BiRewire 1.8.0
Andrea Gobbi
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/BiRewire | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
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### Running command:
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### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings BiRewire_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/BiRewire.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiRewire/DESCRIPTION’ ... OK
* this is package ‘BiRewire’ version ‘1.8.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BiRewire’ can be installed ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘igraph’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
birewire.bipartite.from.incidence: no visible global function
definition for ‘graph.bipartite’
birewire.bipartite.from.incidence: no visible global function
definition for ‘V’
birewire.bipartite.from.incidence: no visible global function
definition for ‘V<-’
birewire.rewire: no visible global function definition for ‘is.igraph’
birewire.rewire.bipartite: no visible global function definition for
‘is.igraph’
birewire.rewire.bipartite.and.projections: no visible global function
definition for ‘is.bipartite’
birewire.rewire.bipartite.and.projections: no visible global function
definition for ‘bipartite.projection’
birewire.rewire.bipartite.and.projections: no visible global function
definition for ‘get.adjacency’
birewire.rewire.bipartite.and.projections: no visible global function
definition for ‘get.incidence’
birewire.rewire.sparse: no visible global function definition for ‘V’
birewire.rewire.sparse: no visible global function definition for ‘E’
birewire.rewire.sparse: no visible global function definition for
‘get.edgelist’
birewire.rewire.sparse.bipartite: no visible global function definition
for ‘is.bipartite’
birewire.rewire.sparse.bipartite: no visible global function definition
for ‘E’
birewire.rewire.sparse.bipartite: no visible global function definition
for ‘get.edgelist’
birewire.rewire.sparse.bipartite: no visible global function definition
for ‘V’
birewire.rewire.sparse.bipartite: no visible global function definition
for ‘graph.bipartite’
* 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 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 compiled code ... NOTE
File ‘BiRewire/libs/BiRewire.so’:
Found ‘rand’, possibly from ‘rand’ (C)
Object: ‘BiRewire.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [5s/5s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘runTests.R’ [1s/1s]
[1s/1s] 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
NOTE: There were 3 notes.
See
‘/home/biocbuild/bbs-3.0-bioc/meat/BiRewire.Rcheck/00check.log’
for details.
* installing *source* package ‘BiRewire’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c BiRewire.c -o BiRewire.o
BiRewire.c: In function ‘rewire_sparse’:
BiRewire.c:1149:9: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
BiRewire.c: In function ‘rewire_sparse_ex’:
BiRewire.c:1265:9: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c interface.c -o interface.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o BiRewire.so BiRewire.o interface.o -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-bioc/meat/BiRewire.Rcheck/BiRewire/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BiRewire)