BioC 3.2: CHECK report for spade on oaxaca

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings spade_1.17.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/spade.Rcheck’
* using R version 3.2.2 beta (2015-08-05 r68859)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spade/DESCRIPTION’ ... OK
* this is package ‘spade’ version ‘1.17.0’
* 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 ‘spade’ can be installed ... [15s/16s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 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 loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
'library' or 'require' calls not declared from:
  ‘hash’ ‘rjson’
'library' or 'require' calls in package code:
  ‘hash’ ‘rjson’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Rclusterpp’ ‘igraph’
  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
SPADE.annotateGraph: no visible global function definition for
  ‘is.igraph’
SPADE.annotateGraph: no visible global function definition for ‘vcount’
SPADE.annotateGraph: no visible global function definition for
  ‘list.vertex.attributes’
SPADE.annotateGraph: no visible global function definition for
  ‘remove.vertex.attribute’
SPADE.annotateGraph: no visible global function definition for
  ‘set.vertex.attribute’
SPADE.annotateGraph: no visible global function definition for ‘V’
SPADE.cluster: no visible global function definition for
  ‘Rclusterpp.hclust’
SPADE.clustersToMST: no visible global function definition for
  ‘graph.adjacency’
SPADE.clustersToMST: no visible global function definition for
  ‘minimum.spanning.tree’
SPADE.createMergeOrderByCellProbability: no visible global function
  definition for ‘read.graph’
SPADE.createMergeOrderByCellProbability: no visible global function
  definition for ‘get.vertex.attribute’
SPADE.createMergeOrderByCellProbability: no visible global function
  definition for ‘V’
SPADE.createPopulationMapping: no visible global function definition
  for ‘hash’
SPADE.driver: no visible global function definition for ‘read.graph’
SPADE.driver: no visible global function definition for ‘vcount’
SPADE.driver: no visible global function definition for ‘fromJSON’
SPADE.evaluateCellTypeRule: no visible global function definition for
  ‘read.graph’
SPADE.layout.arch: no visible global function definition for
  ‘is.igraph’
SPADE.layout.arch: no visible global function definition for
  ‘is.connected’
SPADE.layout.arch: no visible global function definition for ‘girth’
SPADE.layout.arch: no visible global function definition for ‘V’
SPADE.layout.arch: no visible global function definition for
  ‘get.shortest.paths’
SPADE.layout.arch: no visible global function definition for ‘vcount’
SPADE.layout.arch: no visible global function definition for
  ‘neighbors’
SPADE.layout.arch: no visible global function definition for
  ‘subcomponent’
SPADE.layout.arch: no visible global function definition for
  ‘delete.edges’
SPADE.layout.arch: no visible global function definition for ‘E’
SPADE.layout.arch: no visible global function definition for
  ‘as.directed’
SPADE.layout.arch: no visible global function definition for ‘subgraph’
SPADE.layout.arch: no visible global function definition for
  ‘get.edges’
SPADE.layout.arch: no visible global function definition for
  ‘layout.reingold.tilford’
SPADE.plot.trees: no visible global function definition for ‘is.igraph’
SPADE.write.graph: no visible global function definition for
  ‘is.igraph’
SPADE.write.graph : write.gml: no visible global function definition
  for ‘is.directed’
SPADE.write.graph : write.gml: no visible global function definition
  for ‘list.vertex.attributes’
SPADE.write.graph : write.gml: no visible global function definition
  for ‘V’
SPADE.write.graph : write.gml: no visible global function definition
  for ‘get.vertex.attribute’
SPADE.write.graph : write.gml: no visible global function definition
  for ‘list.edge.attributes’
SPADE.write.graph : write.gml: no visible global function definition
  for ‘E’
SPADE.write.graph : write.gml: no visible global function definition
  for ‘get.edges’
SPADE.write.graph : write.gml: no visible global function definition
  for ‘get.edge.attribute’
SPADE.writeGraph: no visible global function definition for
  ‘write.graph’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘SPADE.density’ ‘SPADE.removeExistingDensityAndClusterColumns’
  ‘SPADE.transform.FCS’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'SPADE.downsampleFCS':
SPADE.downsampleFCS
  Code: function(infilename, outfilename, exclude_pctile = 0.01,
                 target_pctile = NULL, target_number = NULL,
                 target_percent = 0.1)
  Docs: function(infilename, outfilename, exclude_pctile = 0.01,
                 target_pctile = 0.05, desired_samples = NULL)
  Argument names in code not in docs:
    target_number target_percent
  Argument names in docs not in code:
    desired_samples
  Mismatches in argument names:
    Position: 5 Code: target_number Docs: desired_samples
  Mismatches in argument default values:
    Name: 'target_pctile' Code: NULL Docs: 0.05

