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CHECK report for ncdfFlow on malbec2

This page was generated on 2018-10-17 08:24:02 -0400 (Wed, 17 Oct 2018).

Package 981/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ncdfFlow 2.26.0
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)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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### Running 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
###
##############################################################################
##############################################################################


* 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.



Installation output

ncdfFlow.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL ncdfFlow
###
##############################################################################
##############################################################################


* 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)

Tests output

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 

Example timings

ncdfFlow.Rcheck/ncdfFlow-Ex.timings

nameusersystemelapsed
Indices0.7760.0320.873
as.flowSet0.6080.0200.629
clone.ncdfFlowSet0.2240.0080.256
extractFlowFrame0.5160.0160.532
ncdfFlowList-class0.6960.0200.718
ncdfFlowSet-constructor0.7080.0160.722
ncfsApply-ncdfFlowSet-method0.9200.0080.928
rbind2-method1.0120.0161.029
read.ncdfFlowSet0.3480.0000.348
replacement-method-for-ncdfFlowSet0.5640.0280.594
save_ncfs000
subset-methods0.5200.0120.534
unlink-ncdfFlowSet-method0.5360.0040.539