BioC 3.2: CHECK report for Cardinal on linux1.bioconductor.org

Package: Cardinal

Version: 1.2.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Cardinal_1.2.0.tar.gz

StartedAt: 2015-10-27 01:43:31 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 01:45:12 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 100.6 seconds

RetCode: 1

Status:  ERROR

CheckDir: Cardinal.Rcheck

Warnings: NA

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Cardinal_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/Cardinal.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ... [10s/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 : .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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [11s/11s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [19s/19s]
 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
  ‘/home/biocbuild/bbs-3.2-bioc/meat/Cardinal.Rcheck/00check.log’
for details.

* installing *source* package ‘Cardinal’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c dynamicAlign.c -o dynamicAlign.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c fastmap.c -o fastmap.o
fastmap.c: In function ‘choose_distant_objects’:
fastmap.c:59:24: warning: ‘o_b’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  pivot_objects->b[col] = o_b;
                        ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c localMaxima.c -o localMaxima.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c pugixml.cpp -o pugixml.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c readAnalyze.cpp -o readAnalyze.o
readAnalyze.cpp: In function ‘SEXPREC* readAnalyzeHDR(SEXP)’:
readAnalyze.cpp:164:47: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
   fread(&header, sizeof(struct dsr), 1, pfile);
                                               ^
readAnalyze.cpp: In function ‘SEXPREC* readAnalyzeT2M(SEXP, SEXP)’:
readAnalyze.cpp:261:49: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
   fread(mz, sizeof(float), INTEGER(n)[0], pfile);
                                                 ^
readAnalyze.cpp: In function ‘SEXPREC* readSimpleIntensityArray(const char*, int, int) [with CType = char; RType = int; SEXP = SEXPREC*]’:
readAnalyze.cpp:143:3: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
   fread(tmp, sizeof(CType), nrow, pfile);
   ^
readAnalyze.cpp: In function ‘SEXPREC* readSimpleIntensityArray(const char*, int, int) [with CType = short int; RType = int; SEXP = SEXPREC*]’:
readAnalyze.cpp:143:3: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
readAnalyze.cpp: In function ‘SEXPREC* readSimpleIntensityArray(const char*, int, int) [with CType = int; RType = int; SEXP = SEXPREC*]’:
readAnalyze.cpp:143:3: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
readAnalyze.cpp: In function ‘SEXPREC* readSimpleIntensityArray(const char*, int, int) [with CType = float; RType = double; SEXP = SEXPREC*]’:
readAnalyze.cpp:143:3: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
readAnalyze.cpp: In function ‘SEXPREC* readSimpleIntensityArray(const char*, int, int) [with CType = double; RType = double; SEXP = SEXPREC*]’:
readAnalyze.cpp:143:3: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c readImzML.cpp -o readImzML.o
readImzML.cpp: In function ‘SEXPREC* readContinuousMzArray(const char*, int, int) [with CType = float; RType = double; SEXP = SEXPREC*]’:
readImzML.cpp:27:2: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  fread(tmp, sizeof(CType), length, pfile);
  ^
readImzML.cpp: In function ‘SEXPREC* readContinuousMzArray(const char*, int, int) [with CType = double; RType = double; SEXP = SEXPREC*]’:
readImzML.cpp:27:2: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
readImzML.cpp: In function ‘SEXPREC* readContinuousMzArray(const char*, int, int) [with CType = int; RType = int; SEXP = SEXPREC*]’:
readImzML.cpp:27:2: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
readImzML.cpp: In function ‘SEXPREC* readContinuousMzArray(const char*, int, int) [with CType = long int; RType = int; SEXP = SEXPREC*]’:
readImzML.cpp:27:2: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
readImzML.cpp: In function ‘SEXPREC* readProcessedIbdArray(const char*, int*, int*, int) [with CType = float; RType = double; SEXP = SEXPREC*]’:
readImzML.cpp:74:3: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
   fread(tmp, sizeof(CType), length[j], pfile);
   ^
readImzML.cpp: In function ‘SEXPREC* readProcessedIbdArray(const char*, int*, int*, int) [with CType = double; RType = double; SEXP = SEXPREC*]’:
readImzML.cpp:74:3: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
readImzML.cpp: In function ‘SEXPREC* readProcessedIbdArray(const char*, int*, int*, int) [with CType = int; RType = int; SEXP = SEXPREC*]’:
readImzML.cpp:74:3: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
readImzML.cpp: In function ‘SEXPREC* readProcessedIbdArray(const char*, int*, int*, int) [with CType = long int; RType = int; SEXP = SEXPREC*]’:
readImzML.cpp:74:3: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
readImzML.cpp: In function ‘SEXPREC* readContinuousIntensityArray(const char*, int, int, int) [with CType = float; RType = double; SEXP = SEXPREC*]’:
readImzML.cpp:49:3: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
   fread(tmp, sizeof(CType), nrow, pfile);
   ^
readImzML.cpp: In function ‘SEXPREC* readContinuousIntensityArray(const char*, int, int, int) [with CType = double; RType = double; SEXP = SEXPREC*]’:
readImzML.cpp:49:3: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
readImzML.cpp: In function ‘SEXPREC* readContinuousIntensityArray(const char*, int, int, int) [with CType = int; RType = int; SEXP = SEXPREC*]’:
readImzML.cpp:49:3: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
readImzML.cpp: In function ‘SEXPREC* readContinuousIntensityArray(const char*, int, int, int) [with CType = long int; RType = int; SEXP = SEXPREC*]’:
readImzML.cpp:49:3: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c smooth.c -o smooth.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c spatial.c -o spatial.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c utils.cpp -o utils.o
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/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 -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/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	0.371	0.012	0.384
IAnnotatedDataFrame-class	0.063	0.000	0.064
ImageData-class	0.008	0.000	0.007
MIAPE-Imaging-class	0.002	0.000	0.003
MSImageData-class	0.059	0.004	0.063
MSImageProcess-class	0.002	0.000	0.001
MSImageSet-class	0.177	0.004	0.181
OPLS-methods	0.062	0.000	0.062
PCA-methods	0.055	0.000	0.054
PLS-methods	0.057	0.000	0.057
SImageData-class	0.042	0.000	0.042
SImageSet-class	0.051	0.000	0.050
colors-functions	0.996	0.000	0.996
generateImage	0.256	0.008	0.264
generateSpectrum	0.036	0.000	0.036
iSet-class	0.041	0.000	0.042
image-methods	0.543	0.004	0.547
normalize-methods	0.142	0.000	0.143
peakAlign-methods	0.351	0.000	0.351
peakFilter-methods	0.379	0.000	0.379
peakPick-methods	0.163	0.000	0.163
pixelApply-methods	0.043	0.000	0.042
pixels-methods	0.115	0.000	0.115
plot-methods	0.713	0.012	0.725
reduceBaseline-methods	0.140	0.000	0.141
reduceDimension-methods	0.172	0.000	0.172
smoothSignal-methods.R	0.14	0.00	0.14
spatialKMeans-methods	0.336	0.000	0.336
spatialShrunkenCentroids-methods	1.042	0.000	1.042
standardizeSamples-methods	0.466	0.000	0.466
topLabels-methods	0.610	0.004	0.614