flowCore 1.38.2
M.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/flowCore | | Last Changed Rev: 117751 / Revision: 122332 | | Last Changed Date: 2016-05-20 15:21:27 -0700 (Fri, 20 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings flowCore_1.38.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/flowCore.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 ‘flowCore/DESCRIPTION’ ... OK
* this is package ‘flowCore’ version ‘1.38.2’
* 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/boost_regex/c_regex_traits.o src/boost_regex/cpp_regex_traits.o
src/boost_regex/cregex.o src/boost_regex/fileiter.o
src/boost_regex/icu.o src/boost_regex/instances.o
src/boost_regex/posix_api.o src/boost_regex/regex.o
src/boost_regex/regex_debug.o src/boost_regex/regex_raw_buffer.o
src/boost_regex/regex_traits_defaults.o
src/boost_regex/static_mutex.o src/boost_regex/usinstances.o
src/boost_regex/w32_regex_traits.o src/boost_regex/wc_regex_traits.o
src/boost_regex/wide_posix_api.o src/boost_regex/winstances.o
Object files/libraries should not be included in a source package.
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘flowCore’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 34.8Mb
sub-directories of 1Mb or more:
data 5.0Mb
doc 1.3Mb
extdata 1.1Mb
lib 20.7Mb
libs 5.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
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 ‘Rgraphviz’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
rbind2,flowSet-flowSet: warning in assign(i, x[[i]], env = env):
partial argument match of 'env' to 'envir'
rbind2,flowSet-flowSet: warning in assign(i, y[[i]], env = env):
partial argument match of 'env' to 'envir'
%in%,flowFrame-norm2Filter: no visible global function definition for
‘cov.rob’
spillover,flowSet: no visible global function definition for
‘devAskNewPage’
spillover,flowSet : <anonymous>: no visible global function definition
for ‘rangeGate’
spillover,flowSet : <anonymous>: no visible global function definition
for ‘density’
spillover,flowSet : <anonymous>: no visible global function definition
for ‘abline’
spillover,flowSet : <anonymous> : <anonymous>: no visible global
function definition for ‘density’
split,flowFrame-factor: no visible binding for global variable ‘i’
summary,workFlow: no visible binding for global variable ‘wf’
Undefined global functions or variables:
abline cov.rob density devAskNewPage i rangeGate wf
Consider adding
importFrom("grDevices", "devAskNewPage")
importFrom("graphics", "abline")
importFrom("stats", "density")
to your NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 6 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/flowCore.Rcheck/00check.log’
for details.
* installing *source* package ‘flowCore’ ...
** libs
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 FastLogicle.cpp -o FastLogicle.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 Hyperlog.cpp -o Hyperlog.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 Logicle.cpp -o Logicle.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 RcppExports.cpp -o RcppExports.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 biexponential.cpp -o biexponential.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 convertRawBytes.cpp -o convertRawBytes.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 fcsTextParse.cpp -o fcsTextParse.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 hyperlogTransform.cpp -o hyperlogTransform.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 inPolygon.cpp -o inPolygon.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 inPolytope.cpp -o inPolytope.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 logicleTransform.cpp -o logicleTransform.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 pairVectorRcppWrap.cpp -o pairVectorRcppWrap.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 uint2double.cpp -o uint2double.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 zeroin.cpp -o zeroin.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 boost_regex/c_regex_traits.cpp -o boost_regex/c_regex_traits.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 boost_regex/cpp_regex_traits.cpp -o boost_regex/cpp_regex_traits.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 boost_regex/cregex.cpp -o boost_regex/cregex.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 boost_regex/fileiter.cpp -o boost_regex/fileiter.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 boost_regex/icu.cpp -o boost_regex/icu.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 boost_regex/instances.cpp -o boost_regex/instances.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 boost_regex/posix_api.cpp -o boost_regex/posix_api.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 boost_regex/regex.cpp -o boost_regex/regex.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 boost_regex/regex_raw_buffer.cpp -o boost_regex/regex_raw_buffer.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 boost_regex/regex_traits_defaults.cpp -o boost_regex/regex_traits_defaults.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 boost_regex/usinstances.cpp -o boost_regex/usinstances.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 boost_regex/w32_regex_traits.cpp -o boost_regex/w32_regex_traits.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 boost_regex/wc_regex_traits.cpp -o boost_regex/wc_regex_traits.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I../inst/include/ -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 boost_regex/winstances.cpp -o boost_regex/winstances.o
mkdir -p "/home/biocbuild/bbs-3.3-bioc/meat/flowCore.Rcheck/flowCore/lib"
ar rs "/home/biocbuild/bbs-3.3-bioc/meat/flowCore.Rcheck/flowCore/lib/libboost_regex.a" boost_regex/c_regex_traits.o boost_regex/cpp_regex_traits.o boost_regex/cregex.o boost_regex/fileiter.o boost_regex/icu.o boost_regex/instances.o boost_regex/posix_api.o boost_regex/regex.o boost_regex/regex_debug.o boost_regex/regex_raw_buffer.o boost_regex/regex_traits_defaults.o boost_regex/static_mutex.o boost_regex/usinstances.o boost_regex/w32_regex_traits.o boost_regex/wc_regex_traits.o boost_regex/wide_posix_api.o boost_regex/winstances.o
ar: creating /home/biocbuild/bbs-3.3-bioc/meat/flowCore.Rcheck/flowCore/lib/libboost_regex.a
g++ -std=c++11 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o flowCore.so FastLogicle.o Hyperlog.o Logicle.o RcppExports.o biexponential.o convertRawBytes.o fcsTextParse.o hyperlogTransform.o inPolygon.o inPolytope.o logicleTransform.o pairVectorRcppWrap.o uint2double.o zeroin.o /home/biocbuild/bbs-3.3-bioc/meat/flowCore.Rcheck/flowCore/lib/libboost_regex.a -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/flowCore.Rcheck/flowCore/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowCore)