CAMERA 1.24.1
Carsten Kuhl
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/CAMERA | | Last Changed Rev: 105917 / Revision: 109384 | | Last Changed Date: 2015-07-08 14:20:51 -0700 (Wed, 08 Jul 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | TIMEOUT | | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |  |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CAMERA_1.24.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/CAMERA.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CAMERA’ can be installed ... [26s/27s] 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
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [74s/76s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
getIsotopeCluster 9.942 0.531 10.481
annotateDiffreport 8.844 0.605 10.427
groupCorr-methods 7.634 0.282 7.921
findAdducts-methods 5.523 0.075 5.604
pspec2metfrag 5.358 0.035 5.395
getPeaklist-methods 5.091 0.033 5.125
annotate-methods 4.886 0.117 5.146
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [67s/68s]
[67s/68s] 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: 5 NOTEs
See
‘/Users/biocbuild/bbs-3.1-bioc/meat/CAMERA.Rcheck/00check.log’
for details.
* installing *source* package ‘CAMERA’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c fastMatch.c -o fastMatch.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o CAMERA.so fastMatch.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-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
** testing if installed package can be loaded
* DONE (CAMERA)