BioC 3.3: CHECK report for Cardinal on morelia

Package: Cardinal

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Cardinal_1.3.0.tar.gz

StartedAt: 2015-10-22 04:10:12 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 04:11:54 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 102.8 seconds

RetCode: 1

Status:  ERROR

CheckDir: Cardinal.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Cardinal_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/Cardinal.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.3.0’
* 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 ... [9s/10s] 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 ... 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 : <anonymous>: no visible binding for global
  variable ‘.Index’
peakAlign,MSImageSet-numeric : <anonymous>: no visible binding for
  global variable ‘.Index’
peakPick,MSImageSet : <anonymous>: no visible binding for global
  variable ‘.Index’
reduceBaseline,MSImageSet : <anonymous>: no visible binding for global
  variable ‘.Index’
reduceDimension,MSImageSet-missing : <anonymous>: no visible binding
  for global variable ‘.Index’
smoothSignal,MSImageSet : <anonymous>: no visible binding for global
  variable ‘.Index’
Undefined global functions or variables:
  .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 ... [10s/10s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [17s/17s]
 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-3.3-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-3.3-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	0.283	0.007	0.290
IAnnotatedDataFrame-class	0.063	0.001	0.063
ImageData-class	0.007	0.001	0.008
MIAPE-Imaging-class	0.003	0.000	0.004
MSImageData-class	0.056	0.007	0.063
MSImageProcess-class	0.001	0.000	0.002
MSImageSet-class	0.172	0.005	0.177
OPLS-methods	0.060	0.001	0.061
PCA-methods	0.058	0.000	0.058
PLS-methods	0.061	0.001	0.062
SImageData-class	0.053	0.001	0.054
SImageSet-class	0.052	0.001	0.053
colors-functions	0.911	0.002	0.914
generateImage	0.233	0.008	0.242
generateSpectrum	0.027	0.002	0.029
iSet-class	0.041	0.001	0.042
image-methods	0.532	0.008	0.541
normalize-methods	0.148	0.001	0.149
peakAlign-methods	0.352	0.001	0.353
peakFilter-methods	0.458	0.001	0.459
peakPick-methods	0.164	0.000	0.165
pixelApply-methods	0.05	0.00	0.05
pixels-methods	0.115	0.001	0.116
plot-methods	0.731	0.020	0.754
reduceBaseline-methods	0.150	0.001	0.151
reduceDimension-methods	0.167	0.000	0.167
smoothSignal-methods.R	0.134	0.000	0.135
spatialKMeans-methods	0.338	0.003	0.341
spatialShrunkenCentroids-methods	1.014	0.007	1.022
standardizeSamples-methods	0.394	0.001	0.395
topLabels-methods	0.583	0.002	0.584