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BioC 3.6: CHECK report for Cardinal on malbec1

This page was generated on 2017-08-16 13:22:52 -0400 (Wed, 16 Aug 2017).

Package 174/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Cardinal 1.9.0
Kylie A. Bemis
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Cardinal
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Cardinal
Version: 1.9.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Cardinal_1.9.0.tar.gz
StartedAt: 2017-08-15 21:45:27 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 21:47:40 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 132.6 seconds
RetCode: 0
Status:  OK 
CheckDir: Cardinal.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Cardinal_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/Cardinal.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.9.0’
* 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
.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.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’
normalize.do: no visible global function definition for ‘lines’
peakAlign.do: no visible global function definition for ‘abline’
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 global function definition for ‘median’
peakPick.limpic: no visible global function definition for ‘quantile’
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’
Undefined global functions or variables:
  .Index abline approx as.formula col2rgb colorRamp dnorm filter
  flush.console kmeans legend lines locator median object.size p.adjust
  packageDescription packageVersion par persp points pt quantile
  rainbow rgb rnorm runif smooth.spline trans3d
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", "smooth.spline")
  importFrom("utils", "flush.console", "object.size",
             "packageDescription", "packageVersion")
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 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/Cardinal.Rcheck/00check.log’
for details.


Cardinal.Rcheck/00install.out:

* installing *source* package ‘Cardinal’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c dynamicAlign.c -o dynamicAlign.o
gcc -I/home/biocbuild/bbs-3.6-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 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c localMaxima.c -o localMaxima.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c pugixml.cpp -o pugixml.o
g++  -I/home/biocbuild/bbs-3.6-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-3.6-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 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c smooth.c -o smooth.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c spatial.c -o spatial.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c utils.cpp -o utils.o
g++ -shared -L/home/biocbuild/bbs-3.6-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-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-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)

Cardinal.Rcheck/Cardinal-Ex.timings:

nameusersystemelapsed
Binmat-class0.0040.0000.001
Hashmat-class0.1320.0080.141
IAnnotatedDataFrame-class0.3360.0040.342
ImageData-class0.0520.0000.053
MIAPE-Imaging-class0.0040.0000.005
MSImageData-class0.3000.0080.306
MSImageProcess-class0.0040.0000.002
MSImageSet-class0.3680.0000.368
OPLS-methods0.2360.0040.241
PCA-methods0.0600.0000.061
PLS-methods0.0560.0000.057
SImageData-class0.0880.0000.089
SImageSet-class0.0720.0000.072
batchProcess-methods0.7520.0040.758
colors-functions0.8280.0000.831
generateImage0.3240.0040.330
generateSpectrum0.0320.0000.034
iSet-class0.0360.0000.034
image-methods0.5320.0040.538
normalize-methods0.0960.0000.099
peakAlign-methods0.3360.0000.336
peakFilter-methods0.3680.0000.368
peakPick-methods0.1160.0000.115
pixelApply-methods0.0320.0000.031
pixels-methods0.0880.0000.086
plot-methods0.5640.0080.571
reduceBaseline-methods0.1160.0000.117
reduceDimension-methods0.1120.0000.112
smoothSignal-methods.R0.1000.0000.097
spatialKMeans-methods0.5360.0000.536
spatialShrunkenCentroids-methods1.3920.0041.395
standardizeSamples-methods0.4080.0000.408
topLabels-methods0.7240.0000.724