Augustin Luna
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/rcellminer |
| Branch: RELEASE_3_9 |
| Last Commit: eeb7968 |
| Last Changed Date: 2019-05-02 11:53:53 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:32:48 -0400 (Wed, 16 Oct 2019).
| Package 1325/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| rcellminer 2.6.0 Augustin Luna
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: rcellminer |
| Version: 2.6.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rcellminer.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings rcellminer_2.6.0.tar.gz |
| StartedAt: 2019-10-16 06:22:54 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:46:59 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 1444.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: rcellminer.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rcellminer.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings rcellminer_2.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/rcellminer.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '2.6.0'
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'rcellminer' can be installed ... 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
* 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
* 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 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
getColumnQuantiles: no visible global function definition for
'quantile'
getDrugActivityRange: no visible global function definition for 'IQR'
getRsd: no visible binding for global variable 'sd'
parCorPatternComparison: no visible global function definition for
'residuals'
parCorPatternComparison: no visible global function definition for 'lm'
parCorPatternComparison: no visible global function definition for
'na.exclude'
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 'axis'
plotCellMiner2D: no visible global function definition for
'element_text'
plotCellMiner2D: no visible global function definition for 'xlim'
plotCellMiner2D: no visible global function definition for 'ylim'
plotDrugActivityRepeats: no visible global function definition for
'pdf'
plotDrugActivityRepeats: no visible global function definition for
'dev.off'
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'
rcdkplot: no visible global function definition for 'par'
rcdkplot: no visible global function definition for 'get.depictor'
rcdkplot: no visible global function definition for 'plot'
rcdkplot: no visible global function definition for 'rasterImage'
Undefined global functions or variables:
IQR axis dev.off element_text get.depictor layout lcm lm na.exclude
par pdf plot quantile rasterImage residuals sd segments xlim ylim
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("graphics", "axis", "layout", "lcm", "par", "plot",
"rasterImage", "segments")
importFrom("stats", "IQR", "lm", "na.exclude", "quantile", "residuals",
"sd")
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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotStructures 1.20 0.25 10.75
compareFingerprints 1.32 0.12 5.41
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotStructures 2.81 0.31 6.39
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.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-3.9-bioc/meat/rcellminer.Rcheck/00check.log'
for details.
rcellminer.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/rcellminer_2.6.0.tar.gz && rm -rf rcellminer.buildbin-libdir && mkdir rcellminer.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rcellminer.buildbin-libdir rcellminer_2.6.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL rcellminer_2.6.0.zip && rm rcellminer_2.6.0.tar.gz rcellminer_2.6.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 3439k 100 3439k 0 0 16.2M 0 --:--:-- --:--:-- --:--:-- 16.8M
install for i386
* installing *source* package 'rcellminer' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'rcellminer'
finding HTML links ... done
DrugData-class html
DrugData-eSet-eSet-MIAxE-method html
DrugData html
Drug_MOA_Key html
MolData-class html
MolData-list-MIAxE-method html
MolData html
cmVersion html
compareFingerprints html
crossCors html
crossCorsSpearman html
drugDB html
elNetMolDataNCI60 html
fingerprintList html
getAct-DrugData-method html
getAct html
getActivityRangeStats html
getAllFeatureData-MolData-method html
getAllFeatureData html
getBinaryMutationData html
getColumnQuantiles html
getDrugActivityData html
getDrugActivityRange html
getDrugActivityRepeatData html
getDrugMoaList html
getDrugName html
getESetList-MolData-method html
getESetList html
getFeatureAnnot-DrugData-method html
getFeatureAnnot-MolData-method html
getFeatureAnnot html
getFeatureDataFromMatList html
getFingerprintList html
getMedSenLineActivity html
getMinDrugActivityRepeatCor html
getMoaStr html
getMoaToCompounds html
getMolDataMatrices html
getMolDataType html
getNumDrugActivityRepeats html
getNumMissingLines html
getRepeatAct-DrugData-method html
getRepeatAct html
getRsd html
getSampleData-DrugData-method html
getSampleData-MolData-method html
getSampleData html
getSmiles html
hasMoa html
initialize-DrugData-method html
initialize-MolData-method html
isPublic html
loadCellminerPlotInfo html
loadNciColorSet html
parCorPatternComparison html
passRuleOf5 html
passRuleOf5FromNsc html
patternComparison html
plotCellMiner html
plotCellMiner2D html
plotDrugActivityRepeats html
plotDrugSets html
plotStructures html
plotStructuresFromNscs html
rcdkplot html
removeMolDataType html
restrictFeatureMat html
rowCors html
runShinyApp html
runShinyComparePlots html
runShinyCompareStructures html
runShinyCompoundBrowser html
searchForNscs html
selectCorrelatedRows html
selectCorrelatedRowsFromMatrices html
sub-sub-MolData-method html
sub-subset-MolData-method html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'rcellminer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rcellminer' as rcellminer_2.6.0.zip
* DONE (rcellminer)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'rcellminer' successfully unpacked and MD5 sums checked
|
rcellminer.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, 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: rcdklibs
Loading required package: rJava
Attaching package: 'rcdk'
The following object is masked from 'package:testthat':
matches
Loading required package: fingerprint
Loading required package: rcellminerData
Consider citing this package: Luna A, et al. rcellminer: exploring molecular profiles and drug response of the NCI-60 cell lines in R. PMID: 26635141; citation("rcellminer")
>
> #test_package("rcellminer")
> test_check("rcellminer")
== testthat results ===========================================================
[ OK: 237 | SKIPPED: 1 | WARNINGS: 2 | FAILED: 0 ]
>
> proc.time()
user system elapsed
576.92 2.20 746.09
|
rcellminer.Rcheck/tests_x64/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, 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: rcdklibs
Loading required package: rJava
Attaching package: 'rcdk'
The following object is masked from 'package:testthat':
matches
Loading required package: fingerprint
Loading required package: rcellminerData
Consider citing this package: Luna A, et al. rcellminer: exploring molecular profiles and drug response of the NCI-60 cell lines in R. PMID: 26635141; citation("rcellminer")
>
> #test_package("rcellminer")
> test_check("rcellminer")
== testthat results ===========================================================
[ OK: 237 | SKIPPED: 1 | WARNINGS: 2 | FAILED: 0 ]
>
> proc.time()
user system elapsed
497.45 2.06 497.14
|
|
rcellminer.Rcheck/examples_i386/rcellminer-Ex.timings
|
rcellminer.Rcheck/examples_x64/rcellminer-Ex.timings
|