BioC 3.3: CHECK report for flowWorkspace on zin2
This page was generated on 2016-10-13 12:42:46 -0700 (Thu, 13 Oct 2016).
flowWorkspace 3.18.11
Greg Finak ,Mike Jiang
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/flowWorkspace | | Last Changed Rev: 121570 / Revision: 122332 | | Last Changed Date: 2016-09-29 15:07:47 -0700 (Thu, 29 Sep 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
Summary
| Package: flowWorkspace |
| Version: 3.18.11 |
| Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings flowWorkspace_3.18.11.tar.gz |
| StartedAt: 2016-10-13 02:08:24 -0700 (Thu, 13 Oct 2016) |
| EndedAt: 2016-10-13 02:15:24 -0700 (Thu, 13 Oct 2016) |
| EllapsedTime: 420.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: flowWorkspace.Rcheck |
| Warnings: 1 |
Command output
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings flowWorkspace_3.18.11.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/flowWorkspace.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowWorkspace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowWorkspace’ version ‘3.18.11’
* 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/pb_build/src/google/protobuf/descriptor.lo
src/pb_build/src/google/protobuf/descriptor.pb.lo
src/pb_build/src/google/protobuf/descriptor_database.lo
src/pb_build/src/google/protobuf/dynamic_message.lo
src/pb_build/src/google/protobuf/extension_set.lo
src/pb_build/src/google/protobuf/extension_set_heavy.lo
src/pb_build/src/google/protobuf/generated_message_reflection.lo
src/pb_build/src/google/protobuf/generated_message_util.lo
src/pb_build/src/google/protobuf/io/coded_stream.lo
src/pb_build/src/google/protobuf/io/gzip_stream.lo
src/pb_build/src/google/protobuf/io/printer.lo
src/pb_build/src/google/protobuf/io/strtod.lo
src/pb_build/src/google/protobuf/io/tokenizer.lo
src/pb_build/src/google/protobuf/io/zero_copy_stream.lo
src/pb_build/src/google/protobuf/io/zero_copy_stream_impl.lo
src/pb_build/src/google/protobuf/io/zero_copy_stream_impl_lite.lo
src/pb_build/src/google/protobuf/message.lo
src/pb_build/src/google/protobuf/message_lite.lo
src/pb_build/src/google/protobuf/reflection_ops.lo
src/pb_build/src/google/protobuf/repeated_field.lo
src/pb_build/src/google/protobuf/service.lo
src/pb_build/src/google/protobuf/stubs/atomicops_internals_x86_gcc.lo
src/pb_build/src/google/protobuf/stubs/atomicops_internals_x86_msvc.lo
src/pb_build/src/google/protobuf/stubs/common.lo
src/pb_build/src/google/protobuf/stubs/once.lo
src/pb_build/src/google/protobuf/stubs/stringprintf.lo
src/pb_build/src/google/protobuf/stubs/structurally_valid.lo
src/pb_build/src/google/protobuf/stubs/strutil.lo
src/pb_build/src/google/protobuf/stubs/substitute.lo
src/pb_build/src/google/protobuf/text_format.lo
src/pb_build/src/google/protobuf/unknown_field_set.lo
src/pb_build/src/google/protobuf/wire_format.lo
src/pb_build/src/google/protobuf/wire_format_lite.lo
src/pb_build/src/libprotobuf.la
src/protobuf-2.6.0/src/solaris/libstdc++.la
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:
src/pb_build/src/google/protobuf/.dirstamp
src/pb_build/src/google/protobuf/io/.dirstamp
src/pb_build/src/google/protobuf/stubs/.dirstamp
src/pb_build/src/.libs
src/pb_build/src/google/protobuf/.libs
src/pb_build/src/google/protobuf/io/.libs
src/pb_build/src/google/protobuf/stubs/.libs
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 ‘flowWorkspace’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 55.0Mb
sub-directories of 1Mb or more:
doc 1.1Mb
lib 21.9Mb
libs 28.4Mb
tests 2.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘gridExtra’
A package should be listed in only one of these fields.
Versioned 'LinkingTo' value for ‘BH’ is only usable in R >= 3.0.2
* 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 ‘RSVGTipsDevice’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
‘RBGL’ ‘graphics’
All declared Imports should be used.
Unexported objects imported by ':::' calls:
‘Rgraphviz:::getRenderPar’ ‘flowCore:::checkClass’
‘flowCore:::copyFlowSet’ ‘flowCore:::guid’
‘flowCore:::logicle_transform’ ‘graph:::.makeEdgeKeys’
‘lattice:::updateList’ ‘ncdfFlow:::.isValidSamples’
‘stats:::.splinefun’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘.load_gs’ ‘.uuid_gen’ ‘isNegated’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GatingSet,GatingHierarchy-character: warning in list.files(pattern =
paste("^", file, "$", sep = ""), path = path, recursive = TRUE, full
= TRUE): partial argument match of 'full' to 'full.names'
getGate,GatingSetList-character: warning in unlist(res, recur = FALSE):
partial argument match of 'recur' to 'recursive'
.addGatingHierarchies: no visible global function definition for
‘read.ncdfFlowSet’
.addGatingHierarchies : <anonymous>: no visible global function
definition for ‘flowFrame’
.addGatingHierarchies: no visible global function definition for
‘flowSet’
.computeCV : <anonymous>: no visible binding for global variable
‘flowJo.count’
.computeCV : <anonymous>: no visible binding for global variable
‘flowCore.count’
.computeCV : <anonymous> : <anonymous>: no visible global function
definition for ‘IQR’
.computeCV : <anonymous> : <anonymous>: no visible global function
definition for ‘median’
.computeCV_gh : <anonymous>: no visible global function definition for
‘IQR’
.computeCV_gh : <anonymous>: no visible global function definition for
‘median’
.convertTrans : <anonymous> : f : <anonymous>: no visible binding for
global variable ‘max_val’
.convertTrans : <anonymous> : f : <anonymous>: no visible binding for
global variable ‘decade’
.convertTrans : <anonymous> : f : <anonymous>: no visible binding for
global variable ‘offset’
.convertTrans : <anonymous> : f : <anonymous>: no visible binding for
global variable ‘min_val’
.convertTrans : <anonymous>: multiple local function definitions for
‘f’ with different formal arguments
.getGraph: no visible global function definition for ‘head’
.getGraph: no visible global function definition for ‘tail’
.graph_handler : asGraphNEL: no visible global function definition for
‘new’
.graph_handler : asGraphNEL: no visible global function definition for
‘validObject’
.load_gs: no visible global function definition for ‘new’
.load_gs: no visible global function definition for ‘.hasSlot’
.load_gs: no visible global function definition for ‘slot’
.mergeGates : <anonymous>: no visible global function definition for
‘extends’
.parse.pData: no visible binding for global variable ‘.’
