Rapid builds (Linux only) of a subset of BioC 3.21<BR>Report updated every 6 hours

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	869
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for ncdfFlow on teran2

To the developers/maintainers of the ncdfFlow package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: ncdfFlow

Version: 2.53.1

Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:ncdfFlow.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings ncdfFlow_2.53.1.tar.gz

StartedAt: 2025-03-22 07:06:54 -0400 (Sat, 22 Mar 2025)

EndedAt: 2025-03-22 07:07:41 -0400 (Sat, 22 Mar 2025)

EllapsedTime: 46.2 seconds

RetCode: 1

Status: ERROR

CheckDir: ncdfFlow.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:ncdfFlow.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings ncdfFlow_2.53.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/ncdfFlow.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘ncdfFlow/DESCRIPTION’ ... OK
* this is package ‘ncdfFlow’ version ‘2.53.1’
* 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
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
  installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
* 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 loading without being on the library search path ... 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 ... WARNING
Note: information on .o files is not available
File ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/ncdfFlow/libs/ncdfFlow.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  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 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ncdfFlow-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getIndices,ncdfFlowSet,character-method
> ### Title: 'getIndices' extracts the event indices of one or multiple
> ###   samples from ncdfFlowSet
> ### Aliases: getIndices,ncdfFlowSet,character-method getIndices
> ###   initIndices,ncdfFlowSet-method initIndices
> ###   updateIndices,ncdfFlowSet,character,logical-method updateIndices
> 
> ### ** Examples
> 
> data(GvHD)
> nc <- ncdfFlowSet(GvHD[1:2])
write s5a01 to empty cdf slot...
     error #000: in H5F_block_write(): line 161
        major: Low-level I/O
        minor: Write failed
     error #001: in H5PB_write(): line 1032
        major: Page Buffering
        minor: Write failed
     error #002: in H5F__accum_write(): line 824
        major: Low-level I/O
        minor: Write failed
     error #003: in H5FD_write(): line 249
        major: Virtual File Layer
        minor: Write failed
     error #004: in H5FD__sec2_write(): line 856
        major: Low-level I/O
        minor: Write failed
     error #005: in H5D_close(): line 1898
        major: Dataset
        minor: Write failed
     error #006: in H5D__flush_real(): line 3022
        major: Dataset
        minor: Unable to flush data from cache
     error #007: in H5D__chunk_flush(): line 2823
        major: Dataset
        minor: Unable to flush data from cache
     error #008: in H5D__chunk_flush_entry(): line 3467
        major: Dataset
        minor: Write failed
     error #009: in H5F_block_write(): line 161
        major: Low-level I/O
        minor: Write failed
     error #010: in H5PB_write(): line 1032
        major: Page Buffering
        minor: Write failed
     error #011: in H5F__accum_write(): line 824
        major: Low-level I/O
        minor: Write failed
     error #012: in H5FD_write(): line 249
        major: Virtual File Layer
        minor: Write failed
     error #013: in H5FD__sec2_write(): line 856
        major: Low-level I/O
        minor: Write failed
     error #014: in H5D__chunk_flush_entry(): line 3467
        major: Dataset
        minor: Write failed
     error #015: in H5F_block_write(): line 161
        major: Low-level I/O
        minor: Write failed
     error #016: in H5PB_write(): line 1032
        major: Page Buffering
        minor: Write failed
     error #017: in H5F__accum_write(): line 824
        major: Low-level I/O
        minor: Write failed
     error #018: in H5FD_write(): line 249
        major: Virtual File Layer
        minor: Write failed
     error #019: in H5FD__sec2_write(): line 856
        major: Low-level I/O
        minor: Write failed
     error #020: in H5D__chunk_flush_entry(): line 3467
        major: Dataset
        minor: Write failed
     error #021: in H5F_block_write(): line 161
        major: Low-level I/O
        minor: Write failed
     error #022: in H5PB_write(): line 1032
        major: Page Buffering
        minor: Write failed
     error #023: in H5F__accum_write(): line 824
        major: Low-level I/O
        minor: Write failed
     error #024: in H5FD_write(): line 249
        major: Virtual File Layer
        minor: Write failed
     error #025: in H5FD__sec2_write(): line 856
        major: Low-level I/O
        minor: Write failed
     error #026: in H5D__chunk_flush_entry(): line 3467
        major: Dataset
        minor: Write failed
     error #027: in H5F_block_write(): line 161
        major: Low-level I/O
        minor: Write failed
     error #028: in H5PB_write(): line 1032
        major: Page Buffering
        minor: Write failed
     error #029: in H5F__accum_write(): line 824
        major: Low-level I/O
        minor: Write failed
     error #030: in H5FD_write(): line 249
        major: Virtual File Layer
        minor: Write failed
     error #031: in H5FD__sec2_write(): line 856
        major: Low-level I/O
        minor: Write failed
Error: hdf Error
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   3. ├─ncdfFlow::ncdfFlowSet(fs)
   4. └─ncdfFlow::ncdfFlowSet(fs)
   5.   └─ncdfFlow (local) .local(x, ...)
   6.     └─ncdfFlow:::createFile(...)
  
