cytofkit 1.7.2
Jinmiao Chen , Hao Chen
| Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cytofkit | | Last Changed Rev: 128824 / Revision: 129046 | | Last Changed Date: 2017-04-18 05:58:07 -0400 (Tue, 18 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | ERROR | OK | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | WARNINGS | 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 cytofkit_1.7.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/cytofkit.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cytofkit/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cytofkit’ version ‘1.7.2’
* 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 ‘cytofkit’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.1Mb
sub-directories of 1Mb or more:
doc 2.7Mb
extdata 4.0Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cytof_clusterPlot: no visible global function definition for
‘geom_text’
cytof_progressionPlot: no visible global function definition for ‘aes’
cytof_progressionPlot: no visible binding for global variable
‘Pseudotime’
cytof_progressionPlot: no visible binding for global variable ‘cluster’
cytofkitShinyAPP2 : <anonymous> : C_ScatterPlotInput: no visible global
function definition for ‘scatterPlot’
cytofkitShinyAPP2 : <anonymous> : C_ScatterPlotInput: no visible global
function definition for ‘plot’
cytofkitShinyAPP2 : <anonymous>: no visible global function definition
for ‘heatMap’
cytofkitShinyAPP2 : <anonymous>: no visible global function definition
for ‘dev.copy2pdf’
cytofkitShinyAPP2 : <anonymous> : M_markerExpressionPlotInput: no
visible global function definition for ‘scatterPlot’
cytofkitShinyAPP2 : <anonymous> : M_markerExpressionPlotInput: no
visible global function definition for ‘plot’
cytofkitShinyAPP2 : <anonymous> : M_stackDensityPlotInput: no visible
global function definition for ‘stackDenistyPlot’
cytofkitShinyAPP2 : <anonymous> : M_stackDensityPlotInput: no visible
global function definition for ‘plot’
cytofkitShinyAPP2 : <anonymous> : S_rateChangePlotInput: no visible
global function definition for ‘plot’
cytofkitShinyAPP2 : <anonymous> : P_scatterPlotInput: no visible global
function definition for ‘plot’
cytofkitShinyAPP2 : <anonymous> : P_markerPlotInput: no visible global
function definition for ‘cytof_expressionTrends’
cytofkitShinyAPP2 : <anonymous> : P_markerPlotInput: no visible global
function definition for ‘plot’
Undefined global functions or variables:
Pseudotime aes cluster cytof_expressionTrends dev.copy2pdf geom_text
heatMap plot scatterPlot stackDenistyPlot
Consider adding
importFrom("grDevices", "dev.copy2pdf")
importFrom("graphics", "plot")
to your NAMESPACE file.
* 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 ... WARNING
Undocumented arguments in documentation object 'cytofkitShinyAPP2'
‘obj’
Documented arguments not in \usage in documentation object 'cytofkitShinyAPP2':
‘objFile’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
cytof_progression 10.768 0.683 11.471
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
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
Status: 1 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/cytofkit.Rcheck/00check.log’
for details.
* installing *source* package ‘cytofkit’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c jaccard_coeff.cpp -o jaccard_coeff.o
clang++ -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 -o cytofkit.so RcppExports.o jaccard_coeff.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/cytofkit.Rcheck/cytofkit/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cytofkit)