Package: simpleaffy

Version: 2.60.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:simpleaffy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings simpleaffy_2.60.0.tar.gz

StartedAt: 2019-10-16 06:56:03 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 06:59:38 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 214.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: simpleaffy.Rcheck

Warnings: 3

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:simpleaffy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings simpleaffy_2.60.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/simpleaffy.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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: incompatible pointer types passing 'FILE *' (aka 'struct __sFILE *') to parameter of type 'const char *' [-Wincompatible-pointer-types]
See ‘/Users/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 ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/simpleaffy/libs/simpleaffy.so’:
  Found ‘___stderrp’, 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 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: 3 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/simpleaffy.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL simpleaffy
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘simpleaffy’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c simpleaffy.c -o simpleaffy.o
simpleaffy.c:440:30: warning: incompatible pointer types passing 'FILE *' (aka 'struct __sFILE *') to parameter of type 'const char *' [-Wincompatible-pointer-types]
    if(gn >= ngrid) REprintf(stderr,"Really ouch! %d %d\n",gn,ends[gn]);
                             ^~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:218:16: note: expanded from macro 'stderr'
#define stderr  __stderrp
                ^~~~~~~~~
/Library/Frameworks/R.framework/Resources/include/R_ext/Print.h:43:27: note: passing argument to parameter here
void REprintf(const char *, ...);
                          ^
1 warning generated.
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 simpleaffy.so simpleaffy.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/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	0	0
bg.correct.sa	0.000	0.001	0.001
call.exprs	0	0	0
detection.p.val	0.000	0.001	0.000
get.annotation	0.000	0.001	0.001
get.array.indices	0.001	0.000	0.000
get.array.subset	0.000	0.000	0.001
get.array.subset.affy	0.001	0.000	0.000
get.fold.change.and.t.test	0	0	0
hmap.colors	0.001	0.000	0.001
hmap.eset	0.000	0.001	0.000
hmap.pc	0	0	0
journalpng	0.001	0.000	0.001
justMAS	0	0	0
pairwise.comparison	0.000	0.000	0.001
pairwise.filter	0	0	0
plot.pairwise.comparison	0	0	0
plot.qc.stats	0.094	0.026	0.121
qc	0.066	0.022	0.089
qc.affy	0.047	0.016	0.063
qc.get.alpha1	0.003	0.001	0.006
qc.get.array	0.000	0.000	0.001
qc.get.probes	0.004	0.002	0.005
qc.get.ratios	0.004	0.002	0.005
qc.get.spikes	0.001	0.001	0.002
qc.have.params	0.008	0.003	0.012
qc.ok	0.003	0.001	0.003
qc.read.file	0.005	0.002	0.006
qc.stats	0.057	0.014	0.071
read.affy	0.000	0.000	0.001
read.affy.mixed	0.000	0.000	0.001
setQCEnvironment	0.007	0.002	0.010
simpleaffy-deprecated	0.015	0.005	0.020
standard.pearson	0.001	0.001	0.001
trad.scatter.plot	0.001	0.001	0.001