BioC 2.13: CHECK report for spade on perceval

Package: spade

Version: 1.10.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch spade_1.10.2.tar.gz

StartedAt: 2014-04-05 04:30:40 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:34:06 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 205.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: spade.Rcheck

Warnings: 3

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/spade.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spade/DESCRIPTION’ ... OK
* this is package ‘spade’ version ‘1.10.2’
* 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 ... [25s/25s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘igraph’ ‘Rclusterpp’
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 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 ... WARNING
‘library’ or ‘require’ calls not declared from:
  ‘hash’ ‘rjson’
Namespaces in Imports field not imported from:
  ‘igraph’ ‘Rclusterpp’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘igraph’ ‘Rclusterpp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SPADE.createPopulationMapping: no visible global function definition
  for ‘hash’
SPADE.driver: no visible global function definition for ‘fromJSON’
* 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 the 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 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘SPADE.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [29s/21s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
SPADE.driver 18.448  0.686  10.915
* 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

WARNING: There were 3 warnings.
NOTE: There were 5 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/spade.Rcheck/00check.log’
for details.

* installing *source* package ‘spade’ ...
checking for gcc... llvm-gcc-4.2 -arch x86_64 -std=gnu99
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 llvm-gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes
checking for llvm-gcc-4.2 -arch x86_64 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... llvm-gcc-4.2 -arch x86_64 -std=gnu99 -E
checking whether we are using the GNU C++ compiler... yes
checking whether llvm-g++-4.2 -arch x86_64 accepts -g... yes
checking how to run the C++ preprocessor... llvm-g++-4.2 -arch x86_64 -E
checking for llvm-gcc-4.2 -arch x86_64 -std=gnu99 option to support OpenMP... -fopenmp
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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -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  -mtune=core2 -g -O2 -Wall  -c cluster.cc -o cluster.o
cluster.cc: In function ‘void<unnamed>::cluster(const <unnamed>::Data_t*, size_t, size_t, size_t, <unnamed>::Idx_t*)’:
cluster.cc:253: warning: comparison between signed and unsigned integer expressions
cluster.cc:253: warning: iteration variable ‘i’ is unsigned
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -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  -mtune=core2 -g -O2 -Wall  -c downsample.cc -o downsample.o
downsample.cc: In function ‘<unnamed>::Dist_t<unnamed>::compute_median_min_dist(<unnamed>::Data_t*, size_t, size_t, size_t)’:
downsample.cc:47: warning: iteration variable ‘i’ is unsigned
downsample.cc: In function ‘void<unnamed>::count_neighbors(<unnamed>::Data_t*, size_t, size_t, <unnamed>::Dist_t, <unnamed>::Dist_t, <unnamed>::Count_t*)’:
downsample.cc:76: warning: iteration variable ‘i’ is unsigned
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -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  -mtune=core2 -g -O2 -Wall  -c spade.cc -o spade.o
spade.cc: In function ‘void R_init_spade(DllInfo*)’:
spade.cc:7: warning: unused variable ‘_CallFun’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -fopenmp -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  -mtune=core2 -g -O2 -Wall  -c upsample.cc -o upsample.o
upsample.cc: In function ‘void<unnamed>::assign_cluster(const <unnamed>::Data_t*, const <unnamed>::Data_t*, <unnamed>::Idx_t*, size_t, size_t, size_t, <unnamed>::Idx_t*)’:
upsample.cc:35: warning: iteration variable ‘i’ is unsigned
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o spade.so cluster.o downsample.o spade.o upsample.o -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.13-bioc/meat/spade.Rcheck/spade/libs
** R
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
* DONE (spade)

name	user	system	elapsed
SPADE.FCSToTree	0.011	0.006	0.018
SPADE.addClusterToFCS	0.011	0.006	0.018
SPADE.addDensityToFCS	0.011	0.002	0.016
SPADE.annotateGraph	0.011	0.003	0.017
SPADE.downsampleFCS	0.382	0.004	0.397
SPADE.driver	18.448	0.686	10.915
SPADE.flattenAnnotations	0.013	0.006	0.020
SPADE.installPlugin	0.007	0.003	0.014
SPADE.layout.arch	0.013	0.006	0.019
SPADE.markerMedians	0.010	0.007	0.016
SPADE.plot.trees	0.009	0.005	0.014
SPADE.read.FCS	0.061	0.015	0.077
SPADE.write.graph	0.011	0.004	0.015