| Back to the "Multiple platform build/check report" | A B C D E F G H I J K L M N O P Q [R] S T U V W X Y Z |
This page was generated on 2016-09-21 03:39:44 -0700 (Wed, 21 Sep 2016).
| Package 983/1257 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| rcellminer 1.5.2 Augustin Luna
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ ERROR ] | ||||||
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | ERROR | skipped | skipped | ||||||
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | ERROR | skipped | skipped |
| Package: rcellminer |
| Version: 1.5.2 |
| Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings rcellminer_1.5.2.tar.gz |
| StartedAt: 2016-09-20 11:18:24 -0700 (Tue, 20 Sep 2016) |
| EndedAt: 2016-09-20 11:19:52 -0700 (Tue, 20 Sep 2016) |
| EllapsedTime: 87.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: rcellminer.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings rcellminer_1.5.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/rcellminer.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rcellminer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rcellminer’ version ‘1.5.2’
* 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 ‘rcellminer’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.4Mb
sub-directories of 1Mb or more:
data 2.9Mb
doc 3.8Mb
* 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 ... 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 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 ... ERROR
Running examples in ‘rcellminer-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotStructures
> ### Title: Plot Structures
> ### Aliases: plotStructures
>
> ### ** Examples
>
> drugAnnot <- as(featureData(getAct(rcellminerData::drugData)), "data.frame")
> plotStructures("94600", drugAnnot["94600","SMILES"])
Error in .jcall(mi, "[B", "getBytes", as.integer(width), as.integer(height)) :
java.awt.AWTError: Can't connect to X11 window server using ':1.0' as the value of the DISPLAY variable.
Calls: plotStructures ... rcdkplot -> view.image.2d -> .jcall -> .jcheck -> .Call
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
java.lang.NoClassDefFoundCould not initialize class sun.awt.X11GraphicsEnvironment
1: plotStructuresFromNscs("94600") at /home/biocbuild/bbs-3.4-bioc/meat/rcellminer.Rcheck/rcellminer/tests/test_plotStructuresFromNscs.R:6
2: plotStructures(nscs, drugAnnot[nscs, "SMILES"], mainLabel = nscs)
3: rcdkplot(tmp[[i]], width = structSize, height = structSize, main = ids[i])
4: view.image.2d(molecule, width, height)
5: .jcall(mi, "[B", "getBytes", as.integer(width), as.integer(height))
6: .jcheck()
DONE ===========================================================================
Error: Test failures
In addition: Warning message:
Placing tests in `inst/tests/` is deprecated. Please use `tests/testthat/` instead
Execution halted
* 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: 2 ERRORs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/rcellminer.Rcheck/00check.log’
for details.
runTests.Rout.fail:
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(rcellminer)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: rcdk
Loading required package: fingerprint
Attaching package: 'rcdk'
The following object is masked from 'package:testthat':
matches
Loading required package: rcellminerData
> test_package("rcellminer")
.........................................................................................................................................................................................W.............................12RCellmine: .
.................
Warnings -----------------------------------------------------------------------
1. getRsd (@test_getRsd.R#4) - Deprecated: please use `expect_gt()` instead
Failed -------------------------------------------------------------------------
1. Error: plotStructures (@test_plotStructures.R#6) ----------------------------
java.awt.AWTCan't connect to X11 window server using ':1.0' as the value of the DISPLAY variable.
1: plotStructures("94600", drugAnnot["94600", "SMILES"]) at /home/biocbuild/bbs-3.4-bioc/meat/rcellminer.Rcheck/rcellminer/tests/test_plotStructures.R:6
2: rcdkplot(tmp[[i]], width = structSize, height = structSize, main = ids[i])
3: view.image.2d(molecule, width, height)
4: .jcall(mi, "[B", "getBytes", as.integer(width), as.integer(height))
5: .jcheck()
2. Error: plotStructuresFromNscs (@test_plotStructuresFromNscs.R#6) ------------
java.lang.NoClassDefFoundCould not initialize class sun.awt.X11GraphicsEnvironment
1: plotStructuresFromNscs("94600") at /home/biocbuild/bbs-3.4-bioc/meat/rcellminer.Rcheck/rcellminer/tests/test_plotStructuresFromNscs.R:6
2: plotStructures(nscs, drugAnnot[nscs, "SMILES"], mainLabel = nscs)
3: rcdkplot(tmp[[i]], width = structSize, height = structSize, main = ids[i])
4: view.image.2d(molecule, width, height)
5: .jcall(mi, "[B", "getBytes", as.integer(width), as.integer(height))
6: .jcheck()
DONE ===========================================================================
Error: Test failures
In addition: Warning message:
Placing tests in `inst/tests/` is deprecated. Please use `tests/testthat/` instead
Execution halted
rcellminer.Rcheck/00install.out:
* 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 * DONE (rcellminer)
rcellminer.Rcheck/rcellminer-Ex.timings:
| name | user | system | elapsed | |
| compareFingerprints | 1.884 | 0.084 | 1.673 | |
| crossCors | 0.004 | 0.000 | 0.006 | |
| crossCorsSpearman | 0 | 0 | 0 | |
| getActivityRangeStats | 0.024 | 0.000 | 0.023 | |
| getColumnQuantiles | 0.000 | 0.000 | 0.002 | |
| getDrugActivityData | 0.004 | 0.000 | 0.005 | |
| getDrugActivityRange | 0.008 | 0.000 | 0.006 | |
| getDrugActivityRepeatData | 0.004 | 0.000 | 0.004 | |
| getDrugMoaList | 0.048 | 0.000 | 0.048 | |
| getDrugName | 0.004 | 0.000 | 0.002 | |
| getFeatureDataFromMatList | 2.104 | 0.756 | 2.946 | |
| getFingerprintList | 0.116 | 0.000 | 0.051 | |
| getMedSenLineActivity | 0.008 | 0.000 | 0.004 | |
| getMinDrugActivityRepeatCor | 0.012 | 0.000 | 0.006 | |
| getMoaStr | 0.168 | 0.004 | 0.171 | |
| getMoaToCompounds | 0.040 | 0.000 | 0.039 | |
| getMolDataMatrices | 0.328 | 0.280 | 0.608 | |
| getMolDataType | 0.000 | 0.000 | 0.001 | |
| getNumDrugActivityRepeats | 0.004 | 0.000 | 0.003 | |
| getNumMissingLines | 0.000 | 0.000 | 0.001 | |
| getRsd | 0.004 | 0.000 | 0.005 | |
| getSmiles | 0.000 | 0.000 | 0.002 | |
| hasMoa | 0.044 | 0.000 | 0.043 | |
| isPublic | 0.004 | 0.000 | 0.002 | |
| loadCellminerPlotInfo | 0.000 | 0.000 | 0.001 | |
| loadNciColorSet | 0.004 | 0.000 | 0.001 | |
| passRuleOf5 | 0.084 | 0.008 | 0.067 | |
| passRuleOf5FromNsc | 0.044 | 0.004 | 0.027 | |
| patternComparison | 0.224 | 0.204 | 0.434 | |
| plotCellMiner | 0.620 | 0.224 | 0.844 | |
| plotDrugActivityRepeats | 0.544 | 0.420 | 0.962 | |
| plotDrugSets | 0.028 | 0.004 | 0.031 | |