  [ FAIL 6 | WARN 13 | SKIP 1 | PASS 24 ]
  Error: Test failures
  In addition: Warning messages:
  1: In for (i in 2:nargs) { :
    closing unused connection 4 (/tmp/Rtmpz1XtqU/filef3b5979479171)
  2: In for (i in seq_len(n)) { :
    closing unused connection 4 (/tmp/Rtmpz1XtqU/filef3b596984455)
  Execution halted
  HDF5: infinite loop closing library
        L,S_top,T_top,F,P,P,Z,FD,E,SL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘ncdfFlow.Rnw’ using knitr
     error #000: in H5Fcreate(): line 366
        major: File accessibility
        minor: Unable to open file
     error #001: in H5F_open(): line 1919
        major: File accessibility
        minor: Unable to close file
     error #002: in H5F__dest(): line 1406
        major: File accessibility
        minor: Unable to release object
     error #003: in H5F__accum_reset(): line 1065
        major: File accessibility
        minor: Unable to flush data from cache
     error #004: in H5F__accum_flush(): line 1029
        major: Low-level I/O
        minor: Write failed
     error #005: in H5FD_write(): line 249
        major: Virtual File Layer
        minor: Write failed
     error #006: in H5FD__sec2_write(): line 856
        major: Low-level I/O
        minor: Write failed
     error #007: in H5F_open(): line 1885
        major: File accessibility
        minor: Unable to flush data from cache
     error #008: in H5F_flush_tagged_metadata(): line 194
        major: Low-level I/O
        minor: Can't reset object
     error #009: in H5F__accum_reset(): line 1065
        major: File accessibility
        minor: Unable to flush data from cache
     error #010: in H5F__accum_flush(): line 1029
        major: Low-level I/O
        minor: Write failed
     error #011: in H5FD_write(): line 249
        major: Virtual File Layer
        minor: Write failed
     error #012: in H5FD__sec2_write(): line 856
        major: Low-level I/O
        minor: Write failed

Quitting from ncdfFlow.Rnw:99-104 [read.ncdfFlowSet]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! hdf Error
---
Backtrace:
    x
 1. \-ncdfFlow::read.ncdfFlowSet(files = files)
 2.   \-ncdfFlow:::createFile(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'ncdfFlow.Rnw' failed with diagnostics:
hdf Error
--- failed re-building ‘ncdfFlow.Rnw’

SUMMARY: processing the following file failed:
  ‘ncdfFlow.Rnw’

Error: Vignette re-building failed.
Execution halted
HDF5: infinite loop closing library
      L,T_top,P,P,FD,E,SL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL

* checking PDF version of manual ... ERROR
Rd conversion errors:
Converting parsed Rd's to LaTeX Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Error in writeLines(x, con, useBytes = TRUE, ...) : 
  Error writing to connection:  No space left on device
* DONE

Status: 4 ERRORs, 3 WARNINGs, 7 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/ncdfFlow.Rcheck/00check.log’
for details.

