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BioC 3.2: CHECK report for spade on moscato1

This page was generated on 2016-04-23 10:18:13 -0700 (Sat, 23 Apr 2016).

Package 1000/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
spade 1.18.2
Zach Bjornson
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/spade
Last Changed Rev: 114031 / Revision: 116712
Last Changed Date: 2016-02-25 14:35:47 -0800 (Thu, 25 Feb 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (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  OK  ERROR  OK 

Summary

Package: spade
Version: 1.18.2
Command: rm -rf spade.buildbin-libdir spade.Rcheck && mkdir spade.buildbin-libdir spade.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=spade.buildbin-libdir spade_1.18.2.tar.gz >spade.Rcheck\00install.out 2>&1 && cp spade.Rcheck\00install.out spade-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=spade.buildbin-libdir --install="check:spade-install.out" --force-multiarch --no-vignettes --timings spade_1.18.2.tar.gz
StartedAt: 2016-04-23 07:48:35 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 07:52:28 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 232.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: spade.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf spade.buildbin-libdir spade.Rcheck && mkdir spade.buildbin-libdir spade.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=spade.buildbin-libdir spade_1.18.2.tar.gz >spade.Rcheck\00install.out 2>&1 && cp spade.Rcheck\00install.out spade-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=spade.buildbin-libdir --install="check:spade-install.out" --force-multiarch --no-vignettes --timings spade_1.18.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/spade.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'spade/DESCRIPTION' ... OK
* this is package 'spade' version '1.18.2'
* 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 whether package 'spade' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.2-bioc/meat/spade.buildbin-libdir/spade/libs/i386/spade.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'rand', possibly from 'rand' (C)
File 'D:/biocbld/bbs-3.2-bioc/meat/spade.buildbin-libdir/spade/libs/x64/spade.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'rand', possibly from 'rand' (C)

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.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [31s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
SPADE.driver 28.01   5.39   25.76
** running examples for arch 'x64' ... [35s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
SPADE.driver 29.88   4.24   28.92
* 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: 3 WARNINGs, 4 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/spade.Rcheck/00check.log'
for details.

spade.Rcheck/00install.out:


install for i386

* installing *source* package 'spade' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c cluster.cc -o cluster.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c downsample.cc -o downsample.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -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]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c upsample.cc -o upsample.o
g++ -m32 -shared -s -static-libgcc -o spade.dll tmp.def cluster.o downsample.o spade.o upsample.o -Ld:/RCompile/r-compiling/local/local323/lib/i386 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/spade.buildbin-libdir/spade/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'spade' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c cluster.cc -o cluster.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c downsample.cc -o downsample.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -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]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c upsample.cc -o upsample.o
g++ -m64 -shared -s -static-libgcc -o spade.dll tmp.def cluster.o downsample.o spade.o upsample.o -Ld:/RCompile/r-compiling/local/local323/lib/x64 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/spade.buildbin-libdir/spade/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'spade' as spade_1.18.2.zip
* DONE (spade)

spade.Rcheck/examples_i386/spade-Ex.timings:

nameusersystemelapsed
SPADE.FCSToTree000
SPADE.addClusterToFCS000
SPADE.addDensityToFCS000
SPADE.annotateGraph0.020.000.02
SPADE.downsampleFCS000
SPADE.driver28.01 5.3925.76
SPADE.flattenAnnotations000
SPADE.installPlugin000
SPADE.layout.arch000
SPADE.markerMedians000
SPADE.plot.trees000
SPADE.read.FCS0.050.000.04
SPADE.write.graph000

spade.Rcheck/examples_x64/spade-Ex.timings:

nameusersystemelapsed
SPADE.FCSToTree0.020.000.02
SPADE.addClusterToFCS000
SPADE.addDensityToFCS000
SPADE.annotateGraph000
SPADE.downsampleFCS000
SPADE.driver29.88 4.2428.92
SPADE.flattenAnnotations000
SPADE.installPlugin000
SPADE.layout.arch000
SPADE.markerMedians000
SPADE.plot.trees000
SPADE.read.FCS0.020.010.03
SPADE.write.graph000