flagme 1.14.0
Mark Robinson
| Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/flagme | | Last Changed Rev: 70050 / Revision: 74773 | | Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | [ WARNINGS ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/flagme.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flagme/DESCRIPTION’ ... OK
* this is package ‘flagme’ version ‘1.14.0’
* 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 whether package ‘flagme’ can be installed ... WARNING
Found the following significant warnings:
Warning: subclass "xcmsPeaks" of class "matrix" is not local and cannot be updated for new inheritance information; consider setClassUnion()
See ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/flagme.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... WARNING
Loading required package: gcspikelite
Loading required package: xcms
Loading required package: methods
Loading required package: mzR
Loading required package: Rcpp
Loading required package: utils
Attaching package: ‘utils’
The following object(s) are masked from ‘package:Rcpp’:
.DollarNames, prompt
Error in eval(expr, envir, enclos) : could not find function "selfStart"
Error : unable to load R code in package ‘xcms’
Error: package ‘xcms’ could not be loaded
Execution halted
It looks like this package (or one of its dependent packages) has an
unstated dependence on a standard package. All dependencies must be
declared in DESCRIPTION.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking whether the package can be unloaded cleanly ... WARNING
Error in eval(expr, envir, enclos) : could not find function "selfStart"
Error : unable to load R code in package ‘xcms’
Error: package ‘xcms’ could not be loaded
Execution halted
* 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 message:
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’
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 ... WARNING
Error: package ‘xcms’ could not be loaded
Call sequence:
3: stop(gettextf("package %s could not be loaded", sQuote(pkg)),
call. = FALSE, domain = NA)
2: .getRequiredPackages2(pkgInfo, quietly = quietly)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* 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 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
parseChromaTOF 5.544 0.012 5.754
* 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 5 warnings.
See
‘/loc/home/biocbuild/bbs-2.11-bioc/meat/flagme.Rcheck/00check.log’
for details.
* installing *source* package ‘flagme’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c dp.c -o dp.o
dp.c: In function ‘dp’:
dp.c:263:26: warning: ‘cur_min’ may be used uninitialized in this function [-Wuninitialized]
dp.c:264:28: warning: ‘tb’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o flagme.so dp.o init.o -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/flagme.Rcheck/flagme/libs
** R
** inst
** preparing package for lazy loading
Warning: subclass "xcmsPeaks" of class "matrix" is not local and cannot be updated for new inheritance information; consider setClassUnion()
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘flagme’
** help
*** installing help indices
** building package indices
** installing vignettes
‘flagme.Rnw’ using ‘UTF-8’
** testing if installed package can be loaded
* DONE (flagme)