Installation output

ncdfFlow.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL ncdfFlow
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘ncdfFlow’ ...
** this is package ‘ncdfFlow’ version ‘2.53.1’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/cpp11/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c cpp11.cpp -o cpp11.o
g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/cpp11/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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 "/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/00LOCK-ncdfFlow/00new/ncdfFlow/lib"
ar rs "/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/00LOCK-ncdfFlow/00new/ncdfFlow/lib/libncdfFlow.a" cpp11.o hdfFlow.o
ar: creating /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/00LOCK-ncdfFlow/00new/ncdfFlow/lib/libncdfFlow.a
g++ -std=gnu++11 -shared -L/usr/local/lib -o ncdfFlow.so cpp11.o hdfFlow.o /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/lib/libhdf5_cpp.a /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/lib/libhdf5.a -L/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/00LOCK-ncdfFlow/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ncdfFlow)

Tests output

ncdfFlow.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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")
     error #000: in H5Fcreate(): line 366
        major: File accessibility
        minor: Unable to open file
     error #001: in H5F_open(): line 1919
        major: File accessibility
        minor: Unable to close file
     error #002: in H5F__dest(): line 1406
        major: File accessibility
        minor: Unable to release object
     error #003: in H5F__accum_reset(): line 1065
        major: File accessibility
        minor: Unable to flush data from cache
     error #004: in H5F__accum_flush(): line 1029
        major: Low-level I/O
        minor: Write failed
     error #005: in H5FD_write(): line 249
        major: Virtual File Layer
        minor: Write failed
     error #006: in H5FD__sec2_write(): line 856
        major: Low-level I/O
        minor: Write failed
     error #007: in H5F_open(): line 1885
        major: File accessibility
        minor: Unable to flush data from cache
     error #008: in H5F_flush_tagged_metadata(): line 194
        major: Low-level I/O
        minor: Can't reset object
     error #009: in H5F__accum_reset(): line 1065
        major: File accessibility
        minor: Unable to flush data from cache
     error #010: in H5F__accum_flush(): line 1029
        major: Low-level I/O
        minor: Write failed
     error #011: in H5FD_write(): line 249
        major: Virtual File Layer
        minor: Write failed
     error #012: in H5FD__sec2_write(): line 856
        major: Low-level I/O
        minor: Write failed
     error #000: in H5Fcreate(): line 366
        major: File accessibility
        minor: Unable to open file
     error #001: in H5F_open(): line 1919
        major: File accessibility
        minor: Unable to close file
     error #002: in H5F__dest(): line 1406
        major: File accessibility
        minor: Unable to release object
     error #003: in H5F__accum_reset(): line 1065
        major: File accessibility
        minor: Unable to flush data from cache
     error #004: in H5F__accum_flush(): line 1029
        major: Low-level I/O
        minor: Write failed
     error #005: in H5FD_write(): line 249
        major: Virtual File Layer
        minor: Write failed
     error #006: in H5FD__sec2_write(): line 856
        major: Low-level I/O
        minor: Write failed
     error #007: in H5F_open(): line 1885
        major: File accessibility
        minor: Unable to flush data from cache
     error #008: in H5F_flush_tagged_metadata(): line 194
        major: Low-level I/O
