Package: NarrowPeaks

Version: 1.26.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:NarrowPeaks.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings NarrowPeaks_1.26.0.tar.gz

StartedAt: 2019-04-16 01:43:13 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 01:45:12 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 119.4 seconds

RetCode: 0

Status:  OK

CheckDir: NarrowPeaks.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:NarrowPeaks.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings NarrowPeaks_1.26.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/NarrowPeaks.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NarrowPeaks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NarrowPeaks’ version ‘1.26.0’
* 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 ‘NarrowPeaks’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘GenomicRanges’ ‘CSAR’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Package in Depends field not imported from: ‘splines’
  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
narrowpeaksDiff: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
* 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
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
NarrowPeaks-package 11.588  0.716  12.343
narrowpeaks          9.744  0.524  10.312
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/NarrowPeaks.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL NarrowPeaks
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘NarrowPeaks’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c wig2CSARScore.c -o wig2CSARScore.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c wig2CSARScore_R_wrapper.c -o wig2CSARScore_R_wrapper.o
gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o NarrowPeaks.so wig2CSARScore.o wig2CSARScore_R_wrapper.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/NarrowPeaks/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 (NarrowPeaks)

name	user	system	elapsed
NarrowPeaks-package	11.588	0.716	12.343
narrowpeaks	9.744	0.524	10.312
narrowpeaksDiff	0.000	0.000	0.001
wig2CSARScore	0.656	0.112	0.792
wigfile_test	0.000	0.000	0.002