BioC 3.5: CHECK report for logitT on malbec2

Package: logitT

Version: 1.34.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings logitT_1.34.0.tar.gz

StartedAt: 2017-10-18 00:23:46 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:24:26 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 39.3 seconds

RetCode: 0

Status:  OK

CheckDir: logitT.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings logitT_1.34.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/logitT.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘logitT/DESCRIPTION’ ... OK
* this is package ‘logitT’ version ‘1.34.0’
* 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 ‘logitT’ can be installed ... OK
* checking installed package size ... OK
* 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 ... NOTE
'library' or 'require' call to ‘affy’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘affy’
  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
logitTAffy: no visible global function definition for ‘featureNames’
logitTAffy: no visible global function definition for ‘pm’
logitTAffy: no visible global function definition for ‘mm’
logitTAffy: no visible global function definition for ‘pmindex’
Undefined global functions or variables:
  featureNames mm pm pmindex
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
File ‘logitT/libs/logitT.so’:
  Found ‘stdout’, possibly from ‘stdout’ (C)
    Object: ‘logitTfunc.o’

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

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
Examples with CPU or elapsed time > 5s
            user system elapsed
logitTAffy 5.356    0.1   5.558
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/logitT.Rcheck/00check.log’
for details.

* installing *source* package ‘logitT’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c logitTfunc.c -o logitTfunc.o
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o logitT.so logitTfunc.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/logitT.Rcheck/logitT/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (logitT)

name	user	system	elapsed
logitTAffy	5.356	0.100	5.558