Mike Jiang
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/ncdfFlow |
| Branch: RELEASE_3_7 |
| Last Commit: 17df36c |
| Last Changed Date: 2018-04-30 10:35:22 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:24:02 -0400 (Wed, 17 Oct 2018).
| Package 981/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ncdfFlow 2.26.0 Mike Jiang
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: ncdfFlow |
| Version: 2.26.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ncdfFlow.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ncdfFlow_2.26.0.tar.gz |
| StartedAt: 2018-10-16 02:19:42 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 02:20:42 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 60.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ncdfFlow.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ncdfFlow.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ncdfFlow_2.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/ncdfFlow.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘2.26.0’
* 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 19.2Mb
sub-directories of 1Mb or more:
lib 6.1Mb
libs 12.5Mb
* 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:::check_channel_alias’ ‘flowCore:::guid’
‘flowCore:::makeFCSparameters’ ‘flowCore:::readFCSgetPar’
‘flowCore:::update_channel_by_alias’
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’
colnames<-,ncdfFlowSet: no visible global function definition for
‘keyword’
colnames<-,ncdfFlowSet: no visible global function definition for
‘keyword<-’
Undefined global functions or variables:
keyword keyword<- 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 ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.7-bioc/R/library/ncdfFlow/libs/ncdfFlow.so’:
Found ‘abort’, possibly from ‘abort’ (C)
Found ‘rand_r’, possibly from ‘rand_r’ (C)
Found ‘stderr’, possibly from ‘stderr’ (C)
Found ‘stdout’, possibly from ‘stdout’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* 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: 5 NOTEs
See
‘/home/biocbuild/bbs-3.7-bioc/meat/ncdfFlow.Rcheck/00check.log’
for details.
ncdfFlow.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL ncdfFlow
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘ncdfFlow’ ...
** libs
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo:54:0,
from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
from ../inst/include/../../src/hdfFlow.h:5,
from ../inst/include/ncdfFlow.h:4,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:509:108: note: #pragma message: NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags
#pragma message ("NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags")
^
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c bitOps.cpp -o bitOps.o
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c hdfFlow.cpp -o hdfFlow.o
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo:54:0,
from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
from hdfFlow.h:5,
from hdfFlow.cpp:1:
/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:509:108: note: #pragma message: NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags
#pragma message ("NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags")
^
hdfFlow.cpp: In function ‘void readSlice_cpp(hid_t, hid_t, hid_t, std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, unsigned int, double*, bool)’:
hdfFlow.cpp:486:14: warning: variable ‘status’ set but not used [-Wunused-but-set-variable]
herr_t status;
^
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c readFrame.cpp -o readFrame.o
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo:54:0,
from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
from hdfFlow.h:5,
from readFrame.cpp:1:
/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:509:108: note: #pragma message: NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags
#pragma message ("NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags")
^
mkdir -p "/home/biocbuild/bbs-3.7-bioc/R/library/ncdfFlow/lib"
ar rs "/home/biocbuild/bbs-3.7-bioc/R/library/ncdfFlow/lib/libncdfFlow.a" RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o
ar: creating /home/biocbuild/bbs-3.7-bioc/R/library/ncdfFlow/lib/libncdfFlow.a
g++ -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o ncdfFlow.so RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o /home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/lib/libsz.a -lz -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/ncdfFlow/libs
** R
** inst
** byte-compile and prepare 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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
Loading required package: RcppArmadillo
Loading required package: BH
>
> test_check("ncdfFlow")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 398 SKIPPED: 0 FAILED: 0
Warning message:
In match.arg(type, c("success", "failure", "error", "skip", "warning")) :
closing unused connection 3 (/tmp/RtmpISXK1E/file27947535b383)
> #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
7.824 0.208 8.202
ncdfFlow.Rcheck/ncdfFlow-Ex.timings
| name | user | system | elapsed | |
| Indices | 0.776 | 0.032 | 0.873 | |
| as.flowSet | 0.608 | 0.020 | 0.629 | |
| clone.ncdfFlowSet | 0.224 | 0.008 | 0.256 | |
| extractFlowFrame | 0.516 | 0.016 | 0.532 | |
| ncdfFlowList-class | 0.696 | 0.020 | 0.718 | |
| ncdfFlowSet-constructor | 0.708 | 0.016 | 0.722 | |
| ncfsApply-ncdfFlowSet-method | 0.920 | 0.008 | 0.928 | |
| rbind2-method | 1.012 | 0.016 | 1.029 | |
| read.ncdfFlowSet | 0.348 | 0.000 | 0.348 | |
| replacement-method-for-ncdfFlowSet | 0.564 | 0.028 | 0.594 | |
| save_ncfs | 0 | 0 | 0 | |
| subset-methods | 0.520 | 0.012 | 0.534 | |
| unlink-ncdfFlowSet-method | 0.536 | 0.004 | 0.539 | |