/libdispatch/ddispatch.o
trimmed_netcdf-4.2.1.1/libdispatch/ddispatch.c:33:20: warning: ‘servers’ defined but not used [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/denum.c -o trimmed_netcdf-4.2.1.1/libdispatch/denum.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/derror.c -o trimmed_netcdf-4.2.1.1/libdispatch/derror.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/dfile.c -o trimmed_netcdf-4.2.1.1/libdispatch/dfile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/dgroup.c -o trimmed_netcdf-4.2.1.1/libdispatch/dgroup.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/dnclog.c -o trimmed_netcdf-4.2.1.1/libdispatch/dnclog.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/dopaque.c -o trimmed_netcdf-4.2.1.1/libdispatch/dopaque.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/dparallel.c -o trimmed_netcdf-4.2.1.1/libdispatch/dparallel.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/dstring.c -o trimmed_netcdf-4.2.1.1/libdispatch/dstring.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/dsubstrate.c -o trimmed_netcdf-4.2.1.1/libdispatch/dsubstrate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/dtype.c -o trimmed_netcdf-4.2.1.1/libdispatch/dtype.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/dutf8proc.c -o trimmed_netcdf-4.2.1.1/libdispatch/dutf8proc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/dv2i.c -o trimmed_netcdf-4.2.1.1/libdispatch/dv2i.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/dvar.c -o trimmed_netcdf-4.2.1.1/libdispatch/dvar.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/dvarget.c -o trimmed_netcdf-4.2.1.1/libdispatch/dvarget.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/dvarinq.c -o trimmed_netcdf-4.2.1.1/libdispatch/dvarinq.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/dvarput.c -o trimmed_netcdf-4.2.1.1/libdispatch/dvarput.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/dvlen.c -o trimmed_netcdf-4.2.1.1/libdispatch/dvlen.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/nc_uri.c -o trimmed_netcdf-4.2.1.1/libdispatch/nc_uri.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/ncaux.c -o trimmed_netcdf-4.2.1.1/libdispatch/ncaux.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/ncbytes.c -o trimmed_netcdf-4.2.1.1/libdispatch/ncbytes.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/nchashmap.c -o trimmed_netcdf-4.2.1.1/libdispatch/nchashmap.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/nclist.c -o trimmed_netcdf-4.2.1.1/libdispatch/nclist.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libdispatch/nctime.c -o trimmed_netcdf-4.2.1.1/libdispatch/nctime.o
trimmed_netcdf-4.2.1.1/libdispatch/nctime.c: In function ‘cdComp2Rel.constprop.7’:
trimmed_netcdf-4.2.1.1/libdispatch/nctime.c:871:15: warning: ‘ndel’ may be used uninitialized in this function [-Wuninitialized]
trimmed_netcdf-4.2.1.1/libdispatch/nctime.c:859:12: warning: ‘delta’ may be used uninitialized in this function [-Wuninitialized]
trimmed_netcdf-4.2.1.1/libdispatch/nctime.c: In function ‘cdRel2Comp’:
