BioC 3.5: CHECK report for FunChIP on malbec2

Package: FunChIP

Version: 1.2.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings FunChIP_1.2.0.tar.gz

StartedAt: 2017-08-15 23:07:53 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 23:10:45 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 171.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: FunChIP.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings FunChIP_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/FunChIP.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FunChIP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FunChIP’ version ‘1.2.0’
* 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 ‘FunChIP’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 25.2Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata  21.5Mb
    libs      1.2Mb
* 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 ... 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
            old_size new_size compress
  peaks.rda    638Kb    112Kb       xz
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
smooth_peak-method 4.932  0.112   5.046
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘BiocStyle’
* 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 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/FunChIP.Rcheck/00check.log’
for details.

* installing *source* package ‘FunChIP’ ...
** libs
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include  `/home/biocbuild/bbs-3.5-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -fpic  -g -O2 -c kmean_function.cpp -o kmean_function.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o FunChIP.so kmean_function.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/FunChIP.Rcheck/FunChIP/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (FunChIP)

name	user	system	elapsed
GR100	0.092	0.000	0.091
bending_index	0.424	0.000	0.424
choose_k-method	0.032	0.000	0.032
cluster_peak-method	3.256	0.008	3.270
compute_fragments_length	4.032	0.080	4.117
distance_peak	0.048	0.000	0.051
peaks	0.000	0.000	0.002
pileup_peak-method	0.952	0.636	1.627
plot_peak-method	0.252	0.000	0.250
silhouette_plot	1.676	0.004	1.682
smooth_peak-method	4.932	0.112	5.046
summit_peak-method	0.004	0.000	0.004