.plotGate: no visible global function definition for ‘new’
.plotGate: no visible global function definition for ‘as.formula’
.plotGatingTree: no visible global function definition for ‘dev.prev’
.plotGatingTree: no visible global function definition for ‘dev.off’
.plotGatingTree: no visible global function definition for ‘dev.set’
.preplot: no visible global function definition for ‘as’
.preprocessMap: no visible binding for global variable ‘old’
.preprocessMap: no visible binding for global variable ‘.’
.preprocessor: no visible binding for global variable ‘groupName’
.renderNodes.svgAnno: no visible global function definition for ‘nodes’
.renderNodes.svgAnno : <anonymous>: no visible global function
definition for ‘symbols’
.renderNodes.svgAnno: no visible global function definition for ‘rect’
.renderNodes.svgAnno : <anonymous>: no visible global function
definition for ‘polygon’
.renderNodes.svgAnno: no visible global function definition for
‘polygon’
.renderNodes.svgAnno: no visible global function definition for
‘strwidth’
.renderNodes.svgAnno: no visible global function definition for
‘strheight’
.renderNodes.svgAnno: no visible global function definition for
‘dev.prev’
.renderNodes.svgAnno: no visible global function definition for
‘dev.off’
.renderNodes.svgAnno: no visible global function definition for
‘dev.set’
.renderNodes.svgAnno: no visible global function definition for ‘text’
GatingSetList: no visible global function definition for ‘ncdfFlowList’
GatingSetList: no visible global function definition for ‘as’
GatingSetList: no visible global function definition for ‘validObject’
booleanFilter: no visible global function definition for ‘new’
char2booleanFilter: no visible global function definition for ‘new’
flowWorkspace.par.init: no visible global function definition for
‘gray’
logicle_trans: no visible global function definition for
‘logicleTransform’
logicle_trans: no visible global function definition for
‘inverseLogicleTransform’
mkformula: no visible global function definition for ‘as.formula’
transformerList: no visible global function definition for ‘is’
transformerList: no visible binding for global variable ‘is’
GatingSet,GatingHierarchy-character: no visible global function
definition for ‘new’
GatingSet,character-character: no visible global function definition
for ‘new’
GatingSet,flowSet-ANY: no visible global function definition for ‘new’
Rm,character-GatingSetList-character: no visible global function
definition for ‘selectMethod’
[,GatingSet-ANY: no visible global function definition for ‘extends’
[,GatingSetList-ANY: no visible global function definition for
‘callNextMethod’
[,GatingSetList-ANY: no visible global function definition for ‘as’
[[,GatingSet-character: no visible global function definition for ‘new’
add,GatingSet-filtersList: no visible global function definition for
‘selectMethod’
add,GatingSet-list : <anonymous>: no visible global function definition
for ‘extends’
add,GatingSet-list: no visible global function definition for
‘selectMethod’
add,GatingSetList-filter: no visible global function definition for
‘selectMethod’
add,GatingSetList-filterList: no visible global function definition for
‘selectMethod’
add,GatingSetList-filters: no visible global function definition for
‘selectMethod’
add,GatingSetList-filtersList: no visible global function definition
for ‘selectMethod’
add,GatingSetList-list: no visible global function definition for
‘selectMethod’
compensate,GatingSetList-compensation : <anonymous>: ... may be used in
an incorrect context: ‘compensate(gs, ...)’
getData,GatingSetList-ANY: no visible global function definition for
‘ncdfFlowList’
getGate,GatingHierarchy-character: no visible global function
definition for ‘ellipsoidGate’
getPopStats,GatingHierarchy: no visible binding for global variable
‘node’
keyword,GatingSetList-character: no visible global function definition
for ‘selectMethod’
keyword,GatingSetList-missing: no visible global function definition
for ‘selectMethod’
openWorkspace,character: no visible global function definition for
‘new’
pData<-,GatingSet-data.frame: no visible global function definition for
‘varMetadata’
pData<-,GatingSet-data.frame: no visible global function definition for
‘phenoData’
pData<-,GatingSet-data.frame: no visible global function definition for
‘varMetadata<-’
pData<-,GatingSet-data.frame: no visible global function definition for
‘phenoData<-’
pData<-,GatingSetList-data.frame: no visible global function definition
for ‘callNextMethod’
pData<-,GatingSetList-data.frame: no visible global function definition
for ‘as’
plotGate,GatingSetList-character: no visible global function definition
for ‘selectMethod’
rbind2,GatingSetList-missing: no visible global function definition for
‘ncdfFlowList’
rbind2,GatingSetList-missing: no visible global function definition for
‘new’
rbind2,GatingSetList-missing: no visible binding for global variable
‘slot’
recompute,GatingSetList: no visible global function definition for
‘selectMethod’
transform,GatingSet: no visible global function definition for ‘is’
transform,GatingSet: no visible global function definition for
‘transformList’
Undefined global functions or variables:
. .hasSlot IQR as as.formula callNextMethod decade dev.off dev.prev
dev.set ellipsoidGate extends flowCore.count flowFrame flowJo.count
flowSet gray groupName head inverseLogicleTransform is
logicleTransform max_val median min_val ncdfFlowList new node nodes
offset old phenoData phenoData<- polygon read.ncdfFlowSet rect
selectMethod slot strheight strwidth symbols tail text transformList
validObject varMetadata varMetadata<-
Consider adding
importFrom("grDevices", "dev.off", "dev.prev", "dev.set", "gray")
importFrom("graphics", "polygon", "rect", "strheight", "strwidth",
"symbols", "text")
importFrom("methods", ".hasSlot", "as", "callNextMethod", "extends",
"is", "new", "selectMethod", "slot", "validObject")
importFrom("stats", "IQR", "as.formula", "median", "offset")
importFrom("utils", "head", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... NOTE
S3 methods shown with full name in documentation object 'subset.GatingSet':
‘subset.GatingSet’
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... NOTE
GNU make is a SystemRequirements.
