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BioC 3.1: CHECK report for pRoloc on morelia

This page was generated on 2015-10-09 09:40:38 -0700 (Fri, 09 Oct 2015).

Package 745/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pRoloc 1.8.0
Laurent Gatto
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/pRoloc
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: pRoloc
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pRoloc_1.8.0.tar.gz
StartedAt: 2015-10-09 05:02:12 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 05:08:28 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 376.1 seconds
RetCode: 0
Status:  OK 
CheckDir: pRoloc.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pRoloc_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/pRoloc.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pRoloc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pRoloc’ 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 for sufficient/correct file permissions ... OK
* checking whether package ‘pRoloc’ can be installed ... [29s/30s] 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
* 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘MLInterfaces:::.macroF1’ ‘MLInterfaces:::.precision’
  ‘MLInterfaces:::.recall’ ‘MLInterfaces:::es2df’
  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
Found the following possibly unsafe calls:
File ‘pRoloc/R/annotation.R’:
  unlockBinding("params", .pRolocEnv)
* 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
  Error in .requirePackage(package) : 
    unable to find required package 'pRoloc2'
  Calls: <Anonymous> ... .findInheritedMethods -> getClass -> getClassDef -> .requirePackage
  Execution halted
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... [74s/78s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
perTurboClassification 18.877  0.591  19.487
rfClassification        7.186  0.423   7.620
svmClassification       5.812  0.452   6.269
nnetClassification      5.571  0.082   5.656
ksvmClassification      4.826  0.272   5.116
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [58s/51s]
 [58s/51s] 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
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/pRoloc.Rcheck/00check.log’
for details.


pRoloc.Rcheck/00install.out:

* installing *source* package ‘pRoloc’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pRoloc.cpp -o pRoloc.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 pRoloc.so pRoloc.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/pRoloc.Rcheck/pRoloc/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
* DONE (pRoloc)

pRoloc.Rcheck/pRoloc-Ex.timings:

nameusersystemelapsed
AnnotationParams-class1.3450.0403.428
GenRegRes-class0.0030.0000.002
addMarkers0.2190.0170.256
checkFeatureNamesOverlap1.1800.0621.257
checkFvarOverlap0.0390.0070.045
chi2-methods0.0060.0000.007
empPvalues0.2090.0060.215
exprsToRatios-methods0.2010.0290.230
filterBinMSnSet0.2760.0010.277
filterZeroCols0.1560.0130.169
getGOFromFeatures0.0690.0101.158
getMarkerClasses0.0420.0080.050
getMarkers0.0320.0060.039
getPredictions0.6070.0720.679
getStockcol0.0860.0220.108
highlightOnPlot0.1150.0140.143
knnClassification1.2590.0461.306
knntlClassification0.0020.0000.001
ksvmClassification4.8260.2725.116
makeGoSet0.1740.0091.789
makeNaData1.3040.0161.321
markerMSnSet0.1430.0310.175
minClassScore0.0580.0190.078
minMarkers0.0550.0260.081
nbClassification3.8060.2614.071
nndist-methods0.2460.0180.279
nnetClassification5.5710.0825.656
pRolocmarkers0.0120.0010.012
perTurboClassification18.877 0.59119.487
phenoDisco0.0010.0000.001
plot2D2.6410.1162.780
plot2D_v12.5620.0732.641
plotDist0.1110.0100.128
plsdaClassification0.0010.0010.001
rfClassification7.1860.4237.620
sampleMSnSet0.0920.0170.109
showGOEvidenceCodes0.0010.0010.001
svmClassification5.8120.4526.269
testMSnSet0.6330.0400.674
testMarkers0.0440.0090.053
thetas0.0180.0020.021