Mike Jiang
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/ncdfFlow |
| Branch: RELEASE_3_6 |
| Last Commit: 41314b4 |
| Last Changed Date: 2017-10-30 12:39:37 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:35:09 -0400 (Thu, 12 Apr 2018).
| Package 930/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ncdfFlow 2.24.0 Mike Jiang
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: ncdfFlow |
| Version: 2.24.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ncdfFlow_2.24.0.tar.gz |
| StartedAt: 2018-04-12 07:01:05 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 07:03:20 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 134.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ncdfFlow.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ncdfFlow_2.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/ncdfFlow.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ncdfFlow/DESCRIPTION’ ... OK
* this is package ‘ncdfFlow’ version ‘2.24.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘ncdfFlow’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.2Mb
sub-directories of 1Mb or more:
lib 2.7Mb
libs 2.9Mb
* 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 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 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 ‘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
‘/Users/biocbuild/bbs-3.6-bioc/meat/ncdfFlow.Rcheck/00check.log’
for details.
ncdfFlow.Rcheck/00install.out
* installing *source* package ‘ncdfFlow’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c bitOps.cpp -o bitOps.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c hdfFlow.cpp -o hdfFlow.o
In file included from hdfFlow.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/lexical_cast.hpp:32:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:42:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:52:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/container/container_fwd.hpp:61:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
#define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
^
/usr/local/clang4/bin/../include/c++/v1/__config:388:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c readFrame.cpp -o readFrame.o
mkdir -p "/Users/biocbuild/bbs-3.6-bioc/meat/ncdfFlow.Rcheck/ncdfFlow/lib"
ar rs "/Users/biocbuild/bbs-3.6-bioc/meat/ncdfFlow.Rcheck/ncdfFlow/lib/libncdfFlow.a" RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o
ar: creating archive /Users/biocbuild/bbs-3.6-bioc/meat/ncdfFlow.Rcheck/ncdfFlow/lib/libncdfFlow.a
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o ncdfFlow.so RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhdf5lib/lib/libsz.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-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)
ncdfFlow.Rcheck/tests/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(ncdfFlow)
Loading required package: flowCore
Attaching package: 'flowCore'
The following object is masked from 'package:base':
sort
Loading required package: RcppArmadillo
Loading required package: BH
>
> test_check("ncdfFlow")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 376 SKIPPED: 0 FAILED: 0
Warning message:
closing unused connection 3 (/tmp/RtmpwWLWfR/file1787460b56e42)
> #devtools::test("˜/rglab/workspace/ncdfFlow")
> #test_file("˜/rglab/workspace/ncdfFlow/inst/tests/test_ncdfFlowSet_accessor.R")
> #test_file("˜/rglab/workspace/ncdfFlow/inst/tests/test_ncdfFlowList.R")
>
>
> proc.time()
user system elapsed
10.252 0.536 10.941
ncdfFlow.Rcheck/ncdfFlow-Ex.timings
| name | user | system | elapsed | |
| Indices | 1.682 | 0.081 | 1.791 | |
| as.flowSet | 0.851 | 0.040 | 0.909 | |
| clone.ncdfFlowSet | 0.875 | 0.029 | 0.913 | |
| extractFlowFrame | 0.617 | 0.043 | 0.673 | |
| ncdfFlowList-class | 0.651 | 0.046 | 0.710 | |
| ncdfFlowSet-constructor | 0.641 | 0.043 | 0.692 | |
| ncfsApply-ncdfFlowSet-method | 0.755 | 0.040 | 0.826 | |
| rbind2-method | 0.916 | 0.044 | 0.978 | |
| read.ncdfFlowSet | 0.576 | 0.016 | 0.603 | |
| replacement-method-for-ncdfFlowSet | 0.696 | 0.056 | 0.758 | |
| save_ncfs | 0.000 | 0.001 | 0.001 | |
| subset-methods | 0.654 | 0.045 | 0.707 | |
| unlink-ncdfFlowSet-method | 0.681 | 0.035 | 0.731 | |