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BioC 3.3: CHECK report for simpleaffy on zin2

This page was generated on 2016-10-13 12:40:50 -0700 (Thu, 13 Oct 2016).

Package 1077/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
simpleaffy 2.48.0
Crispin Miller
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/simpleaffy
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: simpleaffy
Version: 2.48.0
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings simpleaffy_2.48.0.tar.gz
StartedAt: 2016-10-13 06:52:54 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 06:54:49 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 115.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: simpleaffy.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings simpleaffy_2.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/simpleaffy.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘2.48.0’
* 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 ... 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 ... NOTE
hmap.eset : <anonymous>: no visible global function definition for
  ‘var’
hmap.pc : <anonymous>: 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
File ‘simpleaffy/libs/simpleaffy.so’:
  Found ‘stderr’, 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, nor the system RNG.

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 ... 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: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/simpleaffy.Rcheck/00check.log’
for details.


simpleaffy.Rcheck/00install.out:

* installing *source* package ‘simpleaffy’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-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:440:5: warning: passing argument 1 of ‘REprintf’ from incompatible pointer type [enabled by default]
     if(gn >= ngrid) REprintf(stderr,"Really ouch! %d %d\n",gn,ends[gn]);
     ^
In file included from /home/biocbuild/bbs-3.3-bioc/R/include/R.h:72:0,
                 from simpleaffy.c:5:
/home/biocbuild/bbs-3.3-bioc/R/include/R_ext/Print.h:40:6: note: expected ‘const char *’ but argument is of type ‘struct _IO_FILE *’
 void REprintf(const char *, ...);
      ^
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o simpleaffy.so simpleaffy.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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.present0.0010.0000.000
all.present.in.group0.0010.0000.001
bg.correct.sa000
call.exprs0.0010.0000.001
detection.p.val0.0010.0000.000
get.annotation0.0010.0000.001
get.array.indices0.0010.0000.000
get.array.subset0.0000.0000.001
get.array.subset.affy0.0010.0000.001
get.fold.change.and.t.test000
hmap.colors0.0010.0000.001
hmap.eset0.0000.0000.001
hmap.pc0.0010.0000.001
journalpng0.0000.0000.001
justMAS0.0010.0000.001
pairwise.comparison000
pairwise.filter0.0010.0000.001
plot.pairwise.comparison000
plot.qc.stats0.0480.0000.050
qc0.0370.0000.038
qc.affy0.0390.0000.040
qc.get.alpha10.0030.0000.003
qc.get.array000
qc.get.probes0.0030.0000.003
qc.get.ratios0.0030.0000.002
qc.get.spikes0.0010.0000.000
qc.have.params0.0070.0000.006
qc.ok0.0020.0000.002
qc.read.file0.0030.0000.003
qc.stats0.0370.0000.038
read.affy0.0010.0000.000
read.affy.mixed0.0000.0000.001
setQCEnvironment0.0020.0040.005
simpleaffy-deprecated0.0100.0000.011
standard.pearson0.0010.0000.001
trad.scatter.plot000