BioC 3.1: CHECK report for CAMERA on moscato2

Package: CAMERA

Version: 1.24.1

Command: rm -rf CAMERA.buildbin-libdir CAMERA.Rcheck && mkdir CAMERA.buildbin-libdir CAMERA.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CAMERA.buildbin-libdir CAMERA_1.24.1.tar.gz >CAMERA.Rcheck\00install.out 2>&1 && cp CAMERA.Rcheck\00install.out CAMERA-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=CAMERA.buildbin-libdir --install="check:CAMERA-install.out" --force-multiarch --no-vignettes --timings CAMERA_1.24.1.tar.gz

StartedAt: 2015-10-08 23:57:25 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-09 00:02:47 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 321.3 seconds

RetCode: 0

Status:  OK

CheckDir: CAMERA.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf CAMERA.buildbin-libdir CAMERA.Rcheck && mkdir CAMERA.buildbin-libdir CAMERA.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CAMERA.buildbin-libdir CAMERA_1.24.1.tar.gz >CAMERA.Rcheck\00install.out 2>&1 && cp CAMERA.Rcheck\00install.out CAMERA-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=CAMERA.buildbin-libdir --install="check:CAMERA-install.out" --force-multiarch --no-vignettes --timings CAMERA_1.24.1.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/CAMERA.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CAMERA/DESCRIPTION' ... OK
* this is package 'CAMERA' version '1.24.1'
* 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 whether package 'CAMERA' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'xcms' 'igraph'
A package should be listed in only one of these fields.
* 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
* 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 dependencies in R code ... NOTE
'library' or 'require' call to 'methods' which was already attached by Depends.
  Please remove these calls from your code.
Unexported objects imported by ':::' calls:
  'xcms:::descendMin' 'xcms:::xcmsClusterApply'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'annotateGrp' 'combineHypothese' 'fastMatch' 'naOmit'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call("getEIC", ..., PACKAGE = "xcms")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
File 'CAMERA/R/zzz.R':
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.

annotateGrpMPI2: no visible binding for global variable
  'papply_commondata'
cleanParallel: no visible global function definition for
  'mpi.close.Rslaves'
cleanParallel: no visible global function definition for 'stopCluster'
fragments2metfusion : <anonymous>: no visible binding for global
  variable 'object'
xsAnnotate: no visible global function definition for 'mpi.comm.size'
xsAnnotate: no visible global function definition for
  'mpi.spawn.Rslaves'
xsAnnotate: no visible global function definition for 'makeCluster'
xsAnnotate: no visible binding for global variable 'graphMethod'
findAdducts,xsAnnotate: no visible global function definition for
  'mpi.comm.size'
plotPeakEICs,xsAnnotate : .local : <anonymous>: no visible binding for
  global variable 'pc'
plotPeakEICs,xsAnnotate : .local: no visible binding for global
  variable 'pspec'
* checking Rd files ... NOTE
prepare_Rd: findKendrickMasses.Rd:21-22: Dropping empty section \details
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... 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 'E:/biocbld/bbs-3.1-bioc/meat/CAMERA.buildbin-libdir/CAMERA/libs/i386/CAMERA.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'E:/biocbld/bbs-3.1-bioc/meat/CAMERA.buildbin-libdir/CAMERA/libs/x64/CAMERA.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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' ... [52s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
getIsotopeCluster  8.08   0.87    9.04
annotateDiffreport 6.79   0.55    7.44
** running examples for arch 'x64' ... [56s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
annotateDiffreport 6.96   0.81    7.92
getIsotopeCluster  6.63   0.70    7.33
groupCorr-methods  5.24   0.17    5.41
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [53s]
 [53s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [27s]
 [27s] 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: 6 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/CAMERA.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'CAMERA' ...
** libs
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c fastMatch.c -o fastMatch.o
gcc -m32 -shared -s -static-libgcc -o CAMERA.dll tmp.def fastMatch.o -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/CAMERA.buildbin-libdir/CAMERA/libs/i386
** R
** data
** inst
** byte-compile and prepare 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 'CAMERA' ...
** libs
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c fastMatch.c -o fastMatch.o
gcc -m64 -shared -s -static-libgcc -o CAMERA.dll tmp.def fastMatch.o -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/CAMERA.buildbin-libdir/CAMERA/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CAMERA' as CAMERA_1.24.1.zip
* DONE (CAMERA)

name	user	system	elapsed
annotate-methods	3.20	0.09	3.48
annotateDiffreport	6.79	0.55	7.44
calcCaS-methods	1.60	0.09	1.70
cleanParallel	0	0	0
combinexsAnnos	0	0	0
findAdducts-methods	3.52	0.00	3.54
findIsotopes-methods	0.78	0.05	0.82
findKendrickMasses	1.77	0.00	1.77
findNeutralLoss	0.76	0.01	0.78
findNeutralLossSpecs	0.56	0.05	0.61
getAllPeakEICs-methods	1.67	0.03	1.70
getIsotopeCluster	8.08	0.87	9.04
getPeaklist-methods	3.11	0.05	3.16
getpspectra	0.59	0.00	0.59
groupCorr-methods	4.71	0.24	4.96
groupDen-methods	2.01	0.01	2.03
groupFWHM-methods	2.42	0.00	2.42
pspec2metfrag	3.34	0.05	3.38
ruleSet-class	0.06	0.00	0.06
xsAnnotate	1.5	0.0	1.5

name	user	system	elapsed
annotate-methods	3.73	0.05	4.65
annotateDiffreport	6.96	0.81	7.92
calcCaS-methods	1.95	0.08	2.03
cleanParallel	0	0	0
combinexsAnnos	0	0	0
findAdducts-methods	4.33	0.05	4.36
findIsotopes-methods	0.73	0.03	0.77
findKendrickMasses	1.7	0.0	1.7
findNeutralLoss	0.92	0.05	0.97
findNeutralLossSpecs	0.95	0.03	0.98
getAllPeakEICs-methods	1.86	0.01	1.87
getIsotopeCluster	6.63	0.70	7.33
getPeaklist-methods	3.99	0.05	4.04
getpspectra	0.66	0.01	0.67
groupCorr-methods	5.24	0.17	5.41
groupDen-methods	2.42	0.02	2.44
groupFWHM-methods	2.34	0.06	2.40
pspec2metfrag	3.52	0.00	3.52
ruleSet-class	0.08	0.00	0.08
xsAnnotate	1.54	0.00	1.55