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BioC 2.14: CHECK report for simpleaffy on morelia

This page was generated on 2014-10-08 09:02:10 -0700 (Wed, 08 Oct 2014).

Package 728/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
simpleaffy 2.40.0
Crispin Miller
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/simpleaffy
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: simpleaffy
Version: 2.40.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch simpleaffy_2.40.0.tar.gz
StartedAt: 2014-10-08 01:37:36 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 01:40:07 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 151.0 seconds
RetCode: 0
Status:  OK 
CheckDir: simpleaffy.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch simpleaffy_2.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/simpleaffy.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘simpleaffy/DESCRIPTION’ ... OK
* this is package ‘simpleaffy’ version ‘2.40.0’
* 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 ... [14s/14s] OK
* 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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/Users/biocbuild/bbs-2.14-bioc/meat/simpleaffy.Rcheck/simpleaffy/libs/simpleaffy.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Object: ‘simpleaffy.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [7s/7s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/simpleaffy.Rcheck/00check.log’
for details.

simpleaffy.Rcheck/00install.out:

* installing *source* package ‘simpleaffy’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -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]);
                             ^˜˜˜˜˜
/usr/include/stdio.h:216:16: note: expanded from macro 'stderr'
#define stderr  __stderrp
                ^˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Print.h:40:27: 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/usr/local/lib -o simpleaffy.so simpleaffy.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-bioc/meat/simpleaffy.Rcheck/simpleaffy/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 (simpleaffy)

simpleaffy.Rcheck/simpleaffy-Ex.timings:

nameusersystemelapsed
all.present0.0000.0000.001
all.present.in.group0.0010.0000.001
bg.correct.sa0.0010.0000.001
call.exprs0.0000.0000.001
detection.p.val000
get.annotation000
get.array.indices0.0010.0000.000
get.array.subset0.0010.0000.001
get.array.subset.affy0.0010.0000.001
get.fold.change.and.t.test0.0010.0000.000
hmap.colors0.0000.0000.001
hmap.eset0.0010.0000.001
hmap.pc0.0010.0000.000
journalpng0.0010.0000.001
justMAS0.0010.0000.001
pairwise.comparison000
pairwise.filter0.0000.0000.001
plot.pairwise.comparison0.0000.0000.001
plot.qc.stats0.0720.0030.075
qc0.0450.0040.049
qc.affy0.2080.0050.212
qc.get.alpha10.0040.0010.005
qc.get.array0.0010.0000.001
qc.get.probes0.0040.0010.005
qc.get.ratios0.0050.0010.006
qc.get.spikes0.0010.0010.002
qc.have.params0.0180.0040.022
qc.ok0.0060.0010.006
qc.read.file0.0050.0010.006
qc.stats0.0410.0040.045
read.affy0.0010.0000.000
read.affy.mixed0.0000.0000.001
setQCEnvironment0.0100.0020.012
simpleaffy-deprecated0.0230.0040.027
standard.pearson0.0010.0000.000
trad.scatter.plot0.0010.0010.001