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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ncdfFlow.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings ncdfFlow_2.54.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/ncdfFlow.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ncdfFlow/DESCRIPTION' ... OK
* this is package 'ncdfFlow' version '2.54.0'
* 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 whether package 'ncdfFlow' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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.
Non-standard license specification:
  AGPL-3.0-only
Standardizable: FALSE
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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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.
Package in Depends field not imported from: 'BH'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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]]),
  keyword(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 ... NOTE
checkRd: (-1) subset-functions.Rd:20: Lost braces
    20 | a subset of code{ncdfFlowSet} or \code{ncdfFlowList} object
       |                 ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  extractFlowFrame.Rd: [[,flowSet-method
  ncdfFlowSet-class.Rd: flowSet, Subset, exprs,flowFrame-method,
    phenoData,flowSet-method, flowSet-class
  ncdfFlowSet-split.Rd: split-methods
  ncfsApply-ncdfFlowSet-method.Rd: fsApply
  rbind2-method.Rd: rbind2,flowSet,flowSet-method
  read.ncdfFlowSet.Rd: read.FCS
  subset-methods.Rd: [,flowSet-method
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'extractFlowFrame.Rd':
\S4method{[[}{ncdfFlowSet,ANY}
  Code: function(x, i, j, ...)
  Docs: function(x, i, j, use.exprs = TRUE, ...)
  Argument names in docs not in code:
    use.exprs
  Mismatches in argument names:
    Position: 4 Code: ... Docs: use.exprs

* 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 ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section 'Writing portable
packages' in the 'Writing R Extensions' manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/ncdfFlow/libs/x64/ncdfFlow.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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 nor [v]sprintf. 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
Indices 6.58   0.39    8.59
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 8 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/ncdfFlow.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL ncdfFlow
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'ncdfFlow' ...
** this is package 'ncdfFlow' version '2.54.0'
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
using C++11
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/cpp11/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c cpp11.cpp -o cpp11.o
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/cpp11/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/BH/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c hdfFlow.cpp -o hdfFlow.o
hdfFlow.cpp: In function 'void readSlice_cpp(hid_t, hid_t, hid_t, std::vector<int>, int, int, double*, bool)':
hdfFlow.cpp:508:31: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  508 |                 if(sampleIndx >= nSample)
      |                    ~~~~~~~~~~~^~~~~~~~~~
hdfFlow.cpp:493:21: warning: variable 'status' set but not used [-Wunused-but-set-variable]
  493 |         herr_t      status;
      |                     ^~~~~~
mkdir -p "E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-ncdfFlow/00new/ncdfFlow/lib/x64"
ar rs "E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-ncdfFlow/00new/ncdfFlow/lib/x64/libncdfFlow.a" cpp11.o hdfFlow.o
C:\rtools45\x86_64-w64-mingw32.static.posix\bin\ar.exe: creating E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-ncdfFlow/00new/ncdfFlow/lib/x64/libncdfFlow.a
g++ -shared -s -static-libgcc -o ncdfFlow.dll tmp.def cpp11.o hdfFlow.o -LE:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/lib/x64-ucrt -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lsz -laec -lz -lpsapi -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-ncdfFlow/00new/ncdfFlow/libs/x64
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ncdfFlow)

R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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: BH
> 
> test_check("ncdfFlow")
[ FAIL 0 | WARN 1 | SKIP 3 | PASS 335 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• ###this will cause crashing error see #50 (2):
  'test_ncdfFlowSet_accessor.R:51:5', 'test_ncdfFlowSet_accessor.R:267:3'
• file.exists(filename) is not TRUE (1): 'test_IO.R:6:3'

[ FAIL 0 | WARN 1 | SKIP 3 | PASS 335 ]
Warning message:
In for (i in seq_len(n)) { :
  closing unused connection 4 (E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpCEF6Kb\file13bac114623e7)
> #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 
  15.62    1.10   18.46