trimmed_netcdf-4.2.1.1/libdispatch/nctime.c:1066:8: warning: ‘delta’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libsrc/attr.c -o trimmed_netcdf-4.2.1.1/libsrc/attr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libsrc/dim.c -o trimmed_netcdf-4.2.1.1/libsrc/dim.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libsrc/lookup3.c -o trimmed_netcdf-4.2.1.1/libsrc/lookup3.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libsrc/memio.c -o trimmed_netcdf-4.2.1.1/libsrc/memio.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libsrc/nc.c -o trimmed_netcdf-4.2.1.1/libsrc/nc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libsrc/nc3dispatch.c -o trimmed_netcdf-4.2.1.1/libsrc/nc3dispatch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libsrc/ncio.c -o trimmed_netcdf-4.2.1.1/libsrc/ncio.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libsrc/nclistmgr.c -o trimmed_netcdf-4.2.1.1/libsrc/nclistmgr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libsrc/ncx.c -o trimmed_netcdf-4.2.1.1/libsrc/ncx.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libsrc/posixio.c -o trimmed_netcdf-4.2.1.1/libsrc/posixio.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libsrc/putget.c -o trimmed_netcdf-4.2.1.1/libsrc/putget.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libsrc/v1hpg.c -o trimmed_netcdf-4.2.1.1/libsrc/v1hpg.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libsrc/var.c -o trimmed_netcdf-4.2.1.1/libsrc/var.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libsrc4/error4.c -o trimmed_netcdf-4.2.1.1/libsrc4/error4.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libsrc4/nc4attr.c -o trimmed_netcdf-4.2.1.1/libsrc4/nc4attr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libsrc4/nc4dim.c -o trimmed_netcdf-4.2.1.1/libsrc4/nc4dim.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libsrc4/nc4dispatch.c -o trimmed_netcdf-4.2.1.1/libsrc4/nc4dispatch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libsrc4/nc4file.c -o trimmed_netcdf-4.2.1.1/libsrc4/nc4file.o
trimmed_netcdf-4.2.1.1/libsrc4/nc4file.c: In function ‘NC4_inq’:
trimmed_netcdf-4.2.1.1/libsrc4/nc4file.c:3145:11: warning: unused variable ‘found’ [-Wunused-variable]
trimmed_netcdf-4.2.1.1/libsrc4/nc4file.c: In function ‘read_dataset’:
trimmed_netcdf-4.2.1.1/libsrc4/nc4file.c:814:48: warning: ‘t’ may be used uninitialized in this function [-Wuninitialized]
trimmed_netcdf-4.2.1.1/libsrc4/nc4file.c:724:8: note: ‘t’ was declared here
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libsrc4/nc4grp.c -o trimmed_netcdf-4.2.1.1/libsrc4/nc4grp.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libsrc4/nc4hdf.c -o trimmed_netcdf-4.2.1.1/libsrc4/nc4hdf.o
trimmed_netcdf-4.2.1.1/libsrc4/nc4hdf.c: In function ‘nc4_get_vara’:
trimmed_netcdf-4.2.1.1/libsrc4/nc4hdf.c:837:10: warning: unused variable ‘hdf_datasetid’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libsrc4/nc4internal.c -o trimmed_netcdf-4.2.1.1/libsrc4/nc4internal.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libsrc4/nc4type.c -o trimmed_netcdf-4.2.1.1/libsrc4/nc4type.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libsrc4/nc4var.c -o trimmed_netcdf-4.2.1.1/libsrc4/nc4var.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/include -Itrimmed_netcdf-4.2.1.1/ -Itrimmed_netcdf-4.2.1.1/include -I/usr/local/include -fpic -g -O2 -Wall -c trimmed_netcdf-4.2.1.1/libsrc4/ncfunc.c -o trimmed_netcdf-4.2.1.1/libsrc4/ncfunc.o
