openCyto 1.4.0
Mike Jiang
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/openCyto | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch openCyto_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/openCyto.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘openCyto/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘openCyto’ version ‘1.4.0’
* 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 ‘openCyto’ can be installed ... [38s/44s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* 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 ... NOTE
'library' or 'require' call to ‘parallel’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
‘flowClust:::.ellipsePoints’ ‘flowStats:::warpSetNCDF’
‘flowWorkspace:::.getAllDescendants’ ‘flowWorkspace:::trimWhiteSpace’
‘lattice:::updateList’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘unlockNamespace’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Found the following possibly unsafe calls:
File ‘openCyto/R/pluginFramework.R’:
unlockBinding(methodName, ENV)
unlockBinding(methodName, ENV)
.boundary: no visible global function definition for ‘rectangleGate’
.gateToFilterResult: no visible global function definition for ‘exprs’
.gating_adaptor: no visible global function definition for
‘rectangleGate’
.gating_adaptor: no visible global function definition for ‘filters’
.gating_boolMethod: no visible global function definition for
‘parameters’
.gating_gtMethod: no visible global function definition for
‘parameters’
.gating_gtMethod : <anonymous>: no visible global function definition
for ‘getChannelMarker’
.gating_refGate : <anonymous> : <anonymous>: no visible global function
definition for ‘parameters’
.gating_refGate : <anonymous> : <anonymous>: no visible global function
definition for ‘getChannelMarker’
.gating_refGate : <anonymous>: no visible global function definition
for ‘getChannelMarker’
.gating_refGate : <anonymous>: no visible global function definition
for ‘rectangleGate’
.gating_refGate: no visible global function definition for ‘filterList’
.gatingTemplate: no visible binding for global variable ‘pop’
.gatingTemplate: no visible binding for global variable ‘gating_method’
.gatingTemplate: no visible binding for global variable ‘gating_args’
.gatingTemplate: no visible binding for global variable
‘collapseDataForGating’
.gatingTemplate: no visible binding for global variable
‘preprocessing_method’
.gatingTemplate: no visible binding for global variable
‘preprocessing_args’
.gen_1dgate : <anonymous>: no visible binding for global variable
‘parent’
.gen_1dgate : <anonymous>: no visible binding for global variable
‘gating_method’
.gen_1dgate : <anonymous>: no visible binding for global variable
‘gating_args’
.gen_1dgate : <anonymous>: no visible binding for global variable
‘collapseDataForGating’
.gen_1dgate : <anonymous>: no visible binding for global variable
‘preprocessing_method’
.gen_1dgate : <anonymous>: no visible binding for global variable
‘preprocessing_args’
.gen_dummy_ref_gate: no visible binding for global variable ‘parent’
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
variable ‘pop’
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
variable ‘gating_method’
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
variable ‘gating_args’
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
variable ‘collapseDataForGating’
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
variable ‘preprocessing_method’
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
variable ‘preprocessing_args’
.gen_refGate: no visible binding for global variable ‘parent’
.gen_refGate: no visible binding for global variable ‘gating_args’
.getEllipseGate: no visible global function definition for
‘polygonGate’
.getEllipseGate: no visible global function definition for
‘ellipsoidGate’
.getFullPath: no visible binding for global variable ‘parent’
.preprocess_csv: no visible binding for global variable ‘pop’
.preprocess_csv: no visible binding for global variable ‘parent’
.preprocess_csv: no visible binding for global variable ‘gating_method’
.preprocess_csv: no visible binding for global variable ‘gating_args’
.preprocess_csv: no visible binding for global variable
‘collapseDataForGating’
.preprocess_csv: no visible binding for global variable
‘preprocessing_method’
.preprocess_csv: no visible binding for global variable
‘preprocessing_args’
.preprocess_row: no visible binding for global variable ‘pop’
.preprocess_row: no visible binding for global variable ‘gating_method’
.preprocess_row: no visible binding for global variable ‘parent’