        minor: Can't reset object
     error #009: in H5F__accum_reset(): line 1065
        major: File accessibility
        minor: Unable to flush data from cache
     error #010: in H5F__accum_flush(): line 1029
        major: Low-level I/O
        minor: Write failed
     error #011: in H5FD_write(): line 249
        major: Virtual File Layer
        minor: Write failed
     error #012: in H5FD__sec2_write(): line 856
        major: Low-level I/O
        minor: Write failed
     error #000: in H5FD_write(): line 249
        major: Virtual File Layer
        minor: Write failed
     error #001: in H5FD__sec2_write(): line 856
        major: Low-level I/O
        minor: Write failed
     error #002: in H5D__chunk_flush_entry(): line 3467
        major: Dataset
        minor: Write failed
     error #003: in H5F_block_write(): line 161
        major: Low-level I/O
        minor: Write failed
     error #004: in H5PB_write(): line 1032
        major: Page Buffering
        minor: Write failed
     error #005: in H5F__accum_write(): line 824
        major: Low-level I/O
        minor: Write failed
     error #006: in H5FD_write(): line 249
        major: Virtual File Layer
        minor: Write failed
     error #007: in H5FD__sec2_write(): line 856
        major: Low-level I/O
        minor: Write failed
     error #008: in H5D__chunk_flush_entry(): line 3467
        major: Dataset
        minor: Write failed
     error #009: in H5F_block_write(): line 161
        major: Low-level I/O
        minor: Write failed
     error #010: in H5PB_write(): line 1032
        major: Page Buffering
        minor: Write failed
     error #011: in H5F__accum_write(): line 824
        major: Low-level I/O
        minor: Write failed
     error #012: in H5FD_write(): line 249
        major: Virtual File Layer
        minor: Write failed
     error #013: in H5FD__sec2_write(): line 856
        major: Low-level I/O
        minor: Write failed
     error #014: in H5D__chunk_flush_entry(): line 3467
        major: Dataset
        minor: Write failed
     error #015: in H5F_block_write(): line 161
        major: Low-level I/O
        minor: Write failed
     error #016: in H5PB_write(): line 1032
        major: Page Buffering
        minor: Write failed
     error #017: in H5F__accum_write(): line 824
        major: Low-level I/O
        minor: Write failed
     error #018: in H5FD_write(): line 249
        major: Virtual File Layer
        minor: Write failed
     error #019: in H5FD__sec2_write(): line 856
        major: Low-level I/O
        minor: Write failed
     error #020: in H5D__chunk_flush_entry(): line 3467
        major: Dataset
        minor: Write failed
     error #021: in H5F_block_write(): line 161
        major: Low-level I/O
        minor: Write failed
     error #022: in H5PB_write(): line 1032
        major: Page Buffering
        minor: Write failed
     error #023: in H5F__accum_write(): line 824
        major: Low-level I/O
        minor: Write failed
     error #024: in H5FD_write(): line 249
        major: Virtual File Layer
        minor: Write failed
     error #025: in H5FD__sec2_write(): line 856
        major: Low-level I/O
        minor: Write failed
     error #026: in H5D__chunk_flush_entry(): line 3467
        major: Dataset
        minor: Write failed
     error #027: in H5F_block_write(): line 161
        major: Low-level I/O
        minor: Write failed
     error #028: in H5PB_write(): line 1032
        major: Page Buffering
        minor: Write failed
     error #029: in H5F__accum_write(): line 824
        major: Low-level I/O
        minor: Write failed
     error #030: in H5FD_write(): line 249
        major: Virtual File Layer
        minor: Write failed
     error #031: in H5FD__sec2_write(): line 856
        major: Low-level I/O