* 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 ... WARNING
Found the following significant warnings:
Warning: Setting row names on a tibble is deprecated.
Warning: Setting row names on a tibble is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘run-all.R’
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: 1 WARNING, 8 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/flowWorkspace.Rcheck/00check.log’
for details.
flowWorkspace.Rcheck/00install.out:
* installing *source* package ‘flowWorkspace’ ...
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 g++ -std=c++11 accepts -g... yes
checking for gcc... gcc -std=gnu99
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
configure: setting xml2 flags...
configure: No directory was specified for --with-xml2. Trying to find xml2 using other methods.
checking for xml2-config... /usr/bin/xml2-config
configure: setting protobuf flags...
configure: No directory was specified for --with-protobuf. Using bundled protocol buffer.
found protobuf-2.6.0 header sources and tar archive;using what is there.
libtoolize: putting auxiliary files in `.'.
libtoolize: copying file `./ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIR, `m4'.
libtoolize: copying file `m4/libtool.m4'
libtoolize: copying file `m4/ltoptions.m4'
libtoolize: copying file `m4/ltsugar.m4'
libtoolize: copying file `m4/ltversion.m4'
libtoolize: copying file `m4/lt˜obsolete.m4'
/usr/share/automake-1.14/am/ltlibrary.am: warning: 'libprotobuf.la': linking libtool libraries using a non-POSIX
/usr/share/automake-1.14/am/ltlibrary.am: archiver requires 'AM_PROG_AR' in 'configure.ac'
src/Makefile.am:81: while processing Libtool library 'libprotobuf.la'
building protobuf...
found pb_build ;using what is there.
checking whether to enable maintainer-specific portions of Makefiles... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
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
checking whether gcc -std=gnu99 understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of gcc -std=gnu99... gcc3
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=c++11 accepts -g... yes
checking dependency style of g++ -std=c++11... gcc3
checking how to run the C++ preprocessor... g++ -std=c++11 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking C++ compiler flags...... use user-supplied: -g -O2
checking whether __SUNPRO_CC is declared... no
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc -std=gnu99... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc -std=gnu99 object... ok
checking for sysroot... no
checking for mt... mt
checking if mt is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc -std=gnu99 supports -fno-rtti -fno-exceptions... no
checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC
checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes
checking if gcc -std=gnu99 static flag -static works... yes
checking if gcc -std=gnu99 supports -c -o file.o... yes
checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes
checking whether the gcc -std=gnu99 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... g++ -std=c++11 -E
checking for ld used by g++ -std=c++11... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ -std=c++11 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ -std=c++11 option to produce PIC... -fPIC -DPIC
checking if g++ -std=c++11 PIC flag -fPIC -DPIC works... yes
checking if g++ -std=c++11 static flag -static works... yes
checking if g++ -std=c++11 supports -c -o file.o... yes
checking if g++ -std=c++11 supports -c -o file.o... (cached) yes
checking whether the g++ -std=c++11 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for ANSI C header files... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking for inttypes.h... (cached) yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for working memcmp... yes
checking for working strtod... yes
checking for ftruncate... yes
checking for memset... yes
checking for mkdir... yes
checking for strchr... yes
checking for strerror... yes
checking for strtol... yes
checking zlib version... ok (1.2.0.4 or later)
checking for library containing zlibVersion... -lz
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking whether to check for GCC pthread/shared inconsistencies... yes
checking whether -pthread is sufficient with -shared... yes
checking whether what we have so far is sufficient with -nostdlib... no
checking whether -lpthread saves the day... yes
checking the location of hash_map... <unordered_map>
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating protobuf.pc
config.status: creating protobuf-lite.pc
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
CDPATH="${ZSH_VERSION+.}:" && cd ../protobuf-2.6.0 && /bin/bash /home/biocbuild/bbs-3.3-bioc/meat/flowWorkspace.Rcheck/00_pkg_src/flowWorkspace/src/protobuf-2.6.0/missing aclocal-1.14 -I m4
cd ../protobuf-2.6.0 && /bin/bash /home/biocbuild/bbs-3.3-bioc/meat/flowWorkspace.Rcheck/00_pkg_src/flowWorkspace/src/protobuf-2.6.0/missing automake-1.14 --foreign
CDPATH="${ZSH_VERSION+.}:" && cd ../protobuf-2.6.0 && /bin/bash /home/biocbuild/bbs-3.3-bioc/meat/flowWorkspace.Rcheck/00_pkg_src/flowWorkspace/src/protobuf-2.6.0/missing autoconf
/bin/bash ./config.status --recheck
running CONFIG_SHELL=/bin/bash /bin/bash ../protobuf-2.6.0/configure --enable-static=no CXX=g++ -std=c++11 CXXFLAGS=-g -O2 CC=gcc -std=gnu99 CFLAGS=-g -O2 -Wall --no-create --no-recursion
checking whether to enable maintainer-specific portions of Makefiles... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
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configure: creating ./config.status
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(CDPATH="${ZSH_VERSION+.}:" && cd ../protobuf-2.6.0 && /bin/bash /home/biocbuild/bbs-3.3-bioc/meat/flowWorkspace.Rcheck/00_pkg_src/flowWorkspace/src/protobuf-2.6.0/missing autoheader)
rm -f stamp-h1
touch ../protobuf-2.6.0/config.h.in
cd . && /bin/bash ./config.status config.h
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make all-recursive
make[1]: Entering directory `/home/biocbuild/bbs-3.3-bioc/meat/flowWorkspace.Rcheck/00_pkg_src/flowWorkspace/src/pb_build'
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make[2]: Entering directory `/home/biocbuild/bbs-3.3-bioc/meat/flowWorkspace.Rcheck/00_pkg_src/flowWorkspace/src/pb_build/src'