.preprocess_row: no visible binding for global variable ‘gating_args’
.preprocess_row: no visible binding for global variable
‘preprocessing_method’
.preprocess_row: no visible binding for global variable
‘preprocessing_args’
.preprocessing: no visible global function definition for ‘parameters’
.preprocessing : <anonymous>: no visible global function definition for
‘getChannelMarker’
.prior_flowClust1d: no visible global function definition for ‘fsApply’
.prior_flowClust1d : <anonymous>: no visible global function definition
for ‘exprs’
.prior_kmeans : <anonymous>: no visible global function definition for
‘exprs’
.quadGate2rectangleGates: no visible global function definition for
‘rectangleGate’
.quadGate2rectangleGates: no visible global function definition for
‘filters’
.read.FCS.csv: no visible global function definition for ‘parameters’
.read.FCS.csv: no visible global function definition for ‘parameters<-’
.read.flowSet.csv: no visible global function definition for ‘flowSet’
.read.flowSet.csv: no visible global function definition for
‘sampleNames<-’
.standardize_flowFrame: no visible global function definition for
‘exprs’
.standardize_flowFrame: no visible global function definition for
‘exprs<-’
.standardize_flowset: no visible global function definition for
‘fsApply’
.standardize_flowset: no visible global function definition for
‘flowSet’
.tailgate: no visible global function definition for ‘exprs’
.tailgate: no visible global function definition for ‘exprs<-’
.tailgate: no visible global function definition for ‘parameters’
.tailgate: no visible global function definition for ‘rectangleGate’
.truncate_flowframe: no visible global function definition for
‘rectangleGate’
.truncate_flowframe: no visible global function definition for ‘Subset’
.truncate_flowset: no visible global function definition for
‘rectangleGate’
.truncate_flowset: no visible global function definition for ‘Subset’
.unique_check_alias: no visible binding for global variable ‘parent’
fcFilterList: no visible global function definition for ‘filterList’
flowClust.1d: no visible global function definition for ‘exprs’
flowClust.1d: no visible global function definition for ‘rectangleGate’
flowClust.2d: no visible global function definition for ‘exprs’
flowClust.2d: no visible global function definition for ‘polygonGate’
mindensity: no visible global function definition for ‘exprs’
mindensity: no visible global function definition for ‘rectangleGate’
quadGate.seq : <anonymous>: no visible global function definition for
‘exprs’
quadGate.seq : <anonymous>: no visible global function definition for
‘rectangleGate’
quadGate.seq: no visible global function definition for ‘filters’
quadGate.tmix: no visible global function definition for ‘polygonGate’
quadGate.tmix: no visible global function definition for ‘filters’
quantileGate: no visible global function definition for ‘exprs’
quantileGate: no visible global function definition for ‘rectangleGate’
tailgate: no visible global function definition for ‘exprs’
tailgate: no visible global function definition for ‘rectangleGate’
templateGen : <anonymous>: no visible global function definition for
‘parameters’
coerce,ncdfFlowSet-flowFrame: no visible global function definition for
‘parameters’
coerce,ncdfFlowSet-flowFrame: no visible global function definition for
‘fsApply’
coerce,ncdfFlowSet-flowFrame : <anonymous>: no visible global function
definition for ‘exprs’
show,boolMethod: no visible global function definition for ‘parameters’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [15s/16s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘run-all.R’ [31s/34s]
[32s/35s] OK
* 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
NOTE: There were 2 notes.
See
‘/Users/biocbuild/bbs-3.0-bioc/meat/openCyto.Rcheck/00check.log’
for details.
* installing *source* package ‘openCyto’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -Wall -c misc.cpp -o misc.o
misc.cpp: In function ‘Rcpp::NumericMatrix collapseData(Rcpp::List, Rcpp::StringVector)’:
misc.cpp:10: warning: comparison between signed and unsigned integer expressions
misc.cpp:21: warning: comparison between signed and unsigned integer expressions
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -Wall -c unlockNamespace.c -o unlockNamespace.o
llvm-g++-4.2 -arch x86_64 -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 -L/usr/local/lib -o openCyto.so RcppExports.o misc.o unlockNamespace.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/openCyto.Rcheck/openCyto/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 (openCyto)