        minor: Write failed
     error #000: in H5Dclose(): line 340
        major: Dataset
        minor: Unable to decrement reference count
     error #001: in H5I_dec_app_ref_always_close(): line 1362
        major: Object atom
        minor: Unable to decrement reference count
     error #002: in H5I_dec_app_ref(): line 1307
        major: Object atom
        minor: Unable to decrement reference count
     error #003: in H5D__close_cb(): line 1857
        major: Dataset
        minor: Can't close object
     error #004: in H5D_close(): line 1978
        major: Dataset
        minor: Unable to release object
     error #005: in H5D__chunk_dest(): line 2919
        major: Low-level I/O
        minor: Unable to flush data from cache
     error #006: in H5D__chunk_cache_evict(): line 3546
        major: Low-level I/O
        minor: Write failed
     error #007: in H5D__chunk_flush_entry(): line 3467
        major: Dataset
        minor: Write failed
     error #008: in H5F_block_write(): line 161
        major: Low-level I/O
        minor: Write failed
     error #009: in H5PB_write(): line 1032
        major: Page Buffering
        minor: Write failed
     error #010: in H5F__accum_write(): line 824
        major: Low-level I/O
        minor: Write failed
     error #011: in H5FD_write(): line 249
        major: Virtual File Layer
        minor: Write failed
     error #012: in H5FD__sec2_write(): line 856
        major: Low-level I/O
        minor: Write failed
     error #013: in H5D_close(): line 1898
        major: Dataset
        minor: Write failed
     error #014: in H5D__flush_real(): line 3022
        major: Dataset
        minor: Unable to flush data from cache
     error #015: in H5D__chunk_flush(): line 2823
        major: Dataset
        minor: Unable to flush data from cache
     error #016: in H5D__chunk_flush_entry(): line 3467
        major: Dataset
        minor: Write failed
     error #017: in H5F_block_write(): line 161
        major: Low-level I/O
        minor: Write failed
     error #018: in H5PB_write(): line 1032
        major: Page Buffering
        minor: Write failed
     error #019: in H5F__accum_write(): line 824
        major: Low-level I/O
        minor: Write failed
     error #020: in H5FD_write(): line 249
        major: Virtual File Layer
        minor: Write failed
     error #021: in H5FD__sec2_write(): line 856
        major: Low-level I/O
        minor: Write failed
     error #000: in H5Fcreate(): line 366
        major: File accessibility
        minor: Unable to open file
     error #001: in H5F_open(): line 1919
        major: File accessibility
        minor: Unable to close file
     error #002: in H5F__dest(): line 1406
        major: File accessibility
        minor: Unable to release object
     error #003: in H5F__accum_reset(): line 1065
        major: File accessibility
        minor: Unable to flush data from cache
     error #004: in H5F__accum_flush(): line 1029
        major: Low-level I/O
        minor: Write failed
     error #005: in H5FD_write(): line 249
        major: Virtual File Layer
        minor: Write failed
     error #006: in H5FD__sec2_write(): line 856
        major: Low-level I/O
        minor: Write failed
     error #007: in H5F_open(): line 1885
        major: File accessibility
        minor: Unable to flush data from cache
     error #008: in H5F_flush_tagged_metadata(): line 194
        major: Low-level I/O
        minor: Can't reset object
     error #009: in H5F__accum_reset(): line 1065
        major: File accessibility
        minor: Unable to flush data from cache
     error #010: in H5F__accum_flush(): line 1029
        major: Low-level I/O
        minor: Write failed
     error #011: in H5FD_write(): line 249
        major: Virtual File Layer