gcc -std=gnu99 -shared -L/usr/local/lib -o ncdfFlow.so bitOps.o init.o netCDF.o trimmed_netcdf-4.2.1.1/liblib/stub.o trimmed_netcdf-4.2.1.1/libdispatch/datt.o trimmed_netcdf-4.2.1.1/libdispatch/dattget.o trimmed_netcdf-4.2.1.1/libdispatch/dattinq.o trimmed_netcdf-4.2.1.1/libdispatch/dattput.o trimmed_netcdf-4.2.1.1/libdispatch/dcompound.o trimmed_netcdf-4.2.1.1/libdispatch/dcopy.o trimmed_netcdf-4.2.1.1/libdispatch/ddim.o trimmed_netcdf-4.2.1.1/libdispatch/ddispatch.o trimmed_netcdf-4.2.1.1/libdispatch/denum.o trimmed_netcdf-4.2.1.1/libdispatch/derror.o trimmed_netcdf-4.2.1.1/libdispatch/dfile.o trimmed_netcdf-4.2.1.1/libdispatch/dgroup.o trimmed_netcdf-4.2.1.1/libdispatch/dnclog.o trimmed_netcdf-4.2.1.1/libdispatch/dopaque.o trimmed_netcdf-4.2.1.1/libdispatch/dparallel.o trimmed_netcdf-4.2.1.1/libdispatch/dstring.o trimmed_netcdf-4.2.1.1/libdispatch/dsubstrate.o trimmed_netcdf-4.2.1.1/libdispatch/dtype.o trimmed_netcdf-4.2.1.1/libdispatch/dutf8proc.o trimmed_netcdf-4.2.1.1/libdispatch/dv2i.o trimmed_netcdf-4.2.1.1/libdispatch/dvar.o trimmed_netcdf-4.2.1.1/libdispatch/dvarget.o trimmed_netcdf-4.2.1.1/libdispatch/dvarinq.o trimmed_netcdf-4.2.1.1/libdispatch/dvarput.o trimmed_netcdf-4.2.1.1/libdispatch/dvlen.o trimmed_netcdf-4.2.1.1/libdispatch/nc_uri.o trimmed_netcdf-4.2.1.1/libdispatch/ncaux.o trimmed_netcdf-4.2.1.1/libdispatch/ncbytes.o trimmed_netcdf-4.2.1.1/libdispatch/nchashmap.o trimmed_netcdf-4.2.1.1/libdispatch/nclist.o trimmed_netcdf-4.2.1.1/libdispatch/nctime.o trimmed_netcdf-4.2.1.1/libsrc/attr.o trimmed_netcdf-4.2.1.1/libsrc/dim.o trimmed_netcdf-4.2.1.1/libsrc/lookup3.o trimmed_netcdf-4.2.1.1/libsrc/memio.o trimmed_netcdf-4.2.1.1/libsrc/nc.o trimmed_netcdf-4.2.1.1/libsrc/nc3dispatch.o trimmed_netcdf-4.2.1.1/libsrc/ncio.o trimmed_netcdf-4.2.1.1/libsrc/nclistmgr.o trimmed_netcdf-4.2.1.1/libsrc/ncx.o trimmed_netcdf-4.2.1.1/libsrc/posixio.o trimmed_netcdf-4.2.1.1/libsrc/putget.o trimmed_netcdf-4.2.1.1/libsrc/v1hpg.o trimmed_netcdf-4.2.1.1/libsrc/var.o trimmed_netcdf-4.2.1.1/libsrc4/error4.o trimmed_netcdf-4.2.1.1/libsrc4/nc4attr.o trimmed_netcdf-4.2.1.1/libsrc4/nc4dim.o trimmed_netcdf-4.2.1.1/libsrc4/nc4dispatch.o trimmed_netcdf-4.2.1.1/libsrc4/nc4file.o trimmed_netcdf-4.2.1.1/libsrc4/nc4grp.o trimmed_netcdf-4.2.1.1/libsrc4/nc4hdf.o trimmed_netcdf-4.2.1.1/libsrc4/nc4internal.o trimmed_netcdf-4.2.1.1/libsrc4/nc4type.o trimmed_netcdf-4.2.1.1/libsrc4/nc4var.o trimmed_netcdf-4.2.1.1/libsrc4/ncfunc.o -L/usr/lib -lhdf5 -lhdf5_hl -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
cp ncdfFlow.so libncdfFlow.so
cp libncdfFlow.so ../inst/lib
rm libncdfFlow.so
/home/biocbuild/bbs-2.12-bioc/R/share/make/shlib.mk:6: warning: overriding commands for target `ncdfFlow.so'
Makevars:32: warning: ignoring old commands for target `ncdfFlow.so'
installing to /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
** testing if installed package can be loaded
* DONE (ncdfFlow)