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CHECK report for reb on merida1

This page was generated on 2019-04-16 11:54:20 -0400 (Tue, 16 Apr 2019).

Package 1278/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
reb 1.60.0
Karl J. Dykema
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/reb
Branch: RELEASE_3_8
Last Commit: 20e853c
Last Changed Date: 2018-10-30 11:41:42 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: reb
Version: 1.60.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:reb.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings reb_1.60.0.tar.gz
StartedAt: 2019-04-16 02:15:18 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:17:02 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 103.8 seconds
RetCode: 0
Status:  OK 
CheckDir: reb.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:reb.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings reb_1.60.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/reb.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘reb/DESCRIPTION’ ... OK
* this is package ‘reb’ version ‘1.60.0’
* 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 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
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/reb/libs/reb.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)
  Found ‘_putchar’, possibly from ‘putchar’ (C)
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)

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. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/reb.Rcheck/00check.log’
for details.



Installation output

reb.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL reb
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘reb’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c movbin.c -o movbin.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o reb.so movbin.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/reb/libs
** R
** data
** 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 (reb)

Tests output


Example timings

reb.Rcheck/reb-Ex.timings

nameusersystemelapsed
absMax0.0010.0000.000
buildChromCytoband0.0060.0040.012
buildChromMap000
cset2band4.2350.1574.479
fromRevIsh3.1960.0673.302
isAbnormal0.0010.0000.001
mcr.eset0.0660.0050.071
movbin0.0340.0010.035
movt0.6050.0160.625
naMean0.0010.0010.001
regmap0.0080.0000.009
revish0.0850.0030.089
rmAmbigMappings0.0010.0000.001
smoothByRegion3.1340.0803.242
summarizeByRegion0.0010.0010.001
tBinomTest000
writeGFF30.1310.0040.137