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libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/stubs/atomicops_internals_x86_gcc.lo -MD -MP -MF google/protobuf/stubs/.deps/atomicops_internals_x86_gcc.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/stubs/atomicops_internals_x86_gcc.cc -fPIC -DPIC -o google/protobuf/stubs/.libs/atomicops_internals_x86_gcc.o
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libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/stubs/atomicops_internals_x86_msvc.lo -MD -MP -MF google/protobuf/stubs/.deps/atomicops_internals_x86_msvc.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/stubs/atomicops_internals_x86_msvc.cc -fPIC -DPIC -o google/protobuf/stubs/.libs/atomicops_internals_x86_msvc.o
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libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/stubs/common.lo -MD -MP -MF google/protobuf/stubs/.deps/common.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/stubs/common.cc -fPIC -DPIC -o google/protobuf/stubs/.libs/common.o
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libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/stubs/once.lo -MD -MP -MF google/protobuf/stubs/.deps/once.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/stubs/once.cc -fPIC -DPIC -o google/protobuf/stubs/.libs/once.o
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libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/stubs/stringprintf.lo -MD -MP -MF google/protobuf/stubs/.deps/stringprintf.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/stubs/stringprintf.cc -fPIC -DPIC -o google/protobuf/stubs/.libs/stringprintf.o
In file included from ../../protobuf-2.6.0/src/google/protobuf/stubs/stringprintf.h:47:0,
from ../../protobuf-2.6.0/src/google/protobuf/stubs/stringprintf.cc:33:
../../protobuf-2.6.0/src/google/protobuf/stubs/stringprintf.cc: In function 'std::string google::protobuf::StringPrintfVector(const char*, const std::vector<std::basic_string<char> >&)':
../../protobuf-2.6.0/src/google/protobuf/stubs/stringprintf.cc:164:59: warning: typedef 'arg_count_mismatch' locally defined but not used [-Wunused-local-typedefs]
GOOGLE_COMPILE_ASSERT(kStringPrintfVectorMaxArgs == 32, arg_count_mismatch);
^
../../protobuf-2.6.0/src/google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
msg[bool(expr) ? 1 : -1]
^
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libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/extension_set.lo -MD -MP -MF google/protobuf/.deps/extension_set.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/extension_set.cc -fPIC -DPIC -o google/protobuf/.libs/extension_set.o
In file included from ../../protobuf-2.6.0/src/google/protobuf/extension_set.cc:43:0:
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h: In function 'void google::protobuf::InsertOrDie(Collection*, const typename Collection::value_type::first_type&, const typename Collection::value_type::second_type&)':
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h:356:43: warning: typedef 'value_type' locally defined but not used [-Wunused-local-typedefs]
typedef typename Collection::value_type value_type;
^
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h: In function 'void google::protobuf::InsertOrDieNoPrint(Collection*, const typename Collection::value_type::first_type&, const typename Collection::value_type::second_type&)':
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h:367:43: warning: typedef 'value_type' locally defined but not used [-Wunused-local-typedefs]
typedef typename Collection::value_type value_type;
^
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libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/stubs/strutil.lo -MD -MP -MF google/protobuf/stubs/.deps/strutil.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.cc -fPIC -DPIC -o google/protobuf/stubs/.libs/strutil.o
In file included from ../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:38:0,
from ../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.cc:33:
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)':
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:341:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
sizeof_int64_is_not_sizeof_long_long);
^
../../protobuf-2.6.0/src/google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
msg[bool(expr) ? 1 : -1]
^
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)':
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:347:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
sizeof_uint64_is_not_sizeof_long_long);
^
../../protobuf-2.6.0/src/google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
msg[bool(expr) ? 1 : -1]
^
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.cc: In function 'char* google::protobuf::DoubleToBuffer(double, char*)':
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.cc:1172:39: warning: typedef 'DBL_DIG_is_too_big' locally defined but not used [-Wunused-local-typedefs]
GOOGLE_COMPILE_ASSERT(DBL_DIG < 20, DBL_DIG_is_too_big);
^
../../protobuf-2.6.0/src/google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
msg[bool(expr) ? 1 : -1]
^
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.cc: In function 'char* google::protobuf::FloatToBuffer(float, char*)':
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.cc:1227:39: warning: typedef 'FLT_DIG_is_too_big' locally defined but not used [-Wunused-local-typedefs]
GOOGLE_COMPILE_ASSERT(FLT_DIG < 10, FLT_DIG_is_too_big);
^
../../protobuf-2.6.0/src/google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
msg[bool(expr) ? 1 : -1]
^
depbase=`echo google/protobuf/stubs/substitute.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/stubs/substitute.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/stubs/substitute.lo ../../protobuf-2.6.0/src/google/protobuf/stubs/substitute.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/stubs/substitute.lo -MD -MP -MF google/protobuf/stubs/.deps/substitute.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/stubs/substitute.cc -fPIC -DPIC -o google/protobuf/stubs/.libs/substitute.o
In file included from ../../protobuf-2.6.0/src/google/protobuf/stubs/substitute.h:35:0,
