ncdfFlow 2.12.0
Mike Jiang
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/ncdfFlow | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | 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-3.0-bioc/R/bin/R CMD check --no-vignettes --timings ncdfFlow_2.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/ncdfFlow.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ncdfFlow/DESCRIPTION’ ... OK
* this is package ‘ncdfFlow’ version ‘2.12.0’
* 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/libwin/i386/libhdf5ForBioC-7.dll src/libwin/i386/libsz-2.dll
src/libwin/x64/libhdf5ForBioC-7.dll src/libwin/x64/libsz-2.dll
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 ‘ncdfFlow’ can be installed ... [23s/35s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘flowCore’ ‘flowViz’
A package should be listed in only one of these fields.
* 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
Packages in Depends field not imported from:
‘BH’ ‘RcppArmadillo’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
‘flowCore:::makeFCSparameters’ ‘flowCore:::readFCSgetPar’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
pData<-,ncdfFlowList-data.frame : <anonymous>: no visible binding for
global variable ‘name’
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* 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 ... [14s/16s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘run-all.R’ [10s/10s]
[10s/11s] 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
NOTE: There were 4 notes.
See
‘/home/biocbuild/bbs-3.0-bioc/meat/ncdfFlow.Rcheck/00check.log’
for details.
* installing *source* package ‘ncdfFlow’ ...
configure: search for hdf5 library in: /usr/lib
configure: found hdf5 library in: /usr/lib
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/include -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/BH/include" -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/include -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/BH/include" -fpic -g -O2 -Wall -c bitOps.cpp -o bitOps.o
bitOps.cpp: In function ‘Rcpp::LogicalVector toLogical(Rcpp::RawVector)’:
bitOps.cpp:23:11: warning: unused variable ‘nByte’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/include -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/BH/include" -fpic -g -O2 -Wall -c hdfFlow.c -o hdfFlow.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/include -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/BH/include" -fpic -g -O2 -Wall -c init.c -o init.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/include -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/BH/include" -fpic -g -O2 -Wall -c readFrame.cpp -o readFrame.o
readFrame.cpp: In function ‘Rcpp::NumericVector readSlice_cpp(std::string, std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, unsigned int&)’:
readFrame.cpp:140:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readFrame.cpp:237:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
readFrame.cpp: In function ‘Rcpp::S4 readFrame(Rcpp::S4, Rcpp::RObject, Rcpp::RObject, bool)’:
readFrame.cpp:373:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/include -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/BH/include" -fpic -g -O2 -Wall -c wrappers.c -o wrappers.o
wrappers.c: In function ‘readSlice’:
wrappers.c:535:12: warning: unused variable ‘data_out’ [-Wunused-variable]
g++ -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o ncdfFlow.so RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o wrappers.o -L/usr/lib -lhdf5 -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-bioc/meat/ncdfFlow.Rcheck/ncdfFlow/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘lapply’ from package ‘base’ in package ‘ncdfFlow’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ncdfFlow)