Package: simpleaffy

Version: 2.60.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:simpleaffy.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings simpleaffy_2.60.0.tar.gz

StartedAt: 2019-10-16 05:04:27 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:06:52 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 145.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: simpleaffy.Rcheck

Warnings: 3

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:simpleaffy.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings simpleaffy_2.60.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/simpleaffy.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘simpleaffy/DESCRIPTION’ ... OK
* this is package ‘simpleaffy’ version ‘2.60.0’
* 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 ‘simpleaffy’ can be installed ... WARNING
Found the following significant warnings:
  simpleaffy.c:440:30: warning: passing argument 1 of ‘REprintf’ from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/biocbuild/bbs-3.9-bioc/meat/simpleaffy.Rcheck/00install.out’ for details.
* 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:
  ‘methods’ ‘utils’ ‘grDevices’ ‘graphics’ ‘stats’ ‘BiocGenerics’ ‘Biobase’ ‘affy’ ‘genefilter’ ‘gcrma’
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 ... OK
* checking S3 generic/method consistency ... WARNING
all:
  function(..., na.rm)
all.present:
  function(x, calls, no)

all:
  function(..., na.rm)
all.present.in.group:
  function(x, group, members, calls, no)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.

Found the following apparent S3 methods exported but not registered:
  all.present all.present.in.group plot.pairwise.comparison
  plot.qc.stats
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
hmap.eset : : no visible global function definition for
  ‘var’
hmap.pc : : no visible global function definition for ‘var’
qc.affy: no visible binding for global variable ‘var’
standard.pearson: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor var
Consider adding
  importFrom("stats", "cor", "var")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'PairComp,ANY,ANY,ANY'
  generic '[<-' and siglist 'PairComp,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ‘/home/biocbuild/bbs-3.9-bioc/R/library/simpleaffy/libs/simpleaffy.so’:
  Found ‘stderr’, possibly from ‘stderr’ (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 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: 3 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/simpleaffy.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL simpleaffy
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘simpleaffy’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c simpleaffy.c -o simpleaffy.o
simpleaffy.c: In function ‘bgmas’:
simpleaffy.c:440:30: warning: passing argument 1 of ‘REprintf’ from incompatible pointer type [-Wincompatible-pointer-types]
     if(gn >= ngrid) REprintf(stderr,"Really ouch! %d %d\n",gn,ends[gn]);
                              ^~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/include/R.h:88:0,
                 from simpleaffy.c:5:
/home/biocbuild/bbs-3.9-bioc/R/include/R_ext/Print.h:43:6: note: expected ‘const char *’ but argument is of type ‘struct _IO_FILE *’
 void REprintf(const char *, ...);
      ^~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o simpleaffy.so simpleaffy.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-simpleaffy/00new/simpleaffy/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (simpleaffy)

name	user	system	elapsed
all.present	0	0	0
all.present.in.group	0.001	0.000	0.000
bg.correct.sa	0	0	0
call.exprs	0	0	0
detection.p.val	0	0	0
get.annotation	0	0	0
get.array.indices	0	0	0
get.array.subset	0	0	0
get.array.subset.affy	0	0	0
get.fold.change.and.t.test	0	0	0
hmap.colors	0.000	0.000	0.001
hmap.eset	0.000	0.000	0.001
hmap.pc	0.000	0.000	0.001
journalpng	0.000	0.000	0.001
justMAS	0	0	0
pairwise.comparison	0	0	0
pairwise.filter	0	0	0
plot.pairwise.comparison	0	0	0
plot.qc.stats	0.076	0.007	0.100
qc	0.035	0.008	0.044
qc.affy	0.044	0.000	0.043
qc.get.alpha1	0.003	0.000	0.002
qc.get.array	0	0	0
qc.get.probes	0.002	0.000	0.002
qc.get.ratios	0.002	0.000	0.003
qc.get.spikes	0.001	0.000	0.000
qc.have.params	0.006	0.000	0.006
qc.ok	0.001	0.000	0.002
qc.read.file	0.000	0.002	0.002
qc.stats	0.031	0.001	0.032
read.affy	0	0	0
read.affy.mixed	0	0	0
setQCEnvironment	0.004	0.001	0.005
simpleaffy-deprecated	0.010	0.000	0.011
standard.pearson	0.001	0.000	0.000
trad.scatter.plot	0.001	0.000	0.000