from ../../protobuf-2.6.0/src/google/protobuf/stubs/substitute.cc:33:
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)':
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:341:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
sizeof_int64_is_not_sizeof_long_long);
^
../../protobuf-2.6.0/src/google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
msg[bool(expr) ? 1 : -1]
^
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)':
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:347:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
sizeof_uint64_is_not_sizeof_long_long);
^
../../protobuf-2.6.0/src/google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
msg[bool(expr) ? 1 : -1]
^
depbase=`echo google/protobuf/stubs/structurally_valid.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/stubs/structurally_valid.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/stubs/structurally_valid.lo ../../protobuf-2.6.0/src/google/protobuf/stubs/structurally_valid.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/stubs/structurally_valid.lo -MD -MP -MF google/protobuf/stubs/.deps/structurally_valid.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/stubs/structurally_valid.cc -fPIC -DPIC -o google/protobuf/stubs/.libs/structurally_valid.o
depbase=`echo google/protobuf/descriptor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/descriptor.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/descriptor.lo ../../protobuf-2.6.0/src/google/protobuf/descriptor.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/descriptor.lo -MD -MP -MF google/protobuf/.deps/descriptor.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/descriptor.cc -fPIC -DPIC -o google/protobuf/.libs/descriptor.o
In file included from ../../protobuf-2.6.0/src/google/protobuf/stubs/hash.h:39:0,
from ../../protobuf-2.6.0/src/google/protobuf/descriptor.cc:35:
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)':
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:341:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
sizeof_int64_is_not_sizeof_long_long);
^
../../protobuf-2.6.0/src/google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
msg[bool(expr) ? 1 : -1]
^
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)':
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:347:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
sizeof_uint64_is_not_sizeof_long_long);
^
../../protobuf-2.6.0/src/google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
msg[bool(expr) ? 1 : -1]
^
In file included from ../../protobuf-2.6.0/src/google/protobuf/descriptor.cc:59:0:
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h: In function 'void google::protobuf::InsertOrDie(Collection*, const typename Collection::value_type::first_type&, const typename Collection::value_type::second_type&)':
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h:356:43: warning: typedef 'value_type' locally defined but not used [-Wunused-local-typedefs]
typedef typename Collection::value_type value_type;
^
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h: In function 'void google::protobuf::InsertOrDieNoPrint(Collection*, const typename Collection::value_type::first_type&, const typename Collection::value_type::second_type&)':
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h:367:43: warning: typedef 'value_type' locally defined but not used [-Wunused-local-typedefs]
typedef typename Collection::value_type value_type;
^
depbase=`echo google/protobuf/descriptor.pb.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/descriptor.pb.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/descriptor.pb.lo ../../protobuf-2.6.0/src/google/protobuf/descriptor.pb.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/descriptor.pb.lo -MD -MP -MF google/protobuf/.deps/descriptor.pb.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/descriptor.pb.cc -fPIC -DPIC -o google/protobuf/.libs/descriptor.pb.o
depbase=`echo google/protobuf/descriptor_database.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/descriptor_database.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/descriptor_database.lo ../../protobuf-2.6.0/src/google/protobuf/descriptor_database.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/descriptor_database.lo -MD -MP -MF google/protobuf/.deps/descriptor_database.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/descriptor_database.cc -fPIC -DPIC -o google/protobuf/.libs/descriptor_database.o
In file included from ../../protobuf-2.6.0/src/google/protobuf/descriptor_database.h:44:0,
from ../../protobuf-2.6.0/src/google/protobuf/descriptor_database.cc:35:
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)':
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:341:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
sizeof_int64_is_not_sizeof_long_long);
^
../../protobuf-2.6.0/src/google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
msg[bool(expr) ? 1 : -1]
^
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)':
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:347:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
sizeof_uint64_is_not_sizeof_long_long);
^
../../protobuf-2.6.0/src/google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
msg[bool(expr) ? 1 : -1]
^
In file included from ../../protobuf-2.6.0/src/google/protobuf/descriptor_database.cc:43:0:
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h: In function 'void google::protobuf::InsertOrDie(Collection*, const typename Collection::value_type::first_type&, const typename Collection::value_type::second_type&)':
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h:356:43: warning: typedef 'value_type' locally defined but not used [-Wunused-local-typedefs]
typedef typename Collection::value_type value_type;
^
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h: In function 'void google::protobuf::InsertOrDieNoPrint(Collection*, const typename Collection::value_type::first_type&, const typename Collection::value_type::second_type&)':
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h:367:43: warning: typedef 'value_type' locally defined but not used [-Wunused-local-typedefs]
typedef typename Collection::value_type value_type;
^
