flowWorkspace 1.5.62
Greg Finak ,Mike Jiang
| Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowWorkspace | | Last Changed Rev: 72454 / Revision: 72575 | | Last Changed Date: 2013-01-10 17:09:40 -0800 (Thu, 10 Jan 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | ERROR | skipped | |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | ERROR | skipped | skipped |
| petty | Mac OS X Leopard (10.5.8) / i386 | ERROR | skipped | skipped |
* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/flowWorkspace.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowWorkspace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowWorkspace’ version ‘1.5.62’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
‘multicore’ ‘Rmpi’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘flowWorkspace’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 24.1Mb
sub-directories of 1Mb or more:
libs 22.9Mb
* 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 ... NOTE
getTransformations,GatingHierarchyInternal : <anonymous>: multiple
local function definitions for ‘f’ with different formal arguments
rbind2,GatingSetList-missing: no visible global function definition for
‘ncdfFlowList’
* 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 ... NOTE
File ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/libs/flowWorkspace.so’:
Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
Objects: ‘GatingHierarchy.o’, ‘GatingSet.o’, ‘flowJoWorkspace.o’,
‘gate.o’, ‘macFlowJoWorkspace.o’, ‘transformation.o’,
‘winFlowJoWorkspace.o’, ‘workspace.o’
Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
GatingHierarchy-class 10.969 0.256 11.277
GatingSet-class 5.840 0.156 6.001
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There were 4 notes.
See
‘/loc/home/biocbuild/bbs-2.12-bioc/meat/flowWorkspace.Rcheck/00check.log’
for details.
* installing *source* package ‘flowWorkspace’ ...
checking for g++... g++
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++ accepts -g... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/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 for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for size_t... yes
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: No directory was specified for --with-boost. Using bundled boost.
untarring boost include tree...
configure: compiling boost serialization library.
configure: Using the following compilation and linking flags for flowWorkspace
configure: PKG_CPPFLAGS=-I/usr/include/libxml2 -Itrimmed_boost_1_52_0
configure: PKG_LIBS=-lxml2 -lz -lm trimmed_boost_1_52_0/libs/serialization/src/*.o
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/ncdfFlow/include" -fpic -g -O2 -c GatingHierarchy.cpp -o GatingHierarchy.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/ncdfFlow/include" -fpic -g -O2 -c GatingSet.cpp -o GatingSet.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/ncdfFlow/include" -fpic -g -O2 -c POPINDICES.cpp -o POPINDICES.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/ncdfFlow/include" -fpic -g -O2 -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/ncdfFlow/include" -fpic -g -O2 -c R_GatingSet.cpp -o R_GatingSet.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/ncdfFlow/include" -fpic -g -O2 -c bitOps.c -o bitOps.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/ncdfFlow/include" -fpic -g -O2 -c calibrationTable.cpp -o calibrationTable.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/ncdfFlow/include" -fpic -g -O2 -c flowData.cpp -o flowData.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/ncdfFlow/include" -fpic -g -O2 -c flowJoWorkspace.cpp -o flowJoWorkspace.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/ncdfFlow/include" -fpic -g -O2 -c gate.cpp -o gate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/ncdfFlow/include" -fpic -g -O2 -c init.c -o init.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/ncdfFlow/include" -fpic -g -O2 -c macFlowJoWorkspace.cpp -o macFlowJoWorkspace.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/ncdfFlow/include" -fpic -g -O2 -c ncdfFlow.cpp -o ncdfFlow.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/ncdfFlow/include" -fpic -g -O2 -c nodeProperties.cpp -o nodeProperties.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/ncdfFlow/include" -fpic -g -O2 -c spline.cpp -o spline.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/ncdfFlow/include" -fpic -g -O2 -c transformation.cpp -o transformation.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/ncdfFlow/include" -fpic -g -O2 -c winFlowJoWorkspace.cpp -o winFlowJoWorkspace.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/ncdfFlow/include" -fpic -g -O2 -c workspace.cpp -o workspace.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/ncdfFlow/include" -fpic -g -O2 -c wsNode.cpp -o wsNode.o
Scalable Robust Estimators with High Breakdown Point (version 1.3-02)
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
g++ -shared -L/usr/local/lib64 -o flowWorkspace.so GatingHierarchy.o GatingSet.o POPINDICES.o R_GatingHierarchy.o R_GatingSet.o bitOps.o calibrationTable.o flowData.o flowJoWorkspace.o gate.o init.o macFlowJoWorkspace.o ncdfFlow.o nodeProperties.o spline.o transformation.o winFlowJoWorkspace.o workspace.o wsNode.o -L/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/lib -lRcpp -Wl,-rpath,/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/lib /loc/home/biocbuild/bbs-2.12-bioc/R/library/ncdfFlow/libs/ncdfFlow.so -lxml2 -lz -lm trimmed_boost_1_52_0/libs/serialization/src/archive_exception.o trimmed_boost_1_52_0/libs/serialization/src/basic_archive.o trimmed_boost_1_52_0/libs/serialization/src/basic_iarchive.o trimmed_boost_1_52_0/libs/serialization/src/basic_iserializer.o trimmed_boost_1_52_0/libs/serialization/src/basic_oarchive.o trimmed_boost_1_52_0/libs/serialization/src/basic_oserializer.o trimmed_boost_1_52_0/libs/serialization/src/basic_pointer_iserializer.o trimmed_boost_1_52_0/libs/serialization/src/basic_pointer_oserializer.o trimmed_boost_1_52_0/libs/serialization/src/basic_serializer_map.o trimmed_boost_1_52_0/libs/serialization/src/basic_text_iprimitive.o trimmed_boost_1_52_0/libs/serialization/src/basic_text_oprimitive.o trimmed_boost_1_52_0/libs/serialization/src/basic_xml_archive.o trimmed_boost_1_52_0/libs/serialization/src/binary_iarchive.o trimmed_boost_1_52_0/libs/serialization/src/binary_oarchive.o trimmed_boost_1_52_0/libs/serialization/src/extended_type_info.o trimmed_boost_1_52_0/libs/serialization/src/extended_type_info_no_rtti.o trimmed_boost_1_52_0/libs/serialization/src/extended_type_info_typeid.o trimmed_boost_1_52_0/libs/serialization/src/polymorphic_iarchive.o trimmed_boost_1_52_0/libs/serialization/src/polymorphic_oarchive.o trimmed_boost_1_52_0/libs/serialization/src/shared_ptr_helper.o trimmed_boost_1_52_0/libs/serialization/src/stl_port.o trimmed_boost_1_52_0/libs/serialization/src/text_iarchive.o trimmed_boost_1_52_0/libs/serialization/src/text_oarchive.o trimmed_boost_1_52_0/libs/serialization/src/void_cast.o trimmed_boost_1_52_0/libs/serialization/src/xml_archive_exception.o trimmed_boost_1_52_0/libs/serialization/src/xml_grammar.o trimmed_boost_1_52_0/libs/serialization/src/xml_iarchive.o trimmed_boost_1_52_0/libs/serialization/src/xml_oarchive.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
Scalable Robust Estimators with High Breakdown Point (version 1.3-02)
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘flowWorkspace.Rnw’
** testing if installed package can be loaded
* DONE (flowWorkspace)