rcellminer 1.8.0
Augustin Luna , Vinodh Rajapakse
| Snapshot Date: 2017-07-21 17:18:02 -0400 (Fri, 21 Jul 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/rcellminer | | Last Changed Rev: 129126 / Revision: 131496 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf rcellminer.buildbin-libdir rcellminer.Rcheck && mkdir rcellminer.buildbin-libdir rcellminer.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rcellminer.buildbin-libdir rcellminer_1.8.0.tar.gz >rcellminer.Rcheck\00install.out 2>&1 && cp rcellminer.Rcheck\00install.out rcellminer-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=rcellminer.buildbin-libdir --install="check:rcellminer-install.out" --force-multiarch --no-vignettes --timings rcellminer_1.8.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/rcellminer.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rcellminer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rcellminer' version '1.8.0'
* 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 'rcellminer' can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.4Mb
sub-directories of 1Mb or more:
data 2.9Mb
doc 3.0Mb
* 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
* 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 ... NOTE
Warning: no function found corresponding to methods exports from 'rcellminer' for: 'initialize'
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
** 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 ... NOTE
Warning: no function found corresponding to methods exports from 'rcellminer' for: 'initialize'
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
** 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
.DrugData: no visible global function definition for 'new'
.MolData: no visible global function definition for 'new'
compareFingerprints: no visible global function definition for
'txtProgressBar'
compareFingerprints: no visible global function definition for
'setTxtProgressBar'
crossCors: no visible global function definition for 'cor.test'
crossCors: no visible global function definition for 'pt'
crossCorsSpearman: no visible global function definition for 'cor.test'
getActivityRangeStats: no visible global function definition for
'median'
getColumnQuantiles: no visible global function definition for
'quantile'
getDrugActivityRange: no visible global function definition for 'as'
getDrugActivityRange: no visible global function definition for 'IQR'
getDrugActivityRepeatData: no visible global function definition for
'as'
getDrugName: no visible global function definition for 'as'
getFingerprintList: no visible global function definition for
'txtProgressBar'
getFingerprintList: no visible global function definition for
'setTxtProgressBar'
getMedSenLineActivity: no visible global function definition for
'median'
getMinDrugActivityRepeatCor: no visible global function definition for
'as'
getMoaToCompounds: no visible global function definition for 'as'
getNumDrugActivityRepeats: no visible global function definition for
'as'
getRsd: no visible binding for global variable 'sd'
getRsd: no visible global function definition for 'median'
getSmiles: no visible global function definition for 'as'
passRuleOf5FromNsc: no visible global function definition for 'as'
plotCellMiner: no visible global function definition for 'par'
plotCellMiner: no visible global function definition for 'layout'
plotCellMiner: no visible global function definition for 'lcm'
plotCellMiner: no visible global function definition for 'str'
plotCellMiner: no visible global function definition for 'axis'
plotDrugActivityRepeats: no visible global function definition for 'as'
plotDrugActivityRepeats: no visible global function definition for
'pdf'
plotDrugActivityRepeats: no visible global function definition for
'dev.off'
plotDrugSets: no visible binding for global variable 'median'
plotDrugSets: no visible binding for global variable 'sd'
plotDrugSets: no visible global function definition for 'pdf'
plotDrugSets: no visible global function definition for 'par'
plotDrugSets: no visible global function definition for 'axis'
plotDrugSets: no visible global function definition for 'segments'
plotDrugSets: no visible global function definition for 'dev.off'
plotStructures: no visible global function definition for 'par'
plotStructuresFromNscs: no visible global function definition for 'as'
rcdkplot: no visible global function definition for 'par'
rcdkplot: no visible global function definition for 'plot'
rcdkplot: no visible global function definition for 'rasterImage'
rowCors: no visible global function definition for 'pt'
searchForNscs: no visible global function definition for 'as'
[[<-,MolData: no visible global function definition for 'validObject'
getFeatureAnnot,DrugData: no visible global function definition for
'as'
getFeatureAnnot,MolData : <anonymous>: no visible global function
definition for 'as'
initialize,DrugData: no visible global function definition for
'validObject'
initialize,MolData: no visible global function definition for
'validObject'
Undefined global functions or variables:
IQR as axis cor.test dev.off layout lcm median new par pdf plot pt
quantile rasterImage sd segments setTxtProgressBar str txtProgressBar
validObject
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("graphics", "axis", "layout", "lcm", "par", "plot",
"rasterImage", "segments")
importFrom("methods", "as", "new", "validObject")
importFrom("stats", "IQR", "cor.test", "median", "pt", "quantile",
"sd")
importFrom("utils", "setTxtProgressBar", "str", "txtProgressBar")
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 ... 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* 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
compareFingerprints 2.63 0.15 14.86
plotStructures 0.91 0.08 7.41
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotStructures 1.85 0.19 7.03
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
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: 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/rcellminer.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'rcellminer' ...
** R
** data
*** moving datasets to lazyload DB
** 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 'rcellminer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rcellminer' as rcellminer_1.8.0.zip
* DONE (rcellminer)