PGPC 0.99.5
Felix Klein
| Snapshot Date: 2015-11-25 07:17:28 -0800 (Wed, 25 Nov 2015) | | URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/PGPC | | Last Changed Rev: 3496 / Revision: 3504 | | Last Changed Date: 2015-11-12 14:42:08 -0800 (Thu, 12 Nov 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | TIMEOUT | skipped | skipped | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | 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 PGPC_0.99.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-data-experiment/meat/PGPC.Rcheck’
* using R Under development (unstable) (2015-11-08 r69614)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PGPC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PGPC’ version ‘0.99.5’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘EBImage’ ‘imageHTS’ ‘SearchTrees’ ‘limma’ ‘RColorBrewer’ ‘gplots’
‘splots’ ‘ggplot2’ ‘geneplotter’ ‘ChemmineR’ ‘reshape2’ ‘plyr’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘PGPC’ can be installed ... [18s/25s] OK
* checking installed package size ... NOTE
installed size is 251.1Mb
sub-directories of 1Mb or more:
data 172.8Mb
doc 7.3Mb
extdata 70.9Mb
* 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 ... NOTE
Packages in Depends field not imported from:
‘ChemmineR’ ‘RColorBrewer’ ‘geneplotter’ ‘ggplot2’ ‘gplots’ ‘plyr’
‘reshape2’ ‘splots’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘imageHTS:::writeThumbnail’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
myHeatmap: no visible global function definition for ‘pushViewport’
myHeatmap: no visible global function definition for ‘viewport’
myHeatmap: no visible global function definition for ‘unit’
myHeatmap: no visible global function definition for ‘grid.raster’
myHeatmap: no visible global function definition for ‘grid.text’
myHeatmap: no visible global function definition for ‘gpar’
myHeatmap: no visible global function definition for ‘popViewport’
myHeatmapSingle: no visible global function definition for
‘pushViewport’
myHeatmapSingle: no visible global function definition for ‘viewport’
myHeatmapSingle: no visible global function definition for ‘unit’
myHeatmapSingle: no visible global function definition for
‘grid.raster’
myHeatmapSingle: no visible global function definition for ‘grid.text’
myHeatmapSingle: no visible global function definition for ‘gpar’
myHeatmapSingle: no visible global function definition for
‘popViewport’
plotHeatmap: no visible global function definition for ‘heatmap.2’
plotSingleValues: no visible global function definition for ‘ggplot’
plotSingleValues: no visible global function definition for ‘aes’
plotSingleValues: no visible binding for global variable
‘concdrug1.micro_M.’
plotSingleValues: no visible binding for global variable ‘value’
plotSingleValues: no visible binding for global variable ‘identifier’
plotSingleValues: no visible binding for global variable ‘variable’
plotSingleValues: no visible global function definition for
‘scale_x_log10’
plotSingleValues: no visible global function definition for
‘scale_y_continuous’
plotSingleValues: no visible global function definition for ‘theme_bw’
plotSingleValues: no visible global function definition for
‘scale_colour_manual’
plotSingleValues: no visible global function definition for ‘labs’
plotSingleValues: no visible binding for global variable ‘experiment’
plotSingleValues: no visible global function definition for
‘geom_jitter’
plotSingleValues: no visible global function definition for
‘position_jitter’
plotSingleValues: no visible global function definition for
‘geom_vline’
plotSummary: no visible binding for global variable
‘concdrug1.micro_M.’
plotSummary: no visible global function definition for ‘theme’
plotSummary: no visible global function definition for ‘element_text’
plotSummary: no visible global function definition for ‘ggplot’
plotSummary: no visible global function definition for ‘aes’
plotSummary: no visible binding for global variable ‘sem’
plotSummary: no visible binding for global variable ‘identifier’
plotSummary: no visible global function definition for ‘geom_point’
plotSummary: no visible global function definition for ‘geom_line’
plotSummary: no visible global function definition for ‘scale_x_log10’
plotSummary: no visible global function definition for
‘scale_y_continuous’
plotSummary: no visible global function definition for
‘scale_colour_manual’
plotSummary: no visible global function definition for ‘geom_errorbar’
plotSummary: no visible global function definition for ‘labs’
plotSummary: no visible binding for global variable ‘experiment’
plotSummary: no visible global function definition for ‘geom_vline’
plotSummaryBarplot: no visible binding for global variable
‘concdrug1.micro_M.’