Codoc mismatches from documentation object 'SPADE.driver':
SPADE.driver
  Code: function(files, file_pattern = "*.fcs", out_dir = ".",
                 cluster_cols = NULL, panels = NULL, comp = TRUE,
                 arcsinh_cofactor = NULL, transforms =
                 flowCore::arcsinhTransform(a = 0, b = 0.2),
                 downsampling_target_number = NULL,
                 downsampling_target_pctile = NULL,
                 downsampling_target_percent = 0.1,
                 downsampling_exclude_pctile = 0.01, k = 200,
                 clustering_samples = 50000, layout =
                 igraph:::layout.kamada.kawai, pctile_color = c(0.02,
                 0.98), fcs_channel_mappings_json = NULL)
  Docs: function(files, file_pattern = "*.fcs", out_dir = ".",
                 cluster_cols = NULL, panels = NULL, comp = TRUE,
                 arcsinh_cofactor = NULL, transforms =
                 flowCore::arcsinhTransform(a = 0, b = 0.2),
                 downsampling_samples = 20000,
                 downsampling_exclude_pctile = 0.01,
                 downsampling_target_pctile = 0.05, k = 200,
                 clustering_samples = 50000, layout =
                 igraph:::layout.kamada.kawai, pctile_color = c(0.02,
                 0.98))
  Argument names in code not in docs:
    downsampling_target_number downsampling_target_percent
    fcs_channel_mappings_json
  Argument names in docs not in code:
    downsampling_samples
  Mismatches in argument names (first 3):
    Position: 9 Code: downsampling_target_number Docs: downsampling_samples
    Position: 10 Code: downsampling_target_pctile Docs: downsampling_exclude_pctile
    Position: 11 Code: downsampling_target_percent Docs: downsampling_target_pctile
  Mismatches in argument default values:
    Name: 'downsampling_target_pctile' Code: NULL Docs: 0.05

* 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 ... 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ...sh: line 1: 97480 Segmentation fault: 11  LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla > 'spade-Ex.Rout' 2>&1 < spade-Ex.R
 ERROR
Running examples in ‘spade-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SPADE.driver
> ### Title: SPADE workflow driver
> ### Aliases: SPADE.driver
> 
> ### ** Examples
> 
> 	# Load two-parameters sample data included in package
> 	data_file_path = system.file(file.path("extdata","SimulatedRawData.fcs"), package = "spade")
> 
> 	# Run basic SPADE analyses, clustering on two parameters. Annotated graphs will be
> 	# in output_dir. See SPADE.plot.trees to generate PDFs of annotated graphs.
> 	output_dir <- tempdir()
> 	SPADE.driver(data_file_path, out_dir=output_dir, cluster_cols=c("marker1","marker2"))
Downsampling file: /Users/biocbuild/bbs-3.2-bioc/meat/spade.Rcheck/spade/extdata/SimulatedRawData.fcs
  Estimated downsampling-I progress:  0% ...
  Estimated downsampling-I progress: 100% ...
Warning in write.FCS(out_frame, outfilename) :
  'write.FCS' is not fully tested and should be considered as experimental.
Targeting 4925 events for /tmp/Rtmpvi8XQL/SimulatedRawData.fcs.density.fcs
Warning in write.FCS(out_frame, outfilename) :
  'write.FCS' is not fully tested and should be considered as experimental.
Clustering files...

 *** caught segfault ***
address 0x0, cause 'memory not mapped'

Traceback:
 1: .Call("hclust_from_data", data = x, link = as.integer(method),     dist = as.integer(distance), p = as.numeric(p), DUP = FALSE,     NAOK = FALSE, PACKAGE = "Rclusterpp")
 2: Rclusterpp.hclust(tbl)
 3: SPADE.cluster(SPADE.transform.matrix(data, transforms), k)
 4: SPADE.FCSToTree(sampled_files, cells_file, graph_file, clust_file,     cols = cluster_cols, transforms = transforms, k = k, desired_samples = clustering_samples,     comp = comp)
 5: SPADE.driver(data_file_path, out_dir = output_dir, cluster_cols = c("marker1",     "marker2"))
aborting ...
* 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: 1 ERROR, 3 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/spade.Rcheck/00check.log’
for details.

* installing *source* package ‘spade’ ...
checking for gcc... clang
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -E
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ accepts -g... yes
checking how to run the C++ preprocessor... clang++ -E
checking for clang option to support OpenMP... unsupported
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking parallel/algorithm usability... no
checking parallel/algorithm presence... no
checking for parallel/algorithm... no
"Parallel STL not found using default"
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DPACKAGE_NAME=\"spade\" -DPACKAGE_TARNAME=\"spade\" -DPACKAGE_VERSION=\"0.20\" -DPACKAGE_STRING=\"spade\ 0.20\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -fPIC  -Wall -mtune=core2 -g -O2  -c cluster.cc -o cluster.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DPACKAGE_NAME=\"spade\" -DPACKAGE_TARNAME=\"spade\" -DPACKAGE_VERSION=\"0.20\" -DPACKAGE_STRING=\"spade\ 0.20\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -fPIC  -Wall -mtune=core2 -g -O2  -c downsample.cc -o downsample.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DPACKAGE_NAME=\"spade\" -DPACKAGE_TARNAME=\"spade\" -DPACKAGE_VERSION=\"0.20\" -DPACKAGE_STRING=\"spade\ 0.20\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -fPIC  -Wall -mtune=core2 -g -O2  -c spade.cc -o spade.o
spade.cc:7:32: warning: unused variable '_CallFun' [-Wunused-variable]
                static const R_CallMethodDef _CallFun[] = {
                                             ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DPACKAGE_NAME=\"spade\" -DPACKAGE_TARNAME=\"spade\" -DPACKAGE_VERSION=\"0.20\" -DPACKAGE_STRING=\"spade\ 0.20\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -fPIC  -Wall -mtune=core2 -g -O2  -c upsample.cc -o upsample.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o spade.so cluster.o downsample.o spade.o upsample.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/spade.Rcheck/spade/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (spade)

name	user	system	elapsed
SPADE.FCSToTree	0.001	0.000	0.002
SPADE.addClusterToFCS	0.002	0.000	0.001
SPADE.addDensityToFCS	0.001	0.000	0.001
SPADE.annotateGraph	0.001	0.000	0.001
SPADE.downsampleFCS	0.001	0.000	0.001

BioC 3.2: CHECK report for spade on oaxaca

Summary

Command output