depbase=`echo google/protobuf/dynamic_message.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/dynamic_message.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/dynamic_message.lo ../../protobuf-2.6.0/src/google/protobuf/dynamic_message.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/dynamic_message.lo -MD -MP -MF google/protobuf/.deps/dynamic_message.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/dynamic_message.cc -fPIC -DPIC -o google/protobuf/.libs/dynamic_message.o
depbase=`echo google/protobuf/extension_set_heavy.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/extension_set_heavy.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/extension_set_heavy.lo ../../protobuf-2.6.0/src/google/protobuf/extension_set_heavy.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/extension_set_heavy.lo -MD -MP -MF google/protobuf/.deps/extension_set_heavy.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/extension_set_heavy.cc -fPIC -DPIC -o google/protobuf/.libs/extension_set_heavy.o
depbase=`echo google/protobuf/generated_message_reflection.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/generated_message_reflection.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/generated_message_reflection.lo ../../protobuf-2.6.0/src/google/protobuf/generated_message_reflection.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/generated_message_reflection.lo -MD -MP -MF google/protobuf/.deps/generated_message_reflection.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/generated_message_reflection.cc -fPIC -DPIC -o google/protobuf/.libs/generated_message_reflection.o
../../protobuf-2.6.0/src/google/protobuf/generated_message_reflection.cc: In member function 'void google::protobuf::internal::GeneratedMessageReflection::SwapOneofField(google::protobuf::Message*, google::protobuf::Message*, const google::protobuf::OneofDescriptor*) const':
../../protobuf-2.6.0/src/google/protobuf/generated_message_reflection.cc:503:54: warning: 'field1' may be used uninitialized in this function [-Wmaybe-uninitialized]
SetField<TYPE>(message2, field1, temp_##TYPE); \
^
../../protobuf-2.6.0/src/google/protobuf/generated_message_reflection.cc:516:60: warning: 'temp_message' may be used uninitialized in this function [-Wmaybe-uninitialized]
SetAllocatedMessage(message2, temp_message, field1);
^
depbase=`echo google/protobuf/message.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/message.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/message.lo ../../protobuf-2.6.0/src/google/protobuf/message.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/message.lo -MD -MP -MF google/protobuf/.deps/message.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/message.cc -fPIC -DPIC -o google/protobuf/.libs/message.o
In file included from ../../protobuf-2.6.0/src/google/protobuf/stubs/hash.h:39:0,
from ../../protobuf-2.6.0/src/google/protobuf/message.cc:37:
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)':
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:341:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
sizeof_int64_is_not_sizeof_long_long);
^
../../protobuf-2.6.0/src/google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
msg[bool(expr) ? 1 : -1]
^
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)':
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:347:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
sizeof_uint64_is_not_sizeof_long_long);
^
../../protobuf-2.6.0/src/google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
msg[bool(expr) ? 1 : -1]
^
In file included from ../../protobuf-2.6.0/src/google/protobuf/message.cc:51:0:
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h: In function 'void google::protobuf::InsertOrDie(Collection*, const typename Collection::value_type::first_type&, const typename Collection::value_type::second_type&)':
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h:356:43: warning: typedef 'value_type' locally defined but not used [-Wunused-local-typedefs]
typedef typename Collection::value_type value_type;
^
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h: In function 'void google::protobuf::InsertOrDieNoPrint(Collection*, const typename Collection::value_type::first_type&, const typename Collection::value_type::second_type&)':
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h:367:43: warning: typedef 'value_type' locally defined but not used [-Wunused-local-typedefs]
typedef typename Collection::value_type value_type;
^
depbase=`echo google/protobuf/reflection_ops.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/reflection_ops.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/reflection_ops.lo ../../protobuf-2.6.0/src/google/protobuf/reflection_ops.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/reflection_ops.lo -MD -MP -MF google/protobuf/.deps/reflection_ops.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/reflection_ops.cc -fPIC -DPIC -o google/protobuf/.libs/reflection_ops.o
In file included from ../../protobuf-2.6.0/src/google/protobuf/reflection_ops.h:41:0,
from ../../protobuf-2.6.0/src/google/protobuf/reflection_ops.cc:38:
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)':
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:341:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
sizeof_int64_is_not_sizeof_long_long);
^
../../protobuf-2.6.0/src/google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
msg[bool(expr) ? 1 : -1]
^
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)':
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:347:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
sizeof_uint64_is_not_sizeof_long_long);
^
../../protobuf-2.6.0/src/google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
msg[bool(expr) ? 1 : -1]
^
depbase=`echo google/protobuf/service.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool --tag=CXX --mode=compile g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/service.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/service.lo ../../protobuf-2.6.0/src/google/protobuf/service.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/service.lo -MD -MP -MF google/protobuf/.deps/service.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/service.cc -fPIC -DPIC -o google/protobuf/.libs/service.o
