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BioC 3.5: CHECK report for Cardinal on tokay2

This page was generated on 2017-08-16 13:24:10 -0400 (Wed, 16 Aug 2017).

Package 173/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Cardinal 1.8.0
Kylie A. Bemis
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/Cardinal
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Cardinal
Version: 1.8.0
Command: rm -rf Cardinal.buildbin-libdir Cardinal.Rcheck && mkdir Cardinal.buildbin-libdir Cardinal.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Cardinal.buildbin-libdir Cardinal_1.8.0.tar.gz >Cardinal.Rcheck\00install.out 2>&1 && cp Cardinal.Rcheck\00install.out Cardinal-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=Cardinal.buildbin-libdir --install="check:Cardinal-install.out" --force-multiarch --no-vignettes --timings Cardinal_1.8.0.tar.gz
StartedAt: 2017-08-15 22:29:13 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:33:32 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 258.8 seconds
RetCode: 0
Status:  OK  
CheckDir: Cardinal.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Cardinal.buildbin-libdir Cardinal.Rcheck && mkdir Cardinal.buildbin-libdir Cardinal.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Cardinal.buildbin-libdir Cardinal_1.8.0.tar.gz >Cardinal.Rcheck\00install.out 2>&1 && cp Cardinal.Rcheck\00install.out Cardinal-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=Cardinal.buildbin-libdir --install="check:Cardinal-install.out" --force-multiarch --no-vignettes --timings Cardinal_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/Cardinal.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Cardinal/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Cardinal' version '1.8.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
.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'
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'
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 smooth.spline tail 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", "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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.5-bioc/meat/Cardinal.buildbin-libdir/Cardinal/libs/i386/Cardinal.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/Cardinal.Rcheck/00check.log'
for details.

Cardinal.Rcheck/00install.out:


install for i386

* installing *source* package 'Cardinal' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c dynamicAlign.c -o dynamicAlign.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -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;
                        ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c localMaxima.c -o localMaxima.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pugixml.cpp -o pugixml.o
pugixml.cpp:1452:18: warning: 'size_t pugi::impl::{anonymous}::as_utf8_begin(const wchar_t*, size_t)' defined but not used [-Wunused-function]
  PUGI__FN size_t as_utf8_begin(const wchar_t* str, size_t length)
                  ^
pugixml.cpp:1458:16: warning: 'void pugi::impl::{anonymous}::as_utf8_end(char*, size_t, const wchar_t*, size_t)' defined but not used [-Wunused-function]
  PUGI__FN void as_utf8_end(char* buffer, size_t size, const wchar_t* str, size_t length)
                ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c readAnalyze.cpp -o readAnalyze.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c readImzML.cpp -o readImzML.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c smooth.c -o smooth.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c spatial.c -o spatial.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o Cardinal.dll tmp.def dynamicAlign.o fastmap.o localMaxima.o pugixml.o readAnalyze.o readImzML.o smooth.o spatial.o utils.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/Cardinal.buildbin-libdir/Cardinal/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'Cardinal' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c dynamicAlign.c -o dynamicAlign.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -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;
                        ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c localMaxima.c -o localMaxima.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pugixml.cpp -o pugixml.o
pugixml.cpp:1452:18: warning: 'size_t pugi::impl::{anonymous}::as_utf8_begin(const wchar_t*, size_t)' defined but not used [-Wunused-function]
  PUGI__FN size_t as_utf8_begin(const wchar_t* str, size_t length)
                  ^
pugixml.cpp:1458:16: warning: 'void pugi::impl::{anonymous}::as_utf8_end(char*, size_t, const wchar_t*, size_t)' defined but not used [-Wunused-function]
  PUGI__FN void as_utf8_end(char* buffer, size_t size, const wchar_t* str, size_t length)
                ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c readAnalyze.cpp -o readAnalyze.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c readImzML.cpp -o readImzML.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c smooth.c -o smooth.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c spatial.c -o spatial.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o Cardinal.dll tmp.def dynamicAlign.o fastmap.o localMaxima.o pugixml.o readAnalyze.o readImzML.o smooth.o spatial.o utils.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/Cardinal.buildbin-libdir/Cardinal/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Cardinal' as Cardinal_1.8.0.zip
* DONE (Cardinal)

Cardinal.Rcheck/examples_i386/Cardinal-Ex.timings:

nameusersystemelapsed
Binmat-class000
Hashmat-class0.420.020.44
IAnnotatedDataFrame-class0.100.020.11
ImageData-class0.030.000.03
MIAPE-Imaging-class000
MSImageData-class0.190.040.23
MSImageProcess-class000
MSImageSet-class0.200.000.21
OPLS-methods0.160.000.15
PCA-methods0.040.000.08
PLS-methods0.070.000.06
SImageData-class0.070.000.08
SImageSet-class0.070.000.06
batchProcess-methods0.50.00.5
colors-functions0.850.020.86
generateImage0.340.010.36
generateSpectrum0.250.000.25
iSet-class0.050.000.05
image-methods0.550.030.57
normalize-methods0.080.000.08
peakAlign-methods0.290.000.30
peakFilter-methods0.330.000.33
peakPick-methods0.130.000.12
pixelApply-methods0.030.000.03
pixels-methods0.080.000.08
plot-methods0.540.020.56
reduceBaseline-methods0.110.000.11
reduceDimension-methods0.10.00.1
smoothSignal-methods.R0.090.000.10
spatialKMeans-methods0.480.000.48
spatialShrunkenCentroids-methods1.410.001.41
standardizeSamples-methods0.380.000.37
topLabels-methods1.070.001.08

Cardinal.Rcheck/examples_x64/Cardinal-Ex.timings:

nameusersystemelapsed
Binmat-class000
Hashmat-class0.530.000.53
IAnnotatedDataFrame-class0.130.000.12
ImageData-class0.050.000.05
MIAPE-Imaging-class000
MSImageData-class0.260.000.26
MSImageProcess-class000
MSImageSet-class0.280.000.29
OPLS-methods0.220.000.21
PCA-methods0.080.000.10
PLS-methods0.080.000.08
SImageData-class0.170.000.17
SImageSet-class0.140.000.14
batchProcess-methods0.830.000.83
colors-functions1.230.011.25
generateImage0.460.020.47
generateSpectrum0.040.010.06
iSet-class0.100.000.09
image-methods0.700.020.72
normalize-methods0.110.000.11
peakAlign-methods0.370.000.37
peakFilter-methods0.440.000.44
peakPick-methods0.130.000.13
pixelApply-methods0.040.000.04
pixels-methods0.080.000.08
plot-methods0.660.020.67
reduceBaseline-methods0.150.000.16
reduceDimension-methods0.110.000.11
smoothSignal-methods.R0.110.000.10
spatialKMeans-methods0.530.000.54
spatialShrunkenCentroids-methods1.540.001.53
standardizeSamples-methods0.450.000.45
topLabels-methods0.840.000.84