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BioC 2.12: CHECK report for CAMERA on moscato2

This page was generated on 2013-10-09 09:38:40 -0700 (Wed, 09 Oct 2013).

Package 97/671HostnameOS / ArchBUILDCHECKBUILD BIN
CAMERA 1.16.0
Carsten Kuhl
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/CAMERA
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ WARNINGS ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: CAMERA
Version: 1.16.0
Command: rm -rf CAMERA.buildbin-libdir && mkdir CAMERA.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CAMERA.buildbin-libdir CAMERA_1.16.0.tar.gz >CAMERA-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=CAMERA.buildbin-libdir --install="check:CAMERA-install.out" --force-multiarch --no-vignettes --timings CAMERA_1.16.0.tar.gz && mv CAMERA.buildbin-libdir/* CAMERA.Rcheck/ && rmdir CAMERA.buildbin-libdir
StartedAt: 2013-10-09 01:20:48 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 01:27:43 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 415.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: CAMERA.Rcheck
Warnings: 1

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/CAMERA.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CAMERA/DESCRIPTION' ... OK
* this is package 'CAMERA' version '1.16.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'Rmpi'
* 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 ... WARNING
Found the following significant warnings:
  Warning: package 'Rcpp' was built under R version 3.0.2
  Warning: package 'igraph' was built under R version 3.0.2
  Warning: package 'Rcpp' was built under R version 3.0.2
  Warning: package 'igraph' was built under R version 3.0.2
  Warning: package 'Rcpp' was built under R version 3.0.2
  Warning: package 'igraph' was built under R version 3.0.2
See 'E:/biocbld/bbs-2.12-bioc/meat/CAMERA.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package 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
* 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call with 'PACKAGE' argument in a different package:
  .Call("getEIC", ..., PACKAGE = "xcms")
See the chapter 'System and foreign language interfaces' of 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'
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 binding for global variable 'graphMethod'
findAdducts,xsAnnotate: no visible global function definition for
  'mpi.comm.size'
* 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 portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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-2.12-bioc/meat/CAMERA.buildbin-libdir/CAMERA/libs/i386/CAMERA.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'E:/biocbld/bbs-2.12-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.  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 examples ...
** running examples for arch 'i386' ... [77s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
groupCorr-methods   7.58   0.23    7.82
getIsotopeCluster   7.33   0.12    7.46
pspec2metfrag       6.83   0.02    6.85
findAdducts-methods 6.46   0.02    6.49
annotateDiffreport  5.54   0.21    5.85
getPeaklist-methods 5.68   0.05    5.73
annotate-methods    5.42   0.05    5.46
cleanParallel       1.11   0.01    6.04
** running examples for arch 'x64' ... [87s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
groupCorr-methods   9.42   0.31    9.73
getIsotopeCluster   8.02   0.10    8.12
getPeaklist-methods 6.71   0.04    6.74
annotateDiffreport  6.19   0.14    6.37
annotate-methods    5.95   0.05    7.30
findAdducts-methods 5.80   0.01    5.82
pspec2metfrag       5.61   0.02    5.63
cleanParallel       1.17   0.06    6.71
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'runTests.R' [34s]
 [35s] OK
** running tests for arch 'x64'
  Running 'runTests.R' [43s]
 [43s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 5 notes.
See
  'E:/biocbld/bbs-2.12-bioc/meat/CAMERA.Rcheck/00check.log'
for details.

CAMERA.Rcheck/00install.out:


install for i386

* installing *source* package 'CAMERA' ...
** libs
gcc -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/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/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.12-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.12-bioc/meat/CAMERA.buildbin-libdir/CAMERA/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: package 'Rcpp' was built under R version 3.0.2
Warning: package 'igraph' was built under R version 3.0.2
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: package 'Rcpp' was built under R version 3.0.2
Warning: package 'igraph' was built under R version 3.0.2

install for x64

* installing *source* package 'CAMERA' ...
** libs
gcc -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/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/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.12-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.12-bioc/meat/CAMERA.buildbin-libdir/CAMERA/libs/x64
** testing if installed package can be loaded
Warning: package 'Rcpp' was built under R version 3.0.2
Warning: package 'igraph' was built under R version 3.0.2
* MD5 sums
packaged installation of 'CAMERA' as CAMERA_1.16.0.zip
* DONE (CAMERA)