Package: reb

Version: 1.56.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings reb_1.56.0.tar.gz

StartedAt: 2018-04-12 02:16:01 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:17:22 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 81.4 seconds

RetCode: 0

Status:  OK

CheckDir: reb.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings reb_1.56.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/reb.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘reb/DESCRIPTION’ ... OK
* this is package ‘reb’ version ‘1.56.0’
* 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 ‘reb’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
Missing object imported by a ':::' call: ‘Biobase:::EXPRSET_DEPR_MSG’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.MAP2chromLoc: warning in mget(subnames, env = chrEnv, ifnotfound =
  NA): partial argument match of 'env' to 'envir'
rmAmbigMappings: warning in ls(env = get(package)): partial argument
  match of 'env' to 'envir'
.genMeanMatrix: no visible global function definition for ‘t.test’
buildChromCytoband: no visible global function definition for ‘new’
buildChromCytoband: no visible binding for global variable
  ‘Hs.cytoband’
buildChromCytoband: no visible binding for global variable
  ‘Rn.cytoband’
buildChromCytoband: no visible binding for global variable
  ‘Mm.cytoband’
buildChromMap: no visible global function definition for ‘new’
cgma: no visible binding for global variable ‘t.test’
cset2band: no visible global function definition for ‘aggregate’
fromRevIsh: no visible binding for global variable ‘vai.chr’
reb: no visible global function definition for ‘supsmu’
reb: no visible global function definition for ‘lowess’
reb: no visible global function definition for ‘approx’
regmap: no visible global function definition for ‘par’
regmap: no visible global function definition for ‘layout’
regmap: no visible global function definition for ‘image’
regmap: no visible global function definition for ‘axis’
smoothByRegion: no visible global function definition for ‘supsmu’
smoothByRegion: no visible global function definition for ‘lowess’
smoothByRegion: no visible global function definition for ‘approx’
summarizeByRegion: no visible binding for global variable ‘t.test’
tBinomTest: no visible global function definition for ‘binom.test’
writeGFF3: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  Hs.cytoband Mm.cytoband Rn.cytoband aggregate approx axis binom.test
  image layout lowess new par supsmu t.test vai.chr write.table
Consider adding
  importFrom("graphics", "axis", "image", "layout", "par")
  importFrom("methods", "new")
  importFrom("stats", "aggregate", "approx", "binom.test", "lowess",
             "supsmu", "t.test")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ‘reb/libs/reb.so’:
  Found ‘putchar’, possibly from ‘putchar’ (C)
    Object: ‘movbin.o’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Object: ‘movbin.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/reb.Rcheck/00check.log’
for details.

* installing *source* package ‘reb’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c movbin.c -o movbin.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o reb.so movbin.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/reb.Rcheck/reb/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 (reb)

name	user	system	elapsed
absMax	0.000	0.000	0.001
buildChromCytoband	0.004	0.004	0.056
buildChromMap	0	0	0
cset2band	3.692	0.056	3.760
fromRevIsh	2.280	0.008	2.290
isAbnormal	0.000	0.000	0.001
mcr.eset	0.044	0.000	0.044
movbin	0.020	0.000	0.022
movt	0.348	0.004	0.354
naMean	0	0	0
regmap	0.004	0.000	0.007
revish	0.116	0.000	0.113
rmAmbigMappings	0	0	0
smoothByRegion	2.460	0.008	2.469
summarizeByRegion	0.000	0.000	0.001
tBinomTest	0.000	0.004	0.001
writeGFF3	0.080	0.000	0.081