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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Cardinal_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/Cardinal.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.4.0’
* 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 ... 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
.PCA.fit: no visible binding for global variable ‘var’
.PCA.predict: no visible binding for global variable ‘sd’
.calculateSpatialDiscriminantScores: no visible global function
definition for ‘median’
.console: no visible global function definition for ‘flush.console’
.onAttach: no visible global function definition for ‘packageVersion’
.plot.gridsearch: no visible global function definition for ‘points’
.plot.gridsearch: no visible global function definition for ‘abline’
.plot.gridsearch: no visible global function definition for ‘legend’
.setup.layout: no visible global function definition for ‘par’
.spatialKMeans: no visible global function definition for ‘kmeans’
.spatialShrunkenCentroids.fit: no visible global function definition
for ‘median’
.spatialShrunkenCentroids.predict: no visible global function
definition for ‘median’
alpha.colors: no visible global function definition for ‘col2rgb’
alpha.colors: no visible global function definition for ‘rgb’
contrast.enhance.histogram: no visible global function definition for
‘quantile’
contrast.enhance.histogram: no visible global function definition for
‘tail’
contrast.enhance.suppression: no visible global function definition for
‘quantile’
generateSpectrum: no visible global function definition for ‘runif’
generateSpectrum: no visible global function definition for ‘rnorm’
generateSpectrum : <anonymous>: no visible global function definition
for ‘dnorm’
gradient.colors: no visible global function definition for ‘colorRamp’
gradient.colors : <anonymous>: no visible binding for global variable
‘rgb’
image3d: no visible global function definition for ‘persp’
image3d: no visible global function definition for ‘points’
image3d: no visible global function definition for ‘trans3d’
intensity.colors: no visible global function definition for ‘rainbow’
intensity.colors: no visible global function definition for ‘colorRamp’
intensity.colors: no visible global function definition for ‘col2rgb’
intensity.colors : <anonymous>: no visible binding for global variable
‘rgb’
intensity.colors2: no visible global function definition for ‘rainbow’
interp.surface: no visible global function definition for ‘approx’
nipals.PCA: no visible binding for global variable ‘sd’
normalize.do: no visible global function definition for ‘lines’
peakAlign.do: no visible global function definition for ‘abline’
peakPick.adaptive: no visible binding for global variable ‘sd’
peakPick.adaptive: no visible global function definition for
‘smooth.spline’
peakPick.adaptive: no visible global function definition for ‘median’
peakPick.do: no visible global function definition for ‘lines’
peakPick.limpic: no visible binding for global variable ‘sd’
peakPick.limpic: no visible global function definition for ‘median’
peakPick.limpic: no visible global function definition for ‘quantile’
peakPick.simple: no visible binding for global variable ‘sd’
reduceBaseline.do: no visible global function definition for ‘lines’
reduceBaseline.median: no visible global function definition for
‘smooth.spline’
reduceDimension.do: no visible global function definition for ‘points’
reduceDimension.do: no visible global function definition for ‘lines’
risk.colors: no visible global function definition for ‘colorRamp’
risk.colors : <anonymous>: no visible binding for global variable ‘rgb’
smoothSignal.do: no visible global function definition for ‘lines’
smoothSignal.gaussian: no visible global function definition for
‘dnorm’
smoothSignal.ma: no visible global function definition for ‘filter’
batchProcess,MSImageSet : <anonymous>: no visible binding for global
variable ‘.Index’
image,ResultSet: no visible global function definition for ‘rainbow’
image,ResultSet: no visible global function definition for ‘as.formula’
image,SImageSet: no visible global function definition for ‘rainbow’
image,SImageSet: no visible global function definition for ‘as.formula’
image,SImageSet: no visible global function definition for ‘legend’
image,SImageSet: no visible global function definition for ‘rgb’
initialize,MSImageProcess: no visible global function definition for
‘packageDescription’
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’
plot,ResultSet-missing: no visible global function definition for
‘rainbow’
plot,ResultSet-missing: no visible global function definition for
‘as.formula’
plot,SImageSet-missing: no visible global function definition for
‘as.formula’
plot,SImageSet-missing: no visible global function definition for
‘abline’
plot,SImageSet-missing: no visible global function definition for
‘points’
plot,SImageSet-missing: no visible global function definition for
‘legend’
plot,SImageSet-missing: no visible global function definition for ‘rgb’
reduceBaseline,MSImageSet : <anonymous>: no visible binding for global
variable ‘.Index’
reduceDimension,MSImageSet-missing : <anonymous>: no visible binding
for global variable ‘.Index’
select,SImageSet: no visible global function definition for ‘locator’
show,ImageData: no visible global function definition for ‘object.size’
smoothSignal,MSImageSet : <anonymous>: no visible binding for global
variable ‘.Index’
summary,SpatialShrunkenCentroids : <anonymous>: no visible global
function definition for ‘pt’
summary,SpatialShrunkenCentroids : <anonymous>: no visible global
function definition for ‘p.adjust’
summary,iSet : <anonymous>: no visible global function definition for
‘object.size’
summary,iSet: no visible global function definition for ‘object.size’
topLabels,ResultSet: no visible global function definition for ‘head’
Undefined global functions or variables:
.Index abline approx as.formula col2rgb colorRamp dnorm filter
flush.console head kmeans legend lines locator median object.size
p.adjust packageDescription packageVersion par persp points pt
quantile rainbow rgb rnorm runif sd smooth.spline tail trans3d var
Consider adding
importFrom("grDevices", "col2rgb", "colorRamp", "rainbow", "rgb",
"trans3d")
importFrom("graphics", "abline", "legend", "lines", "locator", "par",
"persp", "points")
importFrom("stats", "approx", "as.formula", "dnorm", "filter",
"kmeans", "median", "p.adjust", "pt", "quantile", "rnorm",
"runif", "sd", "smooth.spline", "var")
importFrom("utils", "flush.console", "head", "object.size",
"packageDescription", "packageVersion", "tail")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... NOTE
‘qpdf’ made some significant size reductions:
compacted ‘Cardinal-walkthrough.pdf’ from 1.7Mb to 1.5Mb
consider running tools::compactPDF() on these files
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/Cardinal.Rcheck/00check.log’
for details.
* installing *source* package ‘Cardinal’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-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-3.3-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-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c localMaxima.c -o localMaxima.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c pugixml.cpp -o pugixml.o
g++ -I/home/biocbuild/bbs-3.3-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-3.3-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*, double, 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*, double, 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*, double, 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*, double, 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*, double*, 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*, double*, 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*, double*, 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*, double*, 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*, double, int, int) [with CType = short 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]
fread(tmp, sizeof(CType), nrow, pfile);
^
readImzML.cpp: In function ‘SEXPREC* readContinuousIntensityArray(const char*, double, 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]
readImzML.cpp: In function ‘SEXPREC* readContinuousIntensityArray(const char*, double, 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*, double, 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*, double, 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]
readImzML.cpp: In function ‘SEXPREC* readProcessedIbdArray(const char*, double*, int*, int) [with CType = short 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]
fread(tmp, sizeof(CType), length[j], pfile);
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-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-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c spatial.c -o spatial.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c utils.cpp -o utils.o
g++ -shared -L/home/biocbuild/bbs-3.3-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-3.3-bioc/R/lib -lR
installing to /home/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)
