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BioC 3.3: CHECK report for spade on zin2

This page was generated on 2016-10-13 12:43:03 -0700 (Thu, 13 Oct 2016).

Package 1099/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
spade 1.20.0
Zach Bjornson
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/spade
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: spade
Version: 1.20.0
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings spade_1.20.0.tar.gz
StartedAt: 2016-10-13 07:02:16 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 07:04:36 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 139.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: spade.Rcheck
Warnings: 4

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings spade_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/spade.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spade/DESCRIPTION’ ... OK
* this is package ‘spade’ version ‘1.20.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: Package 'spade' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.3-bioc/meat/spade.Rcheck/00install.out’ for details.
* 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.FCSToTree: no visible global function definition for
  ‘write.table’
SPADE.addClusterToFCS: no visible global function definition for
  ‘na.fail’
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.build.flowFrame: no visible global function definition for ‘as’
SPADE.cluster: no visible global function definition for
  ‘Rclusterpp.hclust’
SPADE.cluster: no visible global function definition for ‘cutree’
SPADE.clustersToMST: no visible global function definition for ‘dist’
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.createMergeOrderByCellProbability: no visible global function
  definition for ‘write.table’
SPADE.createPopulationMapping: no visible global function definition
  for ‘hash’
SPADE.createPopulationMapping: no visible global function definition
  for ‘read.table’
SPADE.downsampleFCS: no visible global function definition for
  ‘quantile’
SPADE.downsampleFCS: no visible global function definition for ‘runif’
SPADE.driver: no visible global function definition for ‘glob2rx’
SPADE.driver: no visible global function definition for ‘read.graph’
SPADE.driver: no visible global function definition for ‘write.table’
SPADE.driver: no visible global function definition for ‘vcount’
SPADE.driver : <anonymous>: no visible global function definition for
  ‘quantile’
SPADE.driver: no visible global function definition for ‘fromJSON’
SPADE.driver: no visible global function definition for ‘write.csv’
SPADE.evaluateCellTypeRule: no visible binding for global variable
  ‘median’
SPADE.evaluateCellTypeRule: no visible global function definition for
  ‘read.graph’
SPADE.evaluateCellTypeRule: no visible global function definition for
  ‘read.table’
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.markerMedians: no visible binding for global variable ‘median’
SPADE.markerMedians : <anonymous>: no visible global function
  definition for ‘sd’
SPADE.plot.trees: no visible global function definition for ‘is.igraph’
SPADE.plot.trees: no visible global function definition for ‘glob2rx’
SPADE.plot.trees: no visible global function definition for ‘quantile’
SPADE.plot.trees: no visible global function definition for
  ‘colorRampPalette’
SPADE.plot.trees: no visible global function definition for ‘pdf’
SPADE.plot.trees: no visible global function definition for ‘title’
SPADE.plot.trees: no visible global function definition for ‘image’
SPADE.plot.trees: no visible global function definition for ‘dev.off’
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’
cnvrt.coords: no visible global function definition for ‘xy.coords’
cnvrt.coords: no visible global function definition for ‘par’
subplot: no visible global function definition for ‘par’
subplot: no visible global function definition for ‘locator’
subplot: no visible global function definition for ‘xy.coords’
Undefined global functions or variables:
  E Rclusterpp.hclust V as as.directed colorRampPalette cutree
  delete.edges dev.off dist fromJSON get.edge.attribute get.edges
  get.shortest.paths get.vertex.attribute girth glob2rx graph.adjacency
  hash image is.connected is.directed is.igraph layout.reingold.tilford
  list.edge.attributes list.vertex.attributes locator median
  minimum.spanning.tree na.fail neighbors par pdf quantile read.graph
  read.table remove.vertex.attribute runif sd set.vertex.attribute
  subcomponent subgraph title vcount write.csv write.graph write.table
  xy.coords
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf",
             "xy.coords")
  importFrom("graphics", "image", "locator", "par", "title")
  importFrom("methods", "as")
  importFrom("stats", "cutree", "dist", "median", "na.fail", "quantile",
             "runif", "sd")
  importFrom("utils", "glob2rx", "read.table", "write.csv",
             "write.table")
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 ... 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 ... NOTE
File ‘spade/libs/spade.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘downsample.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
SPADE.driver 188.563  0.448  78.286
* 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: 4 WARNINGs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/spade.Rcheck/00check.log’
for details.

spade.Rcheck/00install.out:

* installing *source* package ‘spade’ ...
checking for gcc... gcc -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 gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking for gcc -std=gnu99 option to support OpenMP... -fopenmp
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /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... yes
checking parallel/algorithm presence... yes
checking for parallel/algorithm... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/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 -DHAVE_PARALLEL_ALGORITHM=1 -DHAVE_PARALLEL_STL=1 -fpic  -g -O2  -Wall -c cluster.cc -o cluster.o
cluster.cc: In function ‘void {anonymous}::cluster(const Data_t*, std::size_t, std::size_t, std::size_t, {anonymous}::Idx_t*)’:
cluster.cc:253:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (size_t i=0; i < (c_end - c_beg); i++) {
                                         ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/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 -DHAVE_PARALLEL_ALGORITHM=1 -DHAVE_PARALLEL_STL=1 -fpic  -g -O2  -Wall -c downsample.cc -o downsample.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/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 -DHAVE_PARALLEL_ALGORITHM=1 -DHAVE_PARALLEL_STL=1 -fpic  -g -O2  -Wall -c spade.cc -o spade.o
spade.cc: In function ‘void R_init_spade(DllInfo*)’:
spade.cc:7:32: warning: unused variable ‘_CallFun’ [-Wunused-variable]
   static const R_CallMethodDef _CallFun[] = {
                                ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/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 -DHAVE_PARALLEL_ALGORITHM=1 -DHAVE_PARALLEL_STL=1 -fpic  -g -O2  -Wall -c upsample.cc -o upsample.o
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o spade.so cluster.o downsample.o spade.o upsample.o -fopenmp -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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
Warning: Package 'spade' is deprecated and will be removed from Bioconductor
  version 3.3
* DONE (spade)

spade.Rcheck/spade-Ex.timings:

nameusersystemelapsed
SPADE.FCSToTree0.0010.0000.000
SPADE.addClusterToFCS0.0010.0000.001
SPADE.addDensityToFCS0.0000.0000.001
SPADE.annotateGraph0.0010.0000.000
SPADE.downsampleFCS0.0010.0000.001
SPADE.driver188.563 0.448 78.286
SPADE.flattenAnnotations0.0010.0000.001
SPADE.installPlugin0.0010.0000.000
SPADE.layout.arch0.0000.0000.001
SPADE.markerMedians0.0010.0000.001
SPADE.plot.trees0.0010.0000.000
SPADE.read.FCS0.0210.0000.022
SPADE.write.graph0.0010.0000.000