BioC 3.2: CHECK report for Cardinal on oaxaca

Package: Cardinal

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Cardinal_1.2.0.tar.gz

StartedAt: 2015-10-27 01:59:25 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:02:26 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 180.6 seconds

RetCode: 1

Status:  ERROR

CheckDir: Cardinal.Rcheck

Warnings: NA

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Cardinal_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/Cardinal.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 ‘Cardinal/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Cardinal’ version ‘1.2.0’
* 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 ‘Cardinal’ can be installed ... [11s/14s] 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 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
normalize,MSImageSet : .local : <anonymous>: no visible binding for
  global variable ‘.Index’
peakAlign,MSImageSet-numeric : .local : <anonymous>: no visible binding
  for global variable ‘.Index’
peakPick,MSImageSet : .local : <anonymous>: no visible binding for
  global variable ‘.Index’
reduceBaseline,MSImageSet : .local : <anonymous>: no visible binding
  for global variable ‘.Index’
reduceDimension,MSImageSet-missing : .local : <anonymous>: no visible
  binding for global variable ‘.Index’
smoothSignal,MSImageSet : .local : <anonymous>: no visible binding for
  global variable ‘.Index’
* 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 line endings in C/C++/Fortran sources/headers ... 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’ ... OK
* checking examples ... [16s/16s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [25s/25s]
 ERROR
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  iSet class : ...
  nipals : ..............
  processing : .......................Warning message:
  Placing tests in `inst/tests/` is deprecated. Please use `tests/testthat/` instead 
  ...
  SpatialKMeans : ..
  SpatialShrunkenCentroids : ....
  
  1. Failure (at test_SImageSet.R#133): SImageSet pixelApply ---------------------
  t(tmp3) not equal to expected
  current is not list-like
  Error: Test failures
  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: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/Cardinal.Rcheck/00check.log’
for details.

* installing *source* package ‘Cardinal’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c dynamicAlign.c -o dynamicAlign.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c fastmap.c -o fastmap.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c localMaxima.c -o localMaxima.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c pugixml.cpp -o pugixml.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c readAnalyze.cpp -o readAnalyze.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c readImzML.cpp -o readImzML.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c smooth.c -o smooth.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c spatial.c -o spatial.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c utils.cpp -o utils.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 Cardinal.so dynamicAlign.o fastmap.o localMaxima.o pugixml.o readAnalyze.o readImzML.o smooth.o spatial.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/Cardinal.Rcheck/Cardinal/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Cardinal)

name	user	system	elapsed
Hashmat-class	0.447	0.015	0.497
IAnnotatedDataFrame-class	0.105	0.002	0.107
ImageData-class	0.012	0.001	0.013
MIAPE-Imaging-class	0.005	0.001	0.006
MSImageData-class	0.105	0.011	0.116
MSImageProcess-class	0.002	0.000	0.001
MSImageSet-class	0.307	0.006	0.314
OPLS-methods	0.116	0.000	0.116
PCA-methods	0.100	0.001	0.100
PLS-methods	0.100	0.001	0.101
SImageData-class	0.069	0.002	0.071
SImageSet-class	0.096	0.001	0.098
colors-functions	1.523	0.008	1.531
generateImage	0.425	0.005	0.431
generateSpectrum	0.046	0.004	0.050
iSet-class	0.060	0.002	0.061
image-methods	0.902	0.010	0.914
normalize-methods	0.226	0.001	0.227
peakAlign-methods	0.591	0.001	0.594
peakFilter-methods	0.636	0.002	0.639
peakPick-methods	0.263	0.001	0.265
pixelApply-methods	0.073	0.001	0.075
pixels-methods	0.209	0.000	0.210
plot-methods	0.959	0.014	0.993
reduceBaseline-methods	0.283	0.001	0.285
reduceDimension-methods	0.311	0.001	0.311
smoothSignal-methods.R	0.248	0.001	0.249
spatialKMeans-methods	0.503	0.002	0.505
spatialShrunkenCentroids-methods	1.675	0.005	1.682
standardizeSamples-methods	0.738	0.002	0.739
topLabels-methods	0.897	0.007	0.905