BioC 3.2: CHECK report for BiRewire on linux1.bioconductor.org

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings BiRewire_2.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/BiRewire.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiRewire/DESCRIPTION’ ... OK
* this is package ‘BiRewire’ version ‘2.4.0’
* 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 ... NOTE
Malformed Title field: should not end in a period.
* 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 ... OK
* 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 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [75s/75s] OK
Examples with CPU or elapsed time > 5s
                                        user system elapsed
birewire.analysis.undirected          29.825  0.119  29.976
birewire.visual.monitoring.dsg        28.923  0.000  28.932
birewire.visual.monitoring.undirected  9.607  0.040   9.647
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [14s/14s]
 [14s/14s] 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/BiRewire.Rcheck/00check.log’
for details.

* installing *source* package ‘BiRewire’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-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:1151:22: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
         if( a!=c && b!=d & a!=d && c!=b && (( ad==1 && cb==1 )|| (ac==1 && bd==1) ))
                      ^
BiRewire.c: In function ‘rewire_sparse_ex’:
BiRewire.c:1267:22: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
         if( a!=c && b!=d & a!=d && c!=b && (( ad==1 && cb==1 )|| (ac==1 && bd==1) ))
                      ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-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-3.2-bioc/R/lib -L/usr/local/lib -o BiRewire.so BiRewire.o interface.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-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)

name	user	system	elapsed
birewire.analysis.bipartite	0.061	0.092	0.156
birewire.analysis.dsg	0.131	0.000	0.131
birewire.analysis.undirected	29.825	0.119	29.976
birewire.bipartite.from.incidence	0.004	0.008	0.012
birewire.build.dsg	0.003	0.004	0.008
birewire.induced.bipartite	0.002	0.000	0.003
birewire.rewire.bipartite	0.006	0.004	0.011
birewire.rewire.bipartite.and.projections	0.148	0.008	0.156
birewire.rewire.dsg	0.003	0.000	0.004
birewire.rewire.undirected	0.566	0.012	0.578
birewire.sampler.dsg	0.003	0.000	0.003
birewire.similarity	0.008	0.000	0.008
birewire.similarity.dsg	0.033	0.000	0.033
birewire.visual.monitoring.bipartite	4.601	0.004	4.611
birewire.visual.monitoring.dsg	28.923	0.000	28.932
birewire.visual.monitoring.undirected	9.607	0.040	9.647

BioC 3.2: CHECK report for BiRewire on linux1.bioconductor.org

Summary

Command output