CAMERA 1.16.0
Carsten Kuhl
| Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/CAMERA | | Last Changed Rev: 75263 / Revision: 76155 | | 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 | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
| pelham | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ OK ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/CAMERA.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* 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 for sufficient/correct file permissions ... OK
* checking whether package 'CAMERA' can be installed ... [28s/30s] 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 ... 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 ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [88s/97s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
groupCorr-methods 10.759 0.699 11.808
getIsotopeCluster 8.633 0.586 9.406
annotateDiffreport 7.751 0.510 8.937
getPeaklist-methods 6.603 0.111 6.839
findAdducts-methods 6.521 0.095 6.751
pspec2metfrag 6.292 0.122 6.494
annotate-methods 6.041 0.159 6.357
cleanParallel 1.354 0.051 8.174
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running 'runTests.R' [44s/45s]
[45s/45s] 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
NOTE: There were 4 notes.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/CAMERA.Rcheck/00check.log'
for details.
* installing *source* package 'CAMERA' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c fastMatch.c -o fastMatch.o
fastMatch.c:63:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
struct idxStruct * pidxS = calloc(nx, sizeof(struct idxStruct));
˜˜˜˜˜˜ ^˜
fastMatch.c:65:81: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
error("fastMatch/calloc: memory could not be allocated ! (%d bytes)\n", nx * sizeof(struct idxStruct) );
^˜ ˜
2 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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-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
** testing if installed package can be loaded
* DONE (CAMERA)