        minor: Write failed
     error #012: in H5FD__sec2_write(): line 856
        major: Low-level I/O
        minor: Write failed
[ FAIL 6 | WARN 13 | SKIP 1 | PASS 24 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• file.exists(filename) is not TRUE (1): 'test_IO.R:6:3'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_IO.R:52:3'): read.ncdfFlowSet ──────────────────────────────────
Error: hdf Error
Backtrace:
    ▆
 1. └─ncdfFlow::read.ncdfFlowSet(tmp, emptyValue = FALSE) at test_IO.R:52:3
 2.   └─ncdfFlow:::createFile(...)
── Error ('test_IO.R:64:7'): save_ncfs/load_ncfs ───────────────────────────────
Error: hdf Error
Backtrace:
    ▆
 1. ├─ncdfFlow::ncdfFlowSet(GvHD[1:2]) at test_IO.R:64:7
 2. └─ncdfFlow::ncdfFlowSet(GvHD[1:2])
 3.   └─ncdfFlow (local) .local(x, ...)
 4.     └─ncdfFlow:::createFile(...)
── Error ('test_IO.R:148:3'): read.ncdfFlowSet: channel_alias ──────────────────
Error in `FUN(X[[i]], ...)`: Error in if (!version %in% c("FCS2.0", "FCS3.0", "FCS3.1", "FCS3.2")) stop("This does not seem to be a valid FCS2.0, FCS3.0 or FCS3.1 file") : 
  argument is of length zero
/tmp/Rtmpz1XtqU/filef3b596984455
Backtrace:
     ▆
  1. ├─testthat::expect_message(...) at test_IO.R:148:3
  2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. └─ncdfFlow::read.ncdfFlowSet(c(fcs1, fcs2))
  7.   ├─BiocGenerics::lapply(files, getChnlEvt)
  8.   └─base::lapply(files, getChnlEvt)
  9.     └─ncdfFlow (local) FUN(X[[i]], ...)
 10.       ├─BiocGenerics::eval(thisCall)
 11.       ├─base::eval(thisCall)
 12.       │ └─base::eval(thisCall)
 13.       └─flowCore::read.FCSheader(curFile, emptyValue = TRUE)
 14.         └─base::lapply(...)
 15.           └─flowCore (local) FUN(X[[i]], ...)
── Error ('test_compensation.R:2:1'): (code run outside of `test_that()`) ──────
Error: hdf Error
Backtrace:
    ▆
 1. ├─ncdfFlow::ncdfFlowSet(fs) at test_compensation.R:2:1
 2. └─ncdfFlow::ncdfFlowSet(fs)
 3.   └─ncdfFlow (local) .local(x, ...)
 4.     ├─methods (local) `[[<-`(`*tmp*`, guid, compress = compress, value = `<flowFram[,7]>`)
 5.     └─ncdfFlow (local) `[[<-`(`*tmp*`, guid, compress = compress, value = `<flowFram[,7]>`)
 6.       └─ncdfFlow (local) .local(x, i, j, ..., value = value)
 7.         └─ncdfFlow:::writeSlice(...)
── Error ('test_ncdfFlowList.R:6:1'): (code run outside of `test_that()`) ──────
Error: hdf Error
Backtrace:
    ▆
 1. ├─base::suppressMessages(nc2 <- ncdfFlowSet(GvHD[3:4])) at test_ncdfFlowList.R:6:1
 2. │ └─base::withCallingHandlers(...)
 3. ├─ncdfFlow::ncdfFlowSet(GvHD[3:4])
 4. └─ncdfFlow::ncdfFlowSet(GvHD[3:4])
 5.   └─ncdfFlow (local) .local(x, ...)
 6.     ├─methods (local) `[[<-`(`*tmp*`, guid, compress = compress, value = `<flowFram[,8]>`)
 7.     └─ncdfFlow (local) `[[<-`(`*tmp*`, guid, compress = compress, value = `<flowFram[,8]>`)
 8.       └─ncdfFlow (local) .local(x, i, j, ..., value = value)
 9.         └─ncdfFlow:::writeSlice(...)
── Error ('test_ncdfFlowSet_accessor.R:5:1'): (code run outside of `test_that()`) ──
Error: hdf Error
Backtrace:
    ▆
 1. ├─base::suppressMessages(ncfs <- ncdfFlowSet(fs)) at test_ncdfFlowSet_accessor.R:5:1
 2. │ └─base::withCallingHandlers(...)
 3. ├─ncdfFlow::ncdfFlowSet(fs)
 4. └─ncdfFlow::ncdfFlowSet(fs)
 5.   └─ncdfFlow (local) .local(x, ...)
 6.     └─ncdfFlow:::createFile(...)

[ FAIL 6 | WARN 13 | SKIP 1 | PASS 24 ]
Error: Test failures
In addition: Warning messages:
1: In for (i in 2:nargs) { :
  closing unused connection 4 (/tmp/Rtmpz1XtqU/filef3b5979479171)
2: In for (i in seq_len(n)) { :
  closing unused connection 4 (/tmp/Rtmpz1XtqU/filef3b596984455)
Execution halted
HDF5: infinite loop closing library
      L,S_top,T_top,F,P,P,Z,FD,E,SL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL

Example timings

ncdfFlow.Rcheck/ncdfFlow-Ex.timings

name

user

system

elapsed