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/bin/bash ../libtool --tag=CXX --mode=compile g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/text_format.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/text_format.lo ../../protobuf-2.6.0/src/google/protobuf/text_format.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/text_format.lo -MD -MP -MF google/protobuf/.deps/text_format.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/text_format.cc -fPIC -DPIC -o google/protobuf/.libs/text_format.o
In file included from ../../protobuf-2.6.0/src/google/protobuf/text_format.h:46:0,
from ../../protobuf-2.6.0/src/google/protobuf/text_format.cc:43:
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)':
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:341:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
sizeof_int64_is_not_sizeof_long_long);
^
../../protobuf-2.6.0/src/google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
msg[bool(expr) ? 1 : -1]
^
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)':
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:347:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
sizeof_uint64_is_not_sizeof_long_long);
^
../../protobuf-2.6.0/src/google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
msg[bool(expr) ? 1 : -1]
^
In file included from ../../protobuf-2.6.0/src/google/protobuf/text_format.cc:54:0:
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h: In function 'void google::protobuf::InsertOrDie(Collection*, const typename Collection::value_type::first_type&, const typename Collection::value_type::second_type&)':
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h:356:43: warning: typedef 'value_type' locally defined but not used [-Wunused-local-typedefs]
typedef typename Collection::value_type value_type;
^
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h: In function 'void google::protobuf::InsertOrDieNoPrint(Collection*, const typename Collection::value_type::first_type&, const typename Collection::value_type::second_type&)':
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h:367:43: warning: typedef 'value_type' locally defined but not used [-Wunused-local-typedefs]
typedef typename Collection::value_type value_type;
^
depbase=`echo google/protobuf/unknown_field_set.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/unknown_field_set.lo -MD -MP -MF google/protobuf/.deps/unknown_field_set.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/unknown_field_set.cc -fPIC -DPIC -o google/protobuf/.libs/unknown_field_set.o
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libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/wire_format.lo -MD -MP -MF google/protobuf/.deps/wire_format.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/wire_format.cc -fPIC -DPIC -o google/protobuf/.libs/wire_format.o
depbase=`echo google/protobuf/io/gzip_stream.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/io/gzip_stream.lo -MD -MP -MF google/protobuf/io/.deps/gzip_stream.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/io/gzip_stream.cc -fPIC -DPIC -o google/protobuf/io/.libs/gzip_stream.o
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libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/io/printer.lo -MD -MP -MF google/protobuf/io/.deps/printer.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/io/printer.cc -fPIC -DPIC -o google/protobuf/io/.libs/printer.o
depbase=`echo google/protobuf/io/strtod.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/io/strtod.lo -MD -MP -MF google/protobuf/io/.deps/strtod.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/io/strtod.cc -fPIC -DPIC -o google/protobuf/io/.libs/strtod.o
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libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/io/tokenizer.lo -MD -MP -MF google/protobuf/io/.deps/tokenizer.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/io/tokenizer.cc -fPIC -DPIC -o google/protobuf/io/.libs/tokenizer.o
In file included from ../../protobuf-2.6.0/src/google/protobuf/io/tokenizer.h:42:0,
from ../../protobuf-2.6.0/src/google/protobuf/io/tokenizer.cc:91:
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h: In function 'google::protobuf::int64 google::protobuf::strto64(const char*, char**, int)':
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:341:25: warning: typedef 'sizeof_int64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
sizeof_int64_is_not_sizeof_long_long);
^
../../protobuf-2.6.0/src/google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
msg[bool(expr) ? 1 : -1]
^
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h: In function 'google::protobuf::uint64 google::protobuf::strtou64(const char*, char**, int)':
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:347:25: warning: typedef 'sizeof_uint64_is_not_sizeof_long_long' locally defined but not used [-Wunused-local-typedefs]
sizeof_uint64_is_not_sizeof_long_long);
^
../../protobuf-2.6.0/src/google/protobuf/stubs/common.h:382:11: note: in definition of macro 'GOOGLE_COMPILE_ASSERT'
msg[bool(expr) ? 1 : -1]
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libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -pthread -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -g -O2 -MT google/protobuf/io/zero_copy_stream_impl.lo -MD -MP -MF google/protobuf/io/.deps/zero_copy_stream_impl.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/io/zero_copy_stream_impl.cc -fPIC -DPIC -o google/protobuf/io/.libs/zero_copy_stream_impl.o
