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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:CytoML.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings CytoML_2.0.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/CytoML.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CytoML/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CytoML’ version ‘2.0.5’
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  .github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CytoML’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
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.
Namespaces in Imports field not imported from:
  ‘RUnit’ ‘corpcor’ ‘openCyto’ ‘stats’
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  ‘ggcyto:::merge.quad.gates’ ‘lattice:::updateList’
  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
addCustomInfo: no visible global function definition for
  ‘gh_get_transformations’
addGate: no visible binding for global variable ‘id’
addGate: no visible binding for global variable ‘gate_id’
addGate: no visible binding for global variable ‘fcs’
addGate: no visible binding for global variable ‘fcs_file_id’
addGate: no visible binding for global variable ‘gate_def’
addGate: no visible binding for global variable ‘name’
ce_get_panels: no visible binding for global variable ‘panel’
ce_get_panels: no visible binding for global variable ‘n’
constructTree: no visible binding for global variable ‘id’
constructTree: no visible binding for global variable ‘name’
createTransformIdentifier: no visible global function definition for
  ‘slotNames’
cytobank_to_gatingset.cytobank_experiment: no visible binding for
  global variable ‘desc’
diva_to_gatingset: no visible binding for global variable ‘specimen’
diva_to_gatingset: no visible binding for global variable
  ‘sampleSelected’
diva_to_gatingset: no visible global function definition for
  ‘gh_apply_to_new_fcs’
export_comp_trans: no visible global function definition for
  ‘gh_get_compensations’
export_comp_trans: no visible global function definition for
  ‘gh_get_transformations’
export_gates_cytobank: no visible global function definition for
  ‘gs_get_pop_paths’
export_gates_cytobank: no visible global function definition for
  ‘gs_pop_get_gate’
extend.polygonGate: no visible binding for global variable ‘..dim’
extend.polygonGate : <anonymous>: no visible binding for global
  variable ‘y’
extend.polygonGate : <anonymous>: no visible binding for global
  variable ‘x’
extend.polygonGate: no visible binding for global variable ‘id’
extend.polygonGate: no visible binding for global variable ‘x’
extend.polygonGate: no visible binding for global variable ‘y’
extend.polygonGate: no visible binding for global variable ‘is.smaller’
flinTr: no visible global function definition for ‘lintGml2’
fratioTr: no visible global function definition for ‘ratiotGml2’
generate_trans: no visible global function definition for
  ‘flowjo_log_trans’
gs_compare_cytobank_counts: no visible binding for global variable
  ‘population’
gs_compare_cytobank_counts: no visible binding for global variable
  ‘parent’
gs_compare_cytobank_counts: no visible binding for global variable
  ‘parent_count’
gs_compare_cytobank_counts: no visible global function definition for
  ‘.’
gs_compare_cytobank_counts: no visible binding for global variable
  ‘fcs_filename’
hyperlogTr: no visible global function definition for ‘hyperlogtGml2’
open_cytobank_experiment: no visible global function definition for
  ‘unzip’
range.GatingHierarchy: no visible global function definition for
  ‘gh_get_transformations’
read.gatingML.cytobank: no visible binding for global variable ‘id’
read.gatingML.cytobank: no visible binding for global variable
  ‘comp_ref’
transDg1polynomial: no visible global function definition for
  ‘dg1polynomial’
transEH: no visible global function definition for ‘EHtrans’
transExponential: no visible global function definition for
  ‘exponential’
transHyperLog: no visible global function definition for ‘hyperlog’
transHyperbolicSin: no visible global function definition for ‘sinht’
transInvSplitScale: no visible global function definition for
  ‘invsplitscale’
transInverseHyperbolicSin: no visible global function definition for
  ‘asinht’
transLogarithm: no visible global function definition for ‘logarithm’
transQuadratic: no visible global function definition for ‘quadratic’
transRatio: no visible global function definition for ‘ratio’
transSplitScale: no visible global function definition for ‘splitscale’
transSquareroot: no visible global function definition for ‘squareroot’
write.gatingML: no visible global function definition for ‘sessionInfo’
xmlVertexNode : <anonymous>: no visible global function definition for
  ‘format_float’
identifyNode,http...www.isac.net.org.std.Gating.ML.v1.5.gating_DecisionTreeGate:
  no visible binding for global variable ‘expressionFilter’
identifyNode,http...www.isac.net.org.std.Gating.ML.v1.5.gating_PolytopeGate:
  no visible global function definition for ‘polytopeGate’
identifyNode,http...www.isac.net.org.std.Gating.ML.v2.0.transformations_spectrumMatrix:
  no visible global function definition for ‘pseudoinverse’
Undefined global functions or variables:
  . ..dim EHtrans asinht comp_ref desc dg1polynomial exponential
  expressionFilter fcs fcs_file_id fcs_filename flowjo_log_trans
  format_float gate_def gate_id gh_apply_to_new_fcs
  gh_get_compensations gh_get_transformations gs_get_pop_paths
  gs_pop_get_gate hyperlog hyperlogtGml2 id invsplitscale is.smaller
  lintGml2 logarithm n name panel parent parent_count polytopeGate
  population pseudoinverse quadratic ratio ratiotGml2 sampleSelected
  sessionInfo sinht slotNames specimen splitscale squareroot unzip x y
Consider adding
  importFrom("methods", "slotNames")
  importFrom("utils", "sessionInfo", "unzip")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* 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 is not available
File ‘/home/biocbuild/bbs-3.11-bioc/R/library/CytoML/libs/CytoML.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (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: 8 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/CytoML.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL CytoML
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘CytoML’ ...
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++11 accepts -g... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
configure: setting xml2 flags...
configure: No directory was specified for --with-xml2. Trying to find xml2 using other methods.
checking for xml2-config... /usr/bin/xml2-config
configure: setting cytolib-ml commandline tool path...
configure: Using the following compilation and linking flags
configure:    PKG_CPPFLAGS=-I/usr/include/libxml2
configure:    PKG_LIBS=-lxml2 
configure:    CYTOLIBML_BIN=/usr/local/bin
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/cytolibml_bin_path.R
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/flowWorkspace/include' -I/usr/local/include   -fpic  -O3 -march=native -mtune=native -fPIC -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/flowWorkspace/include' -I/usr/local/include   -fpic  -O3 -march=native -mtune=native -fPIC -c parseFlowJoWorkspace.cpp -o parseFlowJoWorkspace.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o CytoML.so RcppExports.o parseFlowJoWorkspace.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.11-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -lxml2 -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-CytoML/00new/CytoML/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 (CytoML)

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(CytoML)
> 
> 
> test_check("CytoML")
As part of improvements to flowWorkspace, some behavior of
GatingSet objects has changed. For details, please read the section
titled "The cytoframe and cytoset classes" in the package vignette:

  vignette("flowWorkspace-Introduction", "flowWorkspace")
Loading required package: ggplot2
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-H. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter SSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 66 | SKIPPED: 4 | WARNINGS: 1 | FAILED: 0 ]
> 
> #devtools::test()
> 
> # test_file("~/rglab/workspace/CytoML/tests/testthat/flowjo2gs_internalTestSuite.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/Cytobank2GatingSet-InternalTestSuite.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/GatingSet2flowJo-InternalTestSuite.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/diva2gs-InternalTestSuite.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/test-cytobank.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/test-diva2gs.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/test-extend.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/test-GatingSet2flowJo.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/test-flowjo2gs.R")
> 
> proc.time()
   user  system elapsed 
 54.581   0.847  55.691