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 | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | ERROR | skipped | skipped | |
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### Running command:
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### rm -rf spade.buildbin-libdir spade.Rcheck && mkdir spade.buildbin-libdir spade.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=spade.buildbin-libdir spade_1.20.0.tar.gz >spade.Rcheck\00install.out 2>&1 && cp spade.Rcheck\00install.out spade-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=spade.buildbin-libdir --install="check:spade-install.out" --force-multiarch --no-vignettes --timings spade_1.20.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/spade.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.20.0'
* 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 whether package 'spade' can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'spade' is deprecated and will be removed from Bioconductor
See 'E:/biocbld/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
* 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.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
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'E:/biocbld/bbs-3.3-bioc/meat/spade.buildbin-libdir/spade/libs/i386/spade.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
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' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
SPADE.driver 23.57 2.3 21.92
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
SPADE.driver 19.75 2.04 18.86
* 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
'E:/biocbld/bbs-3.3-bioc/meat/spade.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'spade' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -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:253:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i=0; i < (c_end - c_beg); i++) {
^
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -c downsample.cc -o downsample.o
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"c:/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]
static const R_CallMethodDef _CallFun[] = {
^
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -c upsample.cc -o upsample.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o spade.dll tmp.def cluster.o downsample.o spade.o upsample.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.3-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
Warning: Package 'spade' is deprecated and will be removed from Bioconductor
version 3.3
install for x64
* installing *source* package 'spade' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -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:253:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i=0; i < (c_end - c_beg); i++) {
^
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -c downsample.cc -o downsample.o
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"c:/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]
static const R_CallMethodDef _CallFun[] = {
^
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"c:/local323/include" -O2 -Wall -mtune=core2 -c upsample.cc -o upsample.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o spade.dll tmp.def cluster.o downsample.o spade.o upsample.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/spade.buildbin-libdir/spade/libs/x64
** testing if installed package can be loaded
Warning: Package 'spade' is deprecated and will be removed from Bioconductor
version 3.3
* MD5 sums
packaged installation of 'spade' as spade_1.20.0.zip
* DONE (spade)