plotSummaryBarplot: no visible global function definition for ‘theme’
plotSummaryBarplot: no visible global function definition for
‘element_text’
plotSummaryBarplot: no visible global function definition for ‘ggplot’
plotSummaryBarplot: no visible global function definition for ‘aes’
plotSummaryBarplot: no visible binding for global variable ‘sem’
plotSummaryBarplot: no visible binding for global variable ‘identifier’
plotSummaryBarplot: no visible global function definition for
‘position_dodge’
plotSummaryBarplot: no visible global function definition for
‘geom_bar’
plotSummaryBarplot: no visible global function definition for
‘scale_y_continuous’
plotSummaryBarplot: no visible global function definition for
‘scale_fill_manual’
plotSummaryBarplot: no visible global function definition for
‘scale_colour_manual’
plotSummaryBarplot: no visible global function definition for
‘geom_errorbar’
plotSummaryBarplot: no visible global function definition for ‘labs’
plotSummaryBarplot: no visible binding for global variable ‘experiment’
plotSummaryBarplot: no visible global function definition for ‘xlab’
plotSummaryBarplot: no visible global function definition for
‘geom_point’
plotSummaryBarplot: no visible binding for global variable ‘pvalue’
plotSummaryBarplotInhibition: no visible binding for global variable
‘concdrug1.micro_M.’
plotSummaryBarplotInhibition: no visible global function definition for
‘theme’
plotSummaryBarplotInhibition: no visible global function definition for
‘element_text’
plotSummaryBarplotInhibition: no visible global function definition for
‘element_blank’
plotSummaryBarplotInhibition: no visible global function definition for
‘ggplot’
plotSummaryBarplotInhibition: no visible global function definition for
‘aes’
plotSummaryBarplotInhibition: no visible binding for global variable
‘inhibition’
plotSummaryBarplotInhibition: no visible binding for global variable
‘sem’
plotSummaryBarplotInhibition: no visible binding for global variable
‘identifier’
plotSummaryBarplotInhibition: no visible global function definition for
‘position_dodge’
plotSummaryBarplotInhibition: no visible global function definition for
‘geom_bar’
plotSummaryBarplotInhibition: no visible global function definition for
‘scale_y_continuous’
plotSummaryBarplotInhibition: no visible global function definition for
‘scale_fill_manual’
plotSummaryBarplotInhibition: no visible global function definition for
‘scale_colour_manual’
plotSummaryBarplotInhibition: no visible global function definition for
‘geom_errorbar’
plotSummaryBarplotInhibition: no visible global function definition for
‘labs’
plotSummaryBarplotInhibition: no visible binding for global variable
‘experiment’
plotSummaryBarplotInhibition: no visible global function definition for
‘xlab’
plotSummaryBarplotInhibition: no visible global function definition for
‘ylab’
plotSummaryBarplotInhibition: no visible global function definition for
‘geom_point’
plotSummaryBarplotInhibition: no visible binding for global variable
‘pvalue’
Undefined global functions or variables:
aes concdrug1.micro_M. element_blank element_text experiment geom_bar
geom_errorbar geom_jitter geom_line geom_point geom_vline ggplot gpar
grid.raster grid.text heatmap.2 identifier inhibition labs
popViewport position_dodge position_jitter pushViewport pvalue
scale_colour_manual scale_fill_manual scale_x_log10
scale_y_continuous sem theme theme_bw unit value variable viewport
xlab ylab
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... NOTE
Note: found 28 marked Latin-1 strings
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [14m/15m] OK
Examples with CPU or elapsed time > 5s
user system elapsed
summarizeWellsExtended 363.347 45.964 430.846
getFeaturesAllSpots 212.587 39.918 257.622
segmentAllSpots 95.468 14.341 118.712
segmentXman 24.786 2.012 26.826
getInteractions 11.707 0.370 12.685
ftrs 9.380 0.211 9.601
datamatrixTransformed 8.402 0.182 8.590
* 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: 5 NOTEs
See
‘/Users/biocbuild/bbs-3.3-data-experiment/meat/PGPC.Rcheck/00check.log’
for details.