CAMERA 1.15.5
Carsten Kuhl
| Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CAMERA | | Last Changed Rev: 74553 / Revision: 74774 | | Last Changed Date: 2013-03-19 00:14:31 -0700 (Tue, 19 Mar 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | [ WARNINGS ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/CAMERA.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAMERA/DESCRIPTION’ ... OK
* this is package ‘CAMERA’ version ‘1.15.5’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CAMERA’ can be installed ... [35s/37s] OK
* 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
* 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 ... WARNING
Error in eval(expr, envir, enclos) : could not find function "selfStart"
In addition: Warning messages:
1: class "C++Object" is defined (with package slot ‘Rcpp’) but no metadata object found to revise subclass information---not exported? Making a copy in package ‘.GlobalEnv’
2: class "characterORconnection" is defined (with package slot ‘BiocGenerics’) but no metadata object found to revise subclass information---not exported? Making a copy in package ‘xcms’
3: class "characterORMIAME" is defined (with package slot ‘Biobase’) but no metadata object found to revise subclass information---not exported? Making a copy in package ‘xcms’
Error: unable to load R code in package ‘xcms’
Execution halted
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* 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 ... WARNING
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/CAMERA.Rcheck/00_pkg_src/CAMERA/man/annotateDiffreport.Rd’:
‘diffreport’
Missing link or links in documentation object ‘/home/biocbuild/bbs-2.12-bioc/meat/CAMERA.Rcheck/00_pkg_src/CAMERA/man/xsAnnotate-class.Rd’:
‘xcmsSet’
See the information in section ‘Cross-references’ of the ‘Writing R
Extensions’ manual.
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [99s/112s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
groupCorr-methods 13.152 0.200 14.230
getIsotopeCluster 10.861 0.116 11.318
annotateDiffreport 10.033 0.104 10.198
getPeaklist-methods 7.173 0.024 7.465
findAdducts-methods 7.029 0.032 8.179
pspec2metfrag 6.928 0.004 7.286
annotate-methods 6.372 0.088 6.476
cleanParallel 1.264 0.052 10.088
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘runTests.R’ [49s/51s]
[49s/51s] 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 were 2 warnings.
NOTE: There were 4 notes.
See
‘/home/biocbuild/bbs-2.12-bioc/meat/CAMERA.Rcheck/00check.log’
for details.
* installing *source* package ‘CAMERA’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fastMatch.c -o fastMatch.o
gcc -std=gnu99 -shared -L/usr/local/lib -o CAMERA.so fastMatch.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/CAMERA.Rcheck/CAMERA/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘CAMERA.Rnw’
** testing if installed package can be loaded
* DONE (CAMERA)