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libtool: link: g++ -std=c++11 -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/4.8/crtbeginS.o google/protobuf/stubs/.libs/atomicops_internals_x86_gcc.o google/protobuf/stubs/.libs/atomicops_internals_x86_msvc.o google/protobuf/stubs/.libs/common.o google/protobuf/stubs/.libs/once.o google/protobuf/stubs/.libs/stringprintf.o google/protobuf/.libs/extension_set.o google/protobuf/.libs/generated_message_util.o google/protobuf/.libs/message_lite.o google/protobuf/.libs/repeated_field.o google/protobuf/.libs/wire_format_lite.o google/protobuf/io/.libs/coded_stream.o google/protobuf/io/.libs/zero_copy_stream.o google/protobuf/io/.libs/zero_copy_stream_impl_lite.o google/protobuf/stubs/.libs/strutil.o google/protobuf/stubs/.libs/substitute.o google/protobuf/stubs/.libs/structurally_valid.o google/protobuf/.libs/descriptor.o google/protobuf/.libs/descriptor.pb.o google/protobuf/.libs/descriptor_database.o google/protobuf/.libs/dynamic_message.o google/protobuf/.libs/extension_set_heavy.o google/protobuf/.libs/generated_message_reflection.o google/protobuf/.libs/message.o google/protobuf/.libs/reflection_ops.o google/protobuf/.libs/service.o google/protobuf/.libs/text_format.o google/protobuf/.libs/unknown_field_set.o google/protobuf/.libs/wire_format.o google/protobuf/io/.libs/gzip_stream.o google/protobuf/io/.libs/printer.o google/protobuf/io/.libs/strtod.o google/protobuf/io/.libs/tokenizer.o google/protobuf/io/.libs/zero_copy_stream_impl.o -lpthread -lz -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/4.8/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/crtn.o -pthread -O2 -pthread -Wl,-soname -Wl,libprotobuf.so.9 -o .libs/libprotobuf.so.9.0.0
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make[2]: Leaving directory `/home/biocbuild/bbs-3.3-bioc/meat/flowWorkspace.Rcheck/00_pkg_src/flowWorkspace/src/pb_build/src'
make[1]: Leaving directory `/home/biocbuild/bbs-3.3-bioc/meat/flowWorkspace.Rcheck/00_pkg_src/flowWorkspace/src/pb_build'
configure: Using the following compilation and linking flags for flowWorkspace
configure: PKG_CPPFLAGS=-I/usr/include/libxml2 -Iprotobuf-2.6.0/src
configure: PKG_LIBS=-lxml2
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -fpic -g -O2 -c GatingHierarchy.cpp -o GatingHierarchy.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -fpic -g -O2 -c GatingSet.cpp -o GatingSet.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -fpic -g -O2 -c GatingSet.pb.cc -o GatingSet.pb.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -fpic -g -O2 -c POPINDICES.cpp -o POPINDICES.o
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g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -fpic -g -O2 -c gate.cpp -o gate.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -fpic -g -O2 -c global.cpp -o global.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -fpic -g -O2 -c macFlowJoWorkspace.cpp -o macFlowJoWorkspace.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -fpic -g -O2 -c nodeProperties.cpp -o nodeProperties.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -fpic -g -O2 -c spline.cpp -o spline.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -fpic -g -O2 -c transformation.cpp -o transformation.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -fpic -g -O2 -c winFlowJoWorkspace.cpp -o winFlowJoWorkspace.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -fpic -g -O2 -c workspace.cpp -o workspace.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -fpic -g -O2 -c wsNode.cpp -o wsNode.o
mkdir -p "/home/biocbuild/bbs-3.3-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/lib"
ar rs "/home/biocbuild/bbs-3.3-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/lib/libprotobuf.a" pb_build/src/google/protobuf/.libs/*.o pb_build/src/google/protobuf/stubs/.libs/*.o pb_build/src/google/protobuf/io/.libs/*.o
ar: creating /home/biocbuild/bbs-3.3-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/lib/libprotobuf.a
g++ -std=c++11 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o flowWorkspace.so GatingHierarchy.o GatingSet.o GatingSet.pb.o POPINDICES.o R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o calibrationTable.o compensation.o delimitedMessage.o flowData.o flowJoWorkspace.o gate.o global.o macFlowJoWorkspace.o nodeProperties.o spline.o transformation.o winFlowJoWorkspace.o workspace.o wsNode.o /home/biocbuild/bbs-3.3-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/lib/libprotobuf.a /home/biocbuild/bbs-3.3-bioc/R/library/flowCore/lib/libboost_regex.a -lxml2 -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/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 (flowWorkspace)
flowWorkspace.Rcheck/flowWorkspace-Ex.timings:
| name | user | system | elapsed
|
| GatingHierarchy-class | 2.314 | 0.167 | 2.765 |
|
| GatingSet-class | 1.865 | 0.132 | 2.019 |
|
| GatingSet-methods | 0 | 0 | 0 |
|
| GatingSetList-class | 0.002 | 0.000 | 0.002 |
|
| add | 0.002 | 0.000 | 0.002 |
|
| asinh_Gml2 | 0.001 | 0.000 | 0.001 |
|
| asinhtGml2_trans | 0.001 | 0.000 | 0.001 |
|
| checkRedundantNodes | 0.001 | 0.000 | 0.001 |
|
| clone | 0 | 0 | 0 |
|
| compensate | 0.000 | 0.004 | 0.001 |
|
| dropRedundantChannels | 0 | 0 | 0 |
|
| dropRedundantNodes | 0 | 0 | 0 |
|
| flowJo.fasinh | 0.001 | 0.000 | 0.001 |
|
| flowJoTrans | 0.003 | 0.000 | 0.003 |
|
| flowJoWorkspace-class | 0.036 | 0.000 | 0.036 |
|
| flowJo_biexp_trans | 0.616 | 0.023 | 0.655 |
|
| flowJo_fasinh_trans | 0.001 | 0.000 | 0.001 |
|
| flowWorkspace.par.get | 0.001 | 0.000 | 0.001 |
|
| flow_breaks | 0.899 | 0.140 | 1.055 |
|
| getCompensationMatrices | 0.000 | 0.000 | 0.001 |
|
| getData-methods | 0.001 | 0.000 | 0.001 |
|
| getGate | 0.001 | 0.000 | 0.000 |
|
| getIndices-GatingSet-name-method | 0.000 | 0.000 | 0.001 |
|
| getIndices | 0.001 | 0.000 | 0.000 |
|
| getKeywords | 0.195 | 0.008 | 0.229 |
|
| getNodes | 0.001 | 0.000 | 0.000 |
|
| getParent | 0.000 | 0.000 | 0.001 |
|
| getPopStats | 0.001 | 0.000 | 0.001 |
|
| getSampleGroups | 0.001 | 0.000 | 0.001 |
|
| getSamples | 0 | 0 | 0 |
|
| getSingleCellExpression | 0.000 | 0.000 | 0.001 |
|
| getTransformations | 0 | 0 | 0 |
|
| groupByChannels | 0.000 | 0.000 | 0.001 |
|
| groupByTree | 0.001 | 0.000 | 0.000 |
|
| insertGate | 0 | 0 | 0 |
|
| keyword | 0.001 | 0.000 | 0.001 |
|
| logicleGml2_trans | 0.002 | 0.000 | 0.001 |
|
| logicle_trans | 0.002 | 0.000 | 0.003 |
|
| loglevel | 0.001 | 0.000 | 0.001 |
|
| markernames | 0.001 | 0.000 | 0.001 |
|
| mkformula | 0.002 | 0.000 | 0.002 |
|
| openWorkspace | 0.001 | 0.000 | 0.000 |
|
| parseWorkspace | 0.001 | 0.000 | 0.001 |
|
| plot-methods | 0.001 | 0.000 | 0.001 |
|
| plotGate-methods | 0.001 | 0.000 | 0.000 |
|
| plotPopCV | 0.000 | 0.000 | 0.001 |
|
| prettyAxis | 0.001 | 0.000 | 0.001 |
|
| sampleNames | 0.001 | 0.000 | 0.000 |
|
| save_gs | 0.000 | 0.000 | 0.001 |
|
| setGate | 0.001 | 0.000 | 0.001 |
|
| setNode-methods | 0.000 | 0.004 | 0.001 |
|
| transform | 0.000 | 0.000 | 0.001 |
|
| transformerList | 0.015 | 0.000 | 0.014 |
|
| updateChannels | 0.000 | 0.004 | 0.001 |
|