ncdfFlow 2.22.2
Mike Jiang
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/ncdfFlow | | Branch: RELEASE_3_5 | | Last Commit: e959176 | | Last Changed Date: 2017-09-12 14:28:30 -0400 (Tue, 12 Sep 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ncdfFlow_2.22.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/ncdfFlow.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ncdfFlow/DESCRIPTION’ ... OK
* this is package ‘ncdfFlow’ version ‘2.22.2’
* 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/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 ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘flowCore’
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
'library' or 'require' call to ‘parallel’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
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
ncdfFlowSet,flowSet: warning in assign(guid, new("flowFrame", exprs =
matrix(numeric(0), nrow = 0, ncol = 0), parameters(x[[guid]]),
description(x[[guid]])), env = e1): partial argument match of 'env'
to 'envir'
rbind2,ncdfFlowList-ANY : <anonymous> : <anonymous>: warning in
assign(curSample, NA, env = indiceEnv): partial argument match of
'env' to 'envir'
read.ncdfFlowSet: no visible global function definition for ‘mclapply’
Undefined global functions or variables:
mclapply
* 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 shell scripts ... 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/ncdfFlow.Rcheck/00check.log’
for details.
* installing *source* package ‘ncdfFlow’ ...
configure: No directory was specified for --with-hdf5. Trying to find hdf5 using pkg-config.
checking for pkg-config... /usr/bin/pkg-config
checking for h5cc... /usr/bin/h5cc
configure: PKG_CPPFLAGS = -I/usr/include/hdf5/serial
configure: PKG_LIBS = -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/include/hdf5/serial -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/armadillo:53:0,
from /home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
from /home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:474:96: note: #pragma message: WARNING: use of OpenMP disabled; this compiler doesn't support OpenMP 3.0+
#pragma message ("WARNING: use of OpenMP disabled; this compiler doesn't support OpenMP 3.0+")
^
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/include/hdf5/serial -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I/usr/local/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]
unsigned nByte = bytes.size();
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/include/hdf5/serial -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c hdfFlow.c -o hdfFlow.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/include/hdf5/serial -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/include/hdf5/serial -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -Wall -c readFrame.cpp -o readFrame.o
In file included from /home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/armadillo:53:0,
from /home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
from /home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
from readFrame.cpp:11:
/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:474:96: note: #pragma message: WARNING: use of OpenMP disabled; this compiler doesn't support OpenMP 3.0+
#pragma message ("WARNING: use of OpenMP disabled; this compiler doesn't support OpenMP 3.0+")
^
readFrame.cpp: In function ‘Rcpp::NumericVector readSlice_cpp(std::__cxx11::string, std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, unsigned int&)’:
readFrame.cpp:140:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i = 0; i < chCount; i++){
^
readFrame.cpp:237:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i = 0; i < chCount; i++){
^
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o ncdfFlow.so RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/ncdfFlow.Rcheck/ncdfFlow/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ncdfFlow)