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BioC 3.2: CHECK report for Cardinal on zin1

This page was generated on 2016-04-23 10:14:28 -0700 (Sat, 23 Apr 2016).

Package 140/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Cardinal 1.2.1
Kyle D. Bemis
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/Cardinal
Last Changed Rev: 111669 / Revision: 116712
Last Changed Date: 2015-12-19 12:06:22 -0800 (Sat, 19 Dec 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Cardinal
Version: 1.2.1
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Cardinal_1.2.1.tar.gz
StartedAt: 2016-04-22 22:48:02 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 22:49:49 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 107.0 seconds
RetCode: 0
Status:  OK 
CheckDir: Cardinal.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Cardinal_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/Cardinal.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.2.1’
* 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 ... [11s/11s] 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 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 ... [12s/12s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [20s/20s]
 [20s/20s] 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-3.2-bioc/meat/Cardinal.Rcheck/00check.log’
for details.


Cardinal.Rcheck/00install.out:

* 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)

Cardinal.Rcheck/Cardinal-Ex.timings:

nameusersystemelapsed
Hashmat-class0.3950.0000.395
IAnnotatedDataFrame-class0.0680.0040.072
ImageData-class0.0090.0000.009
MIAPE-Imaging-class0.0030.0000.003
MSImageData-class0.0690.0040.073
MSImageProcess-class0.0020.0000.001
MSImageSet-class0.2080.0000.209
OPLS-methods0.0760.0000.075
PCA-methods0.0590.0040.063
PLS-methods0.0630.0000.063
SImageData-class0.0490.0000.049
SImageSet-class0.0560.0000.056
colors-functions1.0670.0001.066
generateImage0.3400.0040.344
generateSpectrum0.0490.0000.049
iSet-class0.0550.0000.055
image-methods0.6650.0000.665
normalize-methods0.1640.0000.163
peakAlign-methods0.4190.0000.419
peakFilter-methods0.4670.0000.466
peakPick-methods0.1850.0000.185
pixelApply-methods0.0510.0000.051
pixels-methods0.1310.0000.132
plot-methods0.8050.0090.811
reduceBaseline-methods0.1640.0000.164
reduceDimension-methods0.20.00.2
smoothSignal-methods.R0.1690.0000.169
spatialKMeans-methods0.3870.0000.387
spatialShrunkenCentroids-methods1.2140.0121.225
standardizeSamples-methods0.5060.0000.505
topLabels